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Sornlek W, Sonthirod C, Tangphatsornruang S, Ingsriswang S, Runguphan W, Eurwilaichtr L, Champreda V, Tanapongpipat S, Schaap PJ, Martins Dos Santos VAP. Genes controlling hydrolysate toxin tolerance identified by QTL analysis of the natural Saccharomyces cerevisiae BCC39850. Appl Microbiol Biotechnol 2024; 108:21. [PMID: 38159116 DOI: 10.1007/s00253-023-12843-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 01/03/2024]
Abstract
Lignocellulosic material can be converted to valorized products such as fuels. Pretreatment is an essential step in conversion, which is needed to increase the digestibility of the raw material for microbial fermentation. However, pretreatment generates by-products (hydrolysate toxins) that are detrimental to microbial growth. In this study, natural Saccharomyces strains isolated from habitats in Thailand were screened for their tolerance to synthetic hydrolysate toxins (synHTs). The Saccharomyces cerevisiae natural strain BCC39850 (toxin-tolerant) was crossed with the laboratory strain CEN.PK2-1C (toxin-sensitive), and quantitative trait locus (QTL) analysis was performed on the segregants using phenotypic scores of growth (OD600) and glucose consumption. VMS1, DET1, KCS1, MRH1, YOS9, SYO1, and YDR042C were identified from QTLs as candidate genes associated with the tolerance trait. CEN.PK2-1C knockouts of the VMS1, YOS9, KCS1, and MRH1 genes exhibited significantly greater hydrolysate toxin sensitivity to growth, whereas CEN.PK2-1C knock-ins with replacement of VMS1 and MRH1 genes from the BCC39850 alleles showed significant increased ethanol production titers compared with the CEN.PK2-1C parental strain in the presence of synHTs. The discovery of VMS1, YOS9, MRH1, and KCS1 genes associated with hydrolysate toxin tolerance in S. cerevisiae indicates the roles of the endoplasmic-reticulum-associated protein degradation pathway, plasma membrane protein association, and the phosphatidylinositol signaling system in this trait. KEY POINTS: • QTL analysis was conducted using a hydrolysate toxin-tolerant S. cerevisiae natural strain • Deletion of VMS1, YOS9, MRH1, and KCS1 genes associated with hydrolysate toxin-sensitivity • Replacement of VMS1 and MRH1 with natural strain alleles increased ethanol production titers in the presence of hydrolysate toxins.
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Affiliation(s)
- Warasirin Sornlek
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Lily Eurwilaichtr
- National Energy Technology Center, 114 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
| | - Peter J Schaap
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Bioprocess Engineering Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany.
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Zhou Y, Gu Y, Zhang X, Wang W, Li Q, Wang B. QTL Mapping of Adult Plant Resistance to Powdery Mildew in Chinese Wheat Landrace Baidatou. Plant Dis 2024:PDIS12222894RE. [PMID: 38640452 DOI: 10.1094/pdis-12-22-2894-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Wheat powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is one of the most devastating diseases affecting wheat throughout the world. Breeding and growing resistant wheat cultivars is one of the most economic and effective methods to control the disease, and as such, identifying and mapping the new and effective resistance genes is critical. Baidatou, a Chinese wheat landrace, shows excellent field resistance to powdery mildew. To identify the resistance gene(s) in Baidatou, 170 F7:8 recombinant inbred lines (RILs) derived from the cross Mingxian 169/Baidatou were evaluated for powdery mildew response at the adult-plant stage in the experimental fields in Yangling (YL) of Shaanxi Province and Tianshui (TS) in Gansu Province in 2019, 2020, and 2021. The relative area under disease progress curve (rAUDPC) of Mingxian 169/Baidatou F7:8 RILs indicated that the resistance of Baidatou to powdery mildew was controlled by quantitative trait loci (QTLs). Based on bulk segregation analysis combined with the 660K single nucleotide polymorphism (SNP) array and genotyping by target sequencing (16K SNP) of the entire RIL population, two QTLs, QPmbdt.nwafu-2AS and QPmbdt.nwafu-3AS, were identified, and these accounted for up to 44.5% of the phenotypic variation. One of the QTLs was located on the 3.32 cM genetic interval on wheat chromosome 2AS between the kompetitive allele-specific PCR markers AX-111012288 and AX_174233809, and another was located on the 9.6 cM genetic interval on chromosome 3AS between the SNP markers 3A_684044820 and 3A_686681822. These markers could be useful for successful breeding of powdery mildew resistance in wheat.
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Affiliation(s)
- Yongchao Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yudi Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaomei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenli Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Wang K, Wang X, Zhang L, Chi Y, Luo Y, Xu W, Wang Y, Qu S. Morphological Analyses and QTL Mapping of Mottled Leaf in Zucchini ( Cucurbita pepo L.). Int J Mol Sci 2024; 25:2491. [PMID: 38473740 DOI: 10.3390/ijms25052491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
The mottled leaf is one of the agronomic traits of zucchini and can be applied as a marker trait in aggregation breeding. However, the genetic mechanism responsible for mottled leaf has yet to be elucidated. In the present study, we used two inbred lines (line '19': silver mottled leaf; line '113': normal leaf) as parents for the physiological and genetic analysis of mottled leaf. The synthesis and net photosynthetic rate of chlorophyll were not significantly affected in the mottled areas of leaves. However, we detected a large space between the palisade parenchyma in the leaf mottle area of line '19', which may have caused the mottled leaf phenotype. Light also plays an important role in the formation of mottled leaf, and receiving light during the early stages of leaf development is a necessary factor. Genetic analysis has previously demonstrated that mottled leaf is a quantitative trait that is controlled by multiple genes. Based on the strategy of quantitative trait locus sequencing (QTL-seq), two QTLs were identified on chromosomes 1 and 17, named CpML1.1 and CpML17.1, respectively. Two major loci were identified using R/qtl software version 1.66 under greenhouse conditions in April 2019 (2019A) and April 2020 (2020A) and under open cultivation conditions in May 2020 (2020M). The major QTL, CpML1.1, was located in a 925.2-kb interval on chromosome 1 and explained 10.51%-24.15% of the phenotypic variation. The CpML17.1 was located in a 719.7-kb interval on chromosome 17 and explained 16.25%-38.68% of the phenotypic variation. Based on gene annotation, gene sequence alignment, and qRT-PCR analysis, the Cp4.1LG01g23790 at the CpML1.1 locus encoding a protein of the TPX2 family (target protein of Xklp2) may be a candidate gene for mottled leaf in zucchini. Our findings may provide a theoretical basis for the formation of mottled leaf and provide a foundation for the fine mapping of genes associated with mottled leaf. Molecular markers closely linked to mottled leaf can be used in molecular-assisted selection for the zucchini mottled leaf breeding.
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Affiliation(s)
- Kexin Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xinyu Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Lijing Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Yichen Chi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
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Honda S, Imamura A, Seki Y, Chigira K, Iwasa M, Hayami K, Nomura T, Ohkubo S, Ookawa T, Nagano AJ, Matsuoka M, Tanaka Y, Adachi S. Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice. Photosynth Res 2024; 159:17-28. [PMID: 38112862 DOI: 10.1007/s11120-023-01065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023]
Abstract
Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency. In this study, we aimed to identify novel genomic regions for the net CO2 assimilation rate (A) by combining genome-wide association study (GWAS) and the newly developed rapid closed gas exchange system MIC-100. Using three MIC-100 systems in the field at the vegetative stage, we measured A of 168 temperate japonica rice varieties with six replicates for three years. We found that the modern varieties exhibited higher A than the landraces, while there was no significant relationship between the release year and A among the modern varieties. Our GWAS scan revealed two major peaks located on chromosomes 4 and 8, which were repeatedly detected in the different experiments and in the generalized linear modelling approach. We suggest that high-throughput gas exchange measurements combined with GWAS is a reliable approach for understanding the genetic mechanisms underlying photosynthetic diversities in crop species.
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Affiliation(s)
- Sotaro Honda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ayumu Imamura
- Graduate School of Agriculture, Ibaraki University, Ibaraki, 300-0393, Japan
| | - Yoshiaki Seki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Marina Iwasa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Kentaro Hayami
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Satoshi Ohkubo
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Makoto Matsuoka
- Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima, 960-1296, Japan
| | - Yu Tanaka
- Graduate School of Environment and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan.
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Zhang L, Chen Y, Leng Q, Lin X, Lu J, Xu Y, Li H, Xu S, Huang S, López Hernán A, Wang Y, Yin J, Niu J. A High-Resolution Linkage Map Construction and QTL Analysis for Morphological Traits in Anthurium ( Anthurium andraeanum Linden). Plants (Basel) 2023; 12:4185. [PMID: 38140512 PMCID: PMC10747322 DOI: 10.3390/plants12244185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Anthurium andraeanum Linden is a prominent ornamental plant belonging to the family Araceae and is cultivated worldwide. The morphology characteristics are crucial because they significantly impact ornamental values, commercial properties, and the efficiency of space utilization in production. However, only a few related investigations have been conducted in anthurium to date. In this study, an F1 genetic segregation population containing 160 progenies was generated through hybridization between potted and cut anthurium varieties. Fifteen morphological traits were assessed and revealed substantial levels of genetic variation and widespread positive correlation. Based on specific length amplified fragment (SLAF) sequencing technology, 8171 single nucleotide polymorphism (SNP) markers were developed, and the high-density linkage map of 2202.27 cM in length distributed on 15 linkage groups was constructed successfully, with an average distance of 0.30 cM. Using the inclusive composite interval mapping (ICIM) method, 59 QTLs related to 15 key morphological traits were successfully identified, which explained phenotypic variance (PVE) ranging from 6.21% to 17.74%. Thirty-three of those associated with 13 traits were designated as major QTLs with PVE > 10%. These findings offer valuable insights into the genetic basis of quantitative traits and are beneficial for molecular marker-assisted selection (MAS) in anthurium breeding.
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Affiliation(s)
- Linbi Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Yanyan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- Institute of Crops Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qingyun Leng
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Xinge Lin
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Jinping Lu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Yueting Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Haiyan Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Shisong Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Shaohua Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Ariel López Hernán
- Multidisciplinary Workshop on Vascular Plants, Border Ecology Laboratory, University of Flores, Sede Comahue (UFLO), Rio Negro 8328, Argentina;
- Botanical Garden of Plottier City, Neuquen 8316, Argentina
| | - Yaru Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Junmei Yin
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Junhai Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
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Ahmed MIY, Gorafi YSA, Kamal NM, Balla MY, Tahir ISA, Zheng L, Kawakami N, Tsujimoto H. Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy. Front Plant Sci 2023; 14:1270925. [PMID: 38107013 PMCID: PMC10723804 DOI: 10.3389/fpls.2023.1270925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.
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Affiliation(s)
| | - Yasir Serag Alnor Gorafi
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
| | - Nasrein Mohamed Kamal
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Mohammed Yousif Balla
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Izzat Sidahmed Ali Tahir
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Lipeng Zheng
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
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Yang J, Miao J, Li N, Zhou Z, Dai K, Ji F, Yang M, Tan C, Liu J, Wang H, Tang W. Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population. Plant Physiol Biochem 2023; 204:108086. [PMID: 37890228 DOI: 10.1016/j.plaphy.2023.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.
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Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jiahao Miao
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Nan Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Zixian Zhou
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Kunyan Dai
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Faru Ji
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Min Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Chen Tan
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
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Davis MJ, Martin RE, Pinheiro GM, Hoke ES, Moyer S, Ueno K, Rodriguez-Gil JL, Mallett MA, Khillan JS, Pavan WJ, Chang YC, Kwon-Chung KJ. Inbred SJL mice recapitulate human resistance to Cryptococcus infection due to differential immune activation. mBio 2023; 14:e0212323. [PMID: 37800917 PMCID: PMC10653822 DOI: 10.1128/mbio.02123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Cryptococcosis studies often utilize the common C57BL/6J mouse model. Unfortunately, infection in these mice fails to replicate the basic course of human disease, particularly hampering immunological studies. This work demonstrates that SJL/J mice can recapitulate human infection better than other mouse strains. The immunological response to Cryptococcus infection in SJL/J mice was markedly different from C57BL/6J and much more productive in combating this infection. Characterization of infected mice demonstrated strain-specific genetic linkage and differential regulation of multiple important immune-relevant genes in response to Cryptococcus infection. While our results validate many of the previously identified immunological features of cryptococcosis, we also demonstrate limitations from previous mouse models as they may be less translatable to human disease. We concluded that SJL/J mice more faithfully recapitulate human cryptococcosis serving as an exciting new animal model for immunological and genetic studies.
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Affiliation(s)
- M. J. Davis
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - R. E. Martin
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - G. M. Pinheiro
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - E. S. Hoke
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - S. Moyer
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - K. Ueno
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - J. L. Rodriguez-Gil
- Genomics, Development and Disease Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - M. A. Mallett
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - J. S. Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - W. J. Pavan
- Genomics, Development and Disease Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Y. C. Chang
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - K. J. Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
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9
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Asins MJ, Bullones A, Raga V, Romero-Aranda MR, Espinosa J, Triviño JC, Bernet GP, Traverso JA, Carbonell EA, Claros MG, Belver A. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus. Int J Mol Sci 2023; 24:15759. [PMID: 37958745 PMCID: PMC10650496 DOI: 10.3390/ijms242115759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The excessive accumulation of chloride (Cl-) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl-, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl- (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl- was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.
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Affiliation(s)
- Maria J. Asins
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
| | - Veronica Raga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Maria R. Romero-Aranda
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
| | - Jesus Espinosa
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
| | - Juan C. Triviño
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Guillermo P. Bernet
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Jose A. Traverso
- Department of Cellular Biology, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain;
| | - Emilio A. Carbonell
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Málaga, Spain
| | - Andres Belver
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
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10
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Koji T, Iwata H, Ishimori M, Takanashi H, Yamasaki Y, Tsujimoto H. Genetic Dissection of Seasonal Changes in a Greening Plant Based on Time-Series Multispectral Imaging. Plants (Basel) 2023; 12:3597. [PMID: 37896060 PMCID: PMC10610531 DOI: 10.3390/plants12203597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
Good appearance throughout the year is important for perennial ornamental plants used for rooftop greenery. However, the methods for evaluating appearance throughout the year, such as plant color and growth activity, are not well understood. In this study, evergreen and winter-dormant parents of Phedimus takesimensis and 94 F1 plants were used for multispectral imaging. We took 16 multispectral image measurements from March 2019 to April 2020 and used them to calculate 15 vegetation indices and the area of plant cover. QTL analysis was also performed. Traits such as the area of plant cover and vegetation indices related to biomass were high during spring and summer (growth period), whereas vegetation indices related to anthocyanins were high in winter (dormancy period). According to the PCA, changes in the intensity of light reflected from the plants at different wavelengths over the course of a year were consistent with the changes in plant color and growth activity. Seven QTLs were found to be associated with major seasonal growth changes. This approach, which monitors not only at a single point in time but also over time, can reveal morphological changes during growth, senescence, and dormancy throughout the year.
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Affiliation(s)
- Taeko Koji
- The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyamacho Minami, Tottori 680-8553, Japan;
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan; (H.I.); (M.I.); (H.T.)
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan; (H.I.); (M.I.); (H.T.)
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan; (H.I.); (M.I.); (H.T.)
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
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11
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Xu X, Ni Z, Zou X, Zhang Y, Tong J, Xu X, Dong Y, Han B, Li S, Wang D, Xia X, He Z, Hao Y. QTL Mapping Reveals Both All-Stage and Adult-Plant Resistance to Powdery Mildew in Chinese Elite Wheat Cultivars. Plant Dis 2023; 107:3230-3237. [PMID: 37018212 DOI: 10.1094/pdis-02-23-0399-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. tritici is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of B. graminis f. sp. tritici isolates, named #Bgt-HB and #Bgt-BJ. Using genotypic data obtained from the Wheat TraitBreed 50K single-nucleotide polymorphism array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1, and 6BL.2. The QTL on 2AL conferred all-stage resistance to B. graminis f. sp. tritici race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB. The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL, QPmja.caas-4DL, and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both B. graminis f. sp. tritici mixtures, indicating their probable broad-spectrum resistance. A Kompetitive allele-specific PCR marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Because both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders.
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Affiliation(s)
- Xiaoting Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhongqiu Ni
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050031, Hebei, China
| | - Jingyang Tong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Bin Han
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Simin Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Desen Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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12
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Wang Y, Wang G, Lin D, Luo Q, Xu W, Qu S. QTL mapping and stability analysis of trichome density in zucchini ( Cucurbita pepo L.). Front Plant Sci 2023; 14:1232154. [PMID: 37636121 PMCID: PMC10457680 DOI: 10.3389/fpls.2023.1232154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023]
Abstract
Trichomes provide an excellent model for studying cell differentiation and proliferation. The aboveground tissues of plants with long dense trichomes (LDTs) can cause skin itching in people working in a zucchini field, in which management, pollination, and fruit harvesting are difficult. In this study, an F2 population was constructed with the LDT inbred line "16" and the sparse micro trichome (SMT) inbred line "63" for QTL analysis of type I and II trichome density. Two QTLs were identified on chromosomes 3 and 15 using the QTL-seq method. Additionally, 191 InDel markers were developed on 20 chromosomes, a genetic map was constructed for QTL mapping, and three QTLs were identified on chromosomes 3, 6, and 15. Two QTLs, CpTD3.1 and CpTD15.1, were identified in both QTL-seq and genetic map-based QTL analyses, and CpTD15.1 was the major-effect QTL. The stability of CpTD3.1 and CpTD15.1 was confirmed using data from F2 plants under different environmental conditions. The major-effect QTL CpTD15.1 was located between markers chr15-4991349 and chr15-5766791, with a physical distance of 775.44 kb, and explained 12.71%-29.37% of the phenotypic variation observed in the three environments. CpTD3.1 was located between markers chr3-218350 and chr3-2891236, in a region with a physical distance of 2,672.89 kb, and explained 5.00%-10.64% of the phenotypic variation observed in the three environments. The functional annotations of the genes within the CpTD15.1 region were predicted, and five genes encoding transcription factors regulating trichome development were selected. Cp4.1LG15g04400 encoded zinc finger protein (ZFP) and harbored nonsynonymous SNPs in the conserved ring finger domain between the two parental lines. There were significant differences in Cp4.1LG15g04400 expression between "16" and "63", and a similar pattern was found between germplasm resources of LDT lines and SMT lines. It was presumed that Cp4.1LG15g04400 might regulate trichome density in zucchini. These results lay a foundation for better understanding the density of multicellular nonglandular trichomes and the regulatory mechanism of trichome density in zucchini.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Guichao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Dongjuan Lin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Qinfen Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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13
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De Rouck S, İnak E, Dermauw W, Van Leeuwen T. A review of the molecular mechanisms of acaricide resistance in mites and ticks. Insect Biochem Mol Biol 2023; 159:103981. [PMID: 37391089 DOI: 10.1016/j.ibmb.2023.103981] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/12/2023] [Accepted: 06/11/2023] [Indexed: 07/02/2023]
Abstract
The Arachnida subclass of Acari comprises many harmful pests that threaten agriculture as well as animal health, including herbivorous spider mites, the bee parasite Varroa, the poultry mite Dermanyssus and several species of ticks. Especially in agriculture, acaricides are often used intensively to minimize the damage they inflict, promoting the development of resistance. Beneficial predatory mites used in biological control are also subjected to acaricide selection in the field. The development and use of new genetic and genomic tools such as genome and transcriptome sequencing, bulked segregant analysis (QTL mapping), and reverse genetics via RNAi or CRISPR/Cas9, have greatly increased our understanding of the molecular genetic mechanisms of resistance in Acari, especially in the spider mite Tetranychus urticae which emerged as a model species. These new techniques allowed to uncover and validate new resistance mutations in a larger range of species. In addition, they provided an impetus to start elucidating more challenging questions on mechanisms of gene regulation of detoxification associated with resistance.
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Affiliation(s)
- Sander De Rouck
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Emre İnak
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Department of Plant Protection, Faculty of Agriculture, Ankara University, Dıskapı, 06110, Ankara, Turkiye
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, 9820 Merelbeke, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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14
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Afsharyan NP, Sannemann W, Ballvora A, Léon J. Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population. Plant Direct 2023; 7:e516. [PMID: 37538189 PMCID: PMC10394678 DOI: 10.1002/pld3.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/27/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd-H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.
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Affiliation(s)
- Nazanin P. Afsharyan
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
- Department of Plant BreedingJustus Liebig University GiessenGiessenGermany
| | - Wiebke Sannemann
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
- KWS Saat SE & Co. KGaAEinbeckGermany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant BreedingUniversity of BonnBonnGermany
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15
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Adhikari TB, Siddique MI, Louws FJ, Sim SC, Panthee DR. Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes. Front Plant Sci 2023; 14:1135884. [PMID: 37324699 PMCID: PMC10267708 DOI: 10.3389/fpls.2023.1135884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.
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Affiliation(s)
- Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Muhammad Irfan Siddique
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul, Republic of Korea
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC, United States
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16
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Singh BK, Venkadesan S, Ramkumar MK, Shanmugavadivel PS, Dutta B, Prakash C, Pal M, Solanke AU, Rai A, Singh NK, Mohapatra T, Sevanthi AM. Meta-Analysis of Microarray Data and Their Utility in Dissecting the Mapped QTLs for Heat Acclimation in Rice. Plants (Basel) 2023; 12:1697. [PMID: 37111920 PMCID: PMC10142300 DOI: 10.3390/plants12081697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/19/2023]
Abstract
In the current global warming scenario, it is imperative to develop crops with improved heat tolerance or acclimation, for which knowledge of major heat stress-tolerant genes or genomic regions is a prerequisite. Though several quantitative trait loci (QTLs) for heat tolerance have been mapped in rice, candidate genes from these QTLs have not been reported yet. The meta-analysis of microarray datasets for heat stress in rice can give us a better genomic resource for the dissection of QTLs and the identification of major candidate genes for heat stress tolerance. In the present study, a database, RiceMetaSys-H, comprising 4227 heat stress-responsive genes (HRGs), was created using seven publicly available microarray datasets. This included in-house-generated microarray datasets of Nagina 22 (N22) and IR64 subjected to 8 days of heat stress. The database has provisions for searching the HRGs through genotypes, growth stages, tissues, and physical intervals in the genome, as well as Locus IDs, which provide complete information on the HRGs with their annotations and fold changes, along with the experimental material used for the analysis. The up-regulation of genes involved in hormone biosynthesis and signalling, sugar metabolism, carbon fixation, and the ROS pathway were found to be the key mechanisms of enhanced heat tolerance. Integrating variant and expression analysis, the database was used for the dissection of the major effect of QTLs on chromosomes 4, 5, and 9 from the IR64/N22 mapping population. Out of the 18, 54, and 62 genes in these three QTLs, 5, 15, and 12 genes harboured non-synonymous substitutions. Fifty-seven interacting genes of the selected QTLs were identified by a network analysis of the HRGs in the QTL regions. Variant analysis revealed that the proportion of unique amino acid substitutions (between N22/IR64) in the QTL-specific genes was much higher than the common substitutions, i.e., 2.58:0.88 (2.93-fold), compared to the network genes at a 0.88:0.67 (1.313-fold) ratio. An expression analysis of these 89 genes showed 43 DEGs between IR64/N22. By integrating the expression profiles, allelic variations, and the database, four robust candidates (LOC_Os05g43870, LOC_Os09g27830, LOC_Os09g27650, andLOC_Os09g28000) for enhanced heat stress tolerance were identified. The database thus developed in rice can be used in breeding to combat high-temperature stress.
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Affiliation(s)
- Bablee Kumari Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | | | - M. K. Ramkumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - P. S. Shanmugavadivel
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur 208024, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Chandra Prakash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India
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Pancaldi F, van Loo EN, Senio S, Al Hassan M, van der Cruijsen K, Paulo MJ, Dolstra O, Schranz ME, Trindade LM. Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species. Plants (Basel) 2023; 12:779. [PMID: 36840127 PMCID: PMC9961111 DOI: 10.3390/plants12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence-absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence-absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Eibertus N. van Loo
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sylwia Senio
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mohamad Al Hassan
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kasper van der Cruijsen
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Oene Dolstra
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M. Eric Schranz
- Biosystematics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Wang R, Xing S, Bourke PM, Qi X, Lin M, Esselink D, Arens P, Voorrips RE, Visser RG, Sun L, Zhong Y, Gu H, Li Y, Li S, Maliepaard C, Fang J. Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. Plant Biotechnol J 2023; 21:369-380. [PMID: 36333116 PMCID: PMC9884011 DOI: 10.1111/pbi.13958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 05/11/2023]
Abstract
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.
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Affiliation(s)
- Ran Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Siyuan Xing
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Peter M. Bourke
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Xiuquan Qi
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Miaomiao Lin
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Danny Esselink
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Paul Arens
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | | | - Leiming Sun
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yunpeng Zhong
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Hong Gu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yukuo Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Sikai Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Chris Maliepaard
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jinbao Fang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Li Y, Huo Y, Yang Y, Wang Z, Sun Y, Liu B, Wu X. Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion. Front Plant Sci 2023; 14:1100691. [PMID: 36818885 PMCID: PMC9928573 DOI: 10.3389/fpls.2023.1100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
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Affiliation(s)
| | | | | | | | | | | | - Xiong Wu
- *Correspondence: Bingjiang Liu, ; Xiong Wu,
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20
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Vaishnav S, Chauhan A, Ajay A, Saini BL, Kumar S, Kumar A, Bhushan B, Gaur GK. Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits. Mol Biol Rep 2023; 50:3705-3721. [PMID: 36642776 DOI: 10.1007/s11033-022-08168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/01/2022] [Indexed: 01/17/2023]
Abstract
Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.
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Affiliation(s)
| | - Anuj Chauhan
- Indian Veterinary Research Institute, Bareilly, India.
| | - Argana Ajay
- Indian Veterinary Research Institute, Bareilly, India
| | | | - Subodh Kumar
- Indian Veterinary Research Institute, Bareilly, India
| | - Amit Kumar
- Indian Veterinary Research Institute, Bareilly, India
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Kuzbakova M, Khassanova G, Oshergina I, Ten E, Jatayev S, Yerzhebayeva R, Bulatova K, Khalbayeva S, Schramm C, Anderson P, Sweetman C, Jenkins CLD, Soole KL, Shavrukov Y. Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops. Front Plant Sci 2022; 13:948099. [PMID: 36186054 PMCID: PMC9523450 DOI: 10.3389/fpls.2022.948099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.
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Affiliation(s)
- Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Irina Oshergina
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Sholpan Khalbayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
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Souffriau B, Holt S, Hagman A, De Graeve S, Malcorps P, Foulquié-Moreno MR, Thevelein JM. Polygenic Analysis of Tolerance to Carbon Dioxide Inhibition of Isoamyl Acetate "Banana" Flavor Production in Yeast Reveals MDS3 as Major Causative Gene. Appl Environ Microbiol 2022;:e0081422. [PMID: 36073947 DOI: 10.1128/aem.00814-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The introduction in modern breweries of tall cylindroconical fermentors, replacing the traditional open fermentation vats, unexpectedly revealed strong inhibition of flavor production by the high CO2 pressure in the fermentors. We have screened our collection of Saccharomyces cerevisiae strains for strains displaying elevated tolerance to inhibition of flavor production by +0.65 bar CO2, using a laboratory scale CO2 pressurized fermentation system. We focused on the production of isoamyl acetate, a highly desirable flavor compound conferring fruity banana flavor in beer and other alcoholic beverages, from its precursor isoamyl alcohol (IAAc/Alc ratio). We selected the most tolerant Saccharomyces cerevisiae strain, saké yeast Kyokai no. 1, isolated a stable haploid segregant seg63 with the same high IAAc/Alc ratio under CO2 pressure, crossed seg63 with the unrelated inferior strain ER7A and phenotyped 185 haploid segregants, of which 28 displaying a high IAAc/Alc ratio were pooled. Mapping of Quantitative Trait Loci (QTLs) by whole-genome sequence analysis based on SNP variant frequency revealed two QTLs. In the major QTL, reciprocal hemizygosity analysis identified MDS3 as the causative mutant gene, a putative member of the TOR signaling pathway. The MDS3Seg.63 allele was dominant and contained a single causative point mutation, T2171C, resulting in the F274S substitution. Introduction of MDS3Seg.63 in an industrial tetraploid lager yeast with CRISPR/Cas9 enhanced isoamyl acetate production by 145% under CO2 pressure. This work shows the strong potential of polygenic analysis and targeted genetic modification for creation of cisgenic industrial brewer's yeast strains with specifically improved traits. IMPORTANCE The upscaling of fermentation to very tall cylindroconical tanks is known to negatively impact beer flavor. Most notably, the increased CO2 pressure in such tanks compromises production by the yeast of the desirable fruity “banana” flavor (isoamyl acetate). The cause of the CO2 inhibition of yeast flavor production has always remained enigmatic. Our work has brought the first insight into its molecular-genetic basis and provides a specific gene tool for yeast strain improvement. We first identified a yeast strain with superior tolerance to CO2 inhibition of flavor production, and applied polygenic analysis to identify the responsible gene. We narrowed down the causative element to a single nucleotide difference, MDS3T2171C, and showed that it can be engineered into brewing yeast to obtain strains with superior flavor production in high CO2 pressure conditions, apparently without affecting other traits relevant for beer brewing. Alternatively, such a strain could be obtained through marker-assisted breeding.
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Liu X, Xu Z, Feng B, Zhou Q, Ji G, Guo S, Liao S, Lin D, Fan X, Wang T. Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map. Front Plant Sci 2022; 13:967432. [PMID: 36110352 PMCID: PMC9468616 DOI: 10.3389/fpls.2022.967432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. Ann Bot 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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25
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Williams O, Vander Schoor JK, Butler JB, Ridge S, Sussmilch FC, Hecht VFG, Weller JL. The genetic architecture of flowering time changes in pea from wild to crop. J Exp Bot 2022; 73:3978-3990. [PMID: 35383838 PMCID: PMC9238443 DOI: 10.1093/jxb/erac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Change in phenology has been an important component in crop evolution, and selection for earlier flowering through a reduction in environmental sensitivity has helped broaden adaptation in many species. Natural variation for flowering in domesticated pea (Pisum sativum L.) has been noted and studied for decades, but there has been no clear account of change relative to its wild progenitor. Here we examined the genetic control of differences in flowering time between wild P. sativum ssp. humile and a typical late-flowering photoperiodic P. s. sativum accession in a recombinant inbred population under long and short photoperiods. Our results confirm the importance of the major photoperiod sensitivity locus Hr/PsELF3a and identify two other loci on chromosomes 1 (DTF1) and 3 (DTF3) that contribute to earlier flowering in the domesticated line under both photoperiods. The domesticated allele at a fourth locus on chromosome 6 (DTF6) delays flowering under long days only. Map positions, inheritance patterns, and expression analyses in near-isogenic comparisons imply that DTF1, DTF3, and DTF6 represent gain-of-function alleles of the florigen/antiflorigen genes FTa3, FTa1, and TFL1c/LF, respectively. This echoes similar variation in chickpea and lentil, and suggests a conserved route to reduced photoperiod sensitivity and early phenology in temperate pulses.
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Affiliation(s)
- Owen Williams
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | | | - Jakob B Butler
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Stephen Ridge
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Frances C Sussmilch
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Valerie F G Hecht
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
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26
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Rajandran V, Ortega R, Vander Schoor JK, Butler JB, Freeman JS, Hecht VFG, Erskine W, Murfet IC, Bett KE, Weller JL. Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits. J Exp Bot 2022; 73:3963-3977. [PMID: 35290451 PMCID: PMC9238442 DOI: 10.1093/jxb/erac107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 03/11/2022] [Indexed: 05/25/2023]
Abstract
Modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian, and northern temperate, which correspond to the major global production environments. Reproductive phenology plays a key role in lentil adaptation to this diverse ecogeographic variation. Here, we dissect the characteristic earliness of the pilosae ecotype, suited to the typically short cropping season of South Asian environments. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering, and we show that DTF6a alone is sufficient to confer early flowering under extremely short photoperiods. Genomic synteny confirmed the presence of a conserved cluster of three florigen (FT) gene orthologues among potential candidate genes, and expression analysis in near-isogenic material showed that the early allele is associated with a strong derepression of the FTa1 gene in particular. Sequence analysis revealed a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of >350 accessions with diverse origin showed that the dtf6a allele is predominant in South Asian material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.
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Affiliation(s)
- Vinodan Rajandran
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Raul Ortega
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | | | - Jakob B Butler
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Jules S Freeman
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
- Forest Genetics and Biotechnology, Scion, Private Bag 3020, Rotorua 3046, New Zealand
| | - Valerie F G Hecht
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Willie Erskine
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Ian C Murfet
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
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27
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Nissan N, Hooker J, Pattang A, Charette M, Morrison M, Yu K, Hou A, Golshani A, Molnar SJ, Cober ER, Samanfar B. Novel QTL for Low Seed Cadmium Accumulation in Soybean. Plants (Basel) 2022; 11:1146. [PMID: 35567147 PMCID: PMC9102923 DOI: 10.3390/plants11091146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022]
Abstract
Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg-1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Arezo Pattang
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Malcolm Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Kangfu Yu
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada;
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada;
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Stephen J. Molnar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
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Sugihara Y, Young L, Yaegashi H, Natsume S, Shea DJ, Takagi H, Booker H, Innan H, Terauchi R, Abe A. High-performance pipeline for MutMap and QTL-seq. PeerJ 2022; 10:e13170. [PMID: 35321412 PMCID: PMC8935991 DOI: 10.7717/peerj.13170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/04/2022] [Indexed: 01/12/2023] Open
Abstract
Summary Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).
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Affiliation(s)
- Yu Sugihara
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan,Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Lester Young
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hiroki Yaegashi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Satoshi Natsume
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Daniel J. Shea
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan
| | - Helen Booker
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada,Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Hideki Innan
- Graduate University for Advanced Studies, Hayama, Japan
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan,Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Akira Abe
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
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29
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Jinnan W, Ruyue W, Jihong L, Yanting T, Haoping G, Lili H, Dongyue W, Xueling W. Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar. Mol Genet Genomics 2022; 297:345-356. [PMID: 35015131 DOI: 10.1007/s00438-021-01850-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/18/2021] [Indexed: 11/28/2022]
Abstract
Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64-11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.
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Affiliation(s)
- Wang Jinnan
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Ruyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Li Jihong
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China.
| | - Tian Yanting
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Guo Haoping
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Hou Lili
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Dongyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Xueling
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
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30
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Su X, Wang B, Geng X, Du Y, Yang Q, Liang B, Meng G, Gao Q, Yang W, Zhu Y, Lin T. A high-continuity and annotated tomato reference genome. BMC Genomics 2021; 22:898. [PMID: 34911432 PMCID: PMC8672587 DOI: 10.1186/s12864-021-08212-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. RESULTS Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. CONCLUSION Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.
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Affiliation(s)
- Xiao Su
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Baoan Wang
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaolin Geng
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Yuefan Du
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Qinqin Yang
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Bin Liang
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Ge Meng
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Qiang Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wencai Yang
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China.
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
| | - Tao Lin
- State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China.
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Uwimana B, Mwanje G, Batte M, Akech V, Shah T, Vuylsteke M, Swennen R. Continuous Mapping Identifies Loci Associated With Weevil Resistance [ Cosmopolites sordidus (Germar)] in a Triploid Banana Population. Front Plant Sci 2021; 12:753241. [PMID: 34912355 PMCID: PMC8667469 DOI: 10.3389/fpls.2021.753241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid "Monyet" (2n = 4x) and a 2x "Kokopo" (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker-trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in "Kokopo." Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in "Monyet." The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in "Kokopo" (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
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Affiliation(s)
- Brigitte Uwimana
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Gerald Mwanje
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Michael Batte
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Violet Akech
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), International Livestock Research Institute Campus, Nairobi, Kenya
| | | | - Rony Swennen
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
- Department of Crop Biosystems, KU Leuven, Heverlee, Belgium
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32
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Zhang Y, Gao W, Sonnenberg A, Chen Q, Zhang J, Huang C. Genetic Linkage and Physical Mapping for an Oyster Mushroom ( Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color. Appl Environ Microbiol 2021; 87:e0095321. [PMID: 34406836 DOI: 10.1128/AEM.00953-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.
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33
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Ye W, Yang Y, Wang P, Zhang Y, Zhang L, Tian D, Zhang L, Zhang L, Zhou B. InDel marker development and QTL analysis of agronomic traits in mung bean [ Vigna radiate (L.) Wilczek]. Mol Breed 2021; 41:66. [PMID: 37309317 PMCID: PMC10236061 DOI: 10.1007/s11032-021-01233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/11/2021] [Indexed: 06/14/2023]
Abstract
The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on the main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32 to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two separated F2:3 lines also found that the phenotype was highly corresponded to its genotype which was between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01233-0.
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Affiliation(s)
- Weijun Ye
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
- Anhui Province Key Laboratory of Crop Quality Improvement, Hefei, 230000 Anhui China
| | - Yong Yang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Peiran Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Yin Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Liya Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Dongfeng Tian
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lei Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lingling Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Bin Zhou
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
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34
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Deslauriers SD. High-resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana. AoB Plants 2021; 13:plab063. [PMID: 34729159 PMCID: PMC8557632 DOI: 10.1093/aobpla/plab063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
A primary component of seedling establishment is the photomorphogenic response as seedlings emerge from the soil. This process is characterized by a reduced growth rate in the hypocotyl, increased root growth, opening of the apical hook and expansion of the cotyledons as photosynthetic organs. While fundamental to plant success, the photomorphogenic response can be highly variable. Additionally, studies of Arabidopsis thaliana are made difficult by subtle differences in growth rate between individuals. High-resolution imaging and computational processing have emerged as useful tools for quantification of such phenotypes. This study sought to: (i) develop an imaging methodology which could capture changes in growth rate as seedlings transition from darkness to blue light in real time, and (ii) apply this methodology to single-quantitative trait locus (QTL) analysis using the Cvi × Ler recombinant inbred line (RIL) mapping population. Significant differences in the photomorphogenic response were observed between the parent lines and analysis of 158 RILs revealed a wide range of growth rate phenotypes. Quantitative trait locus analysis detected significant loci associated with dark growth rate on chromosome 5 and significant loci associated with light growth rate on chromosome 2. Candidate genes associated with these loci, such as the previously characterized ER locus, highlight the application of this approach for QTL analysis. Genetic analysis of Landsberg lines without the erecta mutation also supports a role for ER in modulating the photomorphogenic response, consistent with previous QTL analyses of this population. Strengths and limitations of this methodology are presented, as well as means of improvement.
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Affiliation(s)
- Stephen D Deslauriers
- Division of Science and Math, University of Minnesota, Morris, Morris, MN 56267, USA
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35
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Mizuno N, Ishikawa G, Kojima H, Tougou M, Kiribuchi-Otobe C, Fujita M, Nakamura K. Genetic mechanisms determining grain number distribution along the spike and their effect on yield components in wheat. Mol Breed 2021; 41:62. [PMID: 37309314 PMCID: PMC10236116 DOI: 10.1007/s11032-021-01255-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/28/2021] [Indexed: 06/14/2023]
Abstract
The number of wheat grains is one of the major determinants of yield. Many quantitative trait loci (QTLs) and some causal genes such as GNI-A1 and WAPO-A1 that are associated with grain number per spike (GNS) have been identified, but the underlying mechanisms remain largely unknown. We analyzed QTLs for grain number and other related traits using 188 doubled haploid lines derived from the Japanese high-yield variety, Kitahonami, as a parent to elucidate the genetic mechanism determining grain number. The major QTLs for grain number at the apical, central, and basal parts of the spike were identified in different chromosomal regions. We considered GNI-A1 and WAPO-A1 as candidate genes controlling grain number at the central and basal parts of the spike, respectively. Kitahonami had the favorable 105Y allele of GNI-A1 and WAPO-A1b allele and unfavorable alleles of QTLs for grain number at the apical part of spikes. Pyramiding the favorable alleles of these QTLs significantly increased GNS without significantly reducing thousand-grain weight (TGW). In contrast, the accumulation of favorable alleles of QTLs for TGW significantly decreased GNS, whereas days to heading positively correlated with GNS. Late heading increased the spikelet number per spike, resulting in a higher GNS. Pyramiding of the QTLs for TGW and days to heading also altered the GNS. In conclusion, GNS is a complex trait controlled by many QTLs, and it is essential for breeding to design. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01255-8.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Hisayo Kojima
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
| | - Makoto Tougou
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
| | - Kazuhiro Nakamura
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
- Present Address: Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka 833-0041 Japan
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36
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Gould RL, Craig SW, McClatchy S, Churchill GA, Pazdro R. Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation. Free Radic Biol Med 2021; 174:28-39. [PMID: 34324982 PMCID: PMC8597656 DOI: 10.1016/j.freeradbiomed.2021.07.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/14/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Glutathione (GSH) is a critical cellular antioxidant that protects against byproducts of aerobic metabolism and other reactive electrophiles to prevent oxidative stress and cell death. Proper maintenance of its reduced form, GSH, in excess of its oxidized form, GSSG, prevents oxidative stress in the kidney and protects against the development of chronic kidney disease. Evidence has indicated that renal concentrations of GSH and GSSG, as well as their ratio GSH/GSSG, are moderately heritable, and past research has identified polymorphisms and candidate genes associated with these phenotypes in mice. Yet those discoveries were made with in silico mapping methods that are prone to false positives and power limitations, so the true loci and candidate genes that control renal glutathione remain unknown. The present study utilized high-resolution gene mapping with the Diversity Outbred mouse stock to identify causal loci underlying variation in renal GSH levels and redox status. Mapping output identified a suggestive locus associated with renal GSH on murine chromosome X at 51.602 Mbp, and bioinformatic analyses identified apoptosis-inducing factor mitochondria-associated 1 (Aifm1) as the most plausible candidate. Then, mapping outputs were compiled and compared against the genetic architecture of the hepatic GSH system, and we discovered a locus on murine chromosome 14 that overlaps between hepatic GSH concentrations and renal GSH redox potential. Overall, the results support our previously proposed model that the GSH redox system is regulated by both global and tissue-specific loci, vastly improving our understanding of GSH and its regulation and proposing new candidate genes for future mechanistic studies.
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Affiliation(s)
- Rebecca L Gould
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Steven W Craig
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Susan McClatchy
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA.
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Wang T, Liu Y, Yin Q, Geng J, Chen J, Yin X, Wang Y, Shang X, Tian C, Wang Y, Peng J. Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Brief Bioinform 2021; 23:6372935. [PMID: 34545927 DOI: 10.1093/bib/bbab370] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/09/2021] [Accepted: 08/21/2021] [Indexed: 11/13/2022] Open
Abstract
Quantitative trait locus (QTL) analyses of multiomic molecular traits, such as gene transcription (eQTL), DNA methylation (mQTL) and histone modification (haQTL), have been widely used to infer the functional effects of genome variants. However, the QTL discovery is largely restricted by the limited study sample size, which demands higher threshold of minor allele frequency and then causes heavy missing molecular trait-variant associations. This happens prominently in single-cell level molecular QTL studies because of sample availability and cost. It is urgent to propose a method to solve this problem in order to enhance discoveries of current molecular QTL studies with small sample size. In this study, we presented an efficient computational framework called xQTLImp to impute missing molecular QTL associations. In the local-region imputation, xQTLImp uses multivariate Gaussian model to impute the missing associations by leveraging known association statistics of variants and the linkage disequilibrium (LD) around. In the genome-wide imputation, novel procedures are implemented to improve efficiency, including dynamically constructing a reused LD buffer, adopting multiple heuristic strategies and parallel computing. Experiments on various multiomic bulk and single-cell sequencing-based QTL datasets have demonstrated high imputation accuracy and novel QTL discovery ability of xQTLImp. Finally, a C++ software package is freely available at https://github.com/stormlovetao/QTLIMP.
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Affiliation(s)
- Tao Wang
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi St., 150001, Harbin, China
| | - Yongzhuang Liu
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi St., 150001, Harbin, China
| | - Quanwei Yin
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China
| | - Jiaquan Geng
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China
| | - Jin Chen
- Institute for Biomedical Informatics, University of Kentucky, Lexington, 40536, KY, USA
| | - Xipeng Yin
- School of Software, Northwestern Polytechnical University, 1 Dongxiang Road, 710129, Xi'an, China
| | - Yongtian Wang
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China
| | - Chunwei Tian
- Northwestern Polytechnical University, 1 Dongxiang Road, 710129, Xi'an, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi St., 150001, Harbin, China
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China.,Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd, 710129, Xi'an, China
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Yuan HY, Caron CT, Ramsay L, Fratini R, de la Vega MP, Vandenberg A, Weller JL, Bett KE. Genetic and gene expression analysis of flowering time regulation by light quality in lentil. Ann Bot 2021; 128:481-496. [PMID: 34185828 PMCID: PMC8414921 DOI: 10.1093/aob/mcab083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Flowering time is important due to its roles in plant adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, but little is known about light quality-induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil. METHODS We explored variation in flowering time caused by changes in red/far-red-related light quality environments of a lentil interspecific recombinant inbred line (RIL) population developed from a cross between Lens culinaris cv. Lupa and L. orientalis accession BGE 016880. A genetic linkage map was constructed and then used for identifying quantitative trait loci (QTLs) associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes. KEY RESULTS QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9 %. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 (LcFTa1), was located close to three major QTLs. Furthermore, gene expression results suggested that two other florigen genes (LcFTb1 and LcFTb2), MADS-box transcription factors such as LcAGL6/13d, LcSVPb, LcSOC1b and LcFULb, as well as bHLH transcription factor LcPIF6 and Gibberellin 20 oxidase LcGA20oxC,G may also be involved in the light quality response. CONCLUSIONS Our results show that a major component of flowering time sensitivity to light quality is tightly linked to LcFTa1 and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
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Affiliation(s)
- Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Carolyn T Caron
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard Fratini
- Area de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | | | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Ota Y, Matsumoto K, Nakayama Y, Yamakawa T, Ohno T, Mizobuchi R, Sato H. QTL analysis for brown spot resistance in American rice cultivar 'Dawn'. Breed Sci 2021; 71:491-495. [PMID: 34912176 PMCID: PMC8661489 DOI: 10.1270/jsbbs.21015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/18/2021] [Indexed: 06/14/2023]
Abstract
Rice brown spot (BS), caused by Bipolaris oryzae, causes yield loss and deterioration of grain quality. Using single-nucleotide polymorphism (SNP) markers, we conducted quantitative trait locus (QTL) analysis of BS resistance in backcross inbred lines (BILs) from a cross between an American rice cultivar, 'Dawn' (resistant), and 'Koshihikari' (susceptible). Four QTLs for BS resistance were detected in a three-year field evaluation, and 'Dawn' contributed the resistance alleles at all QTLs. The QTL with the greatest effect, qBSR6-kd, explained 15.1% to 20.3% of the total phenotypic variation. Although disease score and days to heading (DTH) were negatively correlated in all three years, qBSR6-kd was located near a QTL for DTH at which the 'Dawn' allele promoted heading. Another BS resistance QTL (qBSR3.1-kd) was unlinked to the QTLs for DTH. Therefore, these two QTLs are likely to be useful for breeding BS-resistant varieties without delaying heading. The other two BS resistance QTLs (qBSR3.2-kd and qBSR7-kd) were located near DTH QTLs at which the 'Dawn' alleles delayed heading. The QTLs reported here will be good candidates for developing BS-resistant cultivars.
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Affiliation(s)
- Yuya Ota
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Kengo Matsumoto
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Yukinori Nakayama
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Tomohiro Yamakawa
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Teppei Ohno
- Kuwana Agricultural Forestry Fisheries Office, Kuwana, Mie 511-8567, Japan
| | - Ritsuko Mizobuchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Sato
- Ministry of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
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Sonnenberg ASM, Sedaghat-Telgerd N, Lavrijssen B, Hendrickx PM, Scholtmeijer K, Baars JJP, Visser RGF, van Peer A. Mapping Recombination Landscape and Basidial Spore Number in the Button Mushroom Agaricus bisporus. Front Fungal Biol 2021; 2:711330. [PMID: 37744108 PMCID: PMC10512247 DOI: 10.3389/ffunb.2021.711330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/30/2021] [Indexed: 09/26/2023]
Abstract
The button mushroom Agaricus bisporus is represented mainly by two varieties, a secondarily homothallic variety with predominantly two heterokaryotic spores per basidia and a heterothallic variety with predominantly four homokaryotic spored basidium. Both varieties also differ in their recombination landscape with the former showing crossovers (CO) predominantly at chromosome ends whereas the latter has a more evenly distribution of CO over the chromosomes. The two varieties are compatible, and this has been used to study segregation of the basidial spore number (BSN) and the genomic positions of recombination, i.e., the CO landscape, in order to find the underlying genetic determinants. Knowledge on genes controlling CO positions might facilitate either the conservation of favorable allele combinations or the disruption of unwanted allele combinations to reduce linkage drag. For BSN, in total seven QTL were found with the major QTL on chromosome 1 explaining ca. 55% of the phenotypic variation. It appeared, however, difficult to map the recombination landscape. This phenotype can only be assessed in the meiotic offspring of an intervarietal hybrid which is a laborious and difficult task. Nevertheless, this was done, and we were able to map three QTLs for this trait, two on chromosome 1 and one on chromosome 2 not overlapping with the QTL for BSN. The hurdles encountered are discussed and a new strategy is proposed that can solves these. We propose to use two genetically unrelated mapping populations both offspring of a cross between a var. bisporus and a var. burnettii homokaryon and thus segregating both for CO and BSN. Homokaryotic offspring of both populations can be intercrossed without limitation of mating incompatibility and marker homozygosity and the hybrid mushrooms directly used to map BSN. Homokaryotic offspring of these hybrid mushrooms can be genotypes to assess CO positions using next generation sequencing technologies that will solve marker problems encountered, especially for genotyping chromosome ends. This new approach can be a useful strategy for a more efficient breeding strategy for mushrooms in general.
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Affiliation(s)
| | | | | | | | | | | | | | - Arend van Peer
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
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Cheng B, Wan H, Han Y, Yu C, Luo L, Pan H, Zhang Q. Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map. Front Plant Sci 2021; 12:682305. [PMID: 34177997 PMCID: PMC8226220 DOI: 10.3389/fpls.2021.682305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/11/2021] [Indexed: 05/27/2023]
Abstract
Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85-47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.
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Affiliation(s)
- Bixuan Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Huihua Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Chao Yu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Le Luo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Shimomura K, Sugiyama M, Kawazu Y, Yoshioka Y. Identification of quantitative trait loci for powdery mildew resistance in highly resistant cucumber ( Cucumis sativus L.) using ddRAD-seq analysis. Breed Sci 2021; 71:326-333. [PMID: 34776739 PMCID: PMC8573554 DOI: 10.1270/jsbbs.20141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew, caused by Podosphaera xanthii (syn. Sphaerotheca fuliginea ex Fr. Poll.), is one of the most economically important foliar diseases in cucumber (Cucumis sativus L.). Cucumber parental line 'Kyuri Chukanbohon Nou 5 Go', developed from weedy cucumber line CS-PMR1, is highly resistant to powdery mildew and is promising breeding material. We performed quantitative trait locus (QTL) analysis using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in a population from a cross between 'Kyuri Chukanbohon Nou 5 Go' and the Japanese native cultivar 'Kaga-aonaga-fushinari', which is susceptible to powdery mildew. The resistance of the population and its parents was evaluated using leaf disc assays and image analysis. We detected one major QTL on Chr. 5 that was effective at both 20°C and 25°C and one minor QTL on Chr. 1 effective at 20°C. We detected two additional QTLs in subpopulation: one on Chr. 3 effective at 20°C and one on Chr. 5 effective at both 20°C and 25°C in a position different from the major QTL. The resistance alleles at all four QTLs were contributed by 'Kyuri Chukanbohon Nou 5 Go'. The results of this study can be used to develop practical DNA markers tightly linked to genes for powdery mildew resistance.
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Affiliation(s)
- Koichiro Shimomura
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Umeda M, Sakaigaichi T, Tanaka M, Tarumoto Y, Adachi K, Hattori T, Hayano M, Takahashi H, Tamura Y, Kimura T, Mori M. Detection of a major QTL related to smut disease resistance inherited from a Japanese wild sugarcane using GRAS-Di technology. Breed Sci 2021; 71:365-374. [PMID: 34776743 PMCID: PMC8573549 DOI: 10.1270/jsbbs.20137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/23/2021] [Indexed: 06/13/2023]
Abstract
Smut disease of sugarcane causes considerable yield losses and the use of resistant varieties is the best control practice. Our group identified a Japanese wild sugarcane with highly smut disease resistance named 'Iriomote8'. In this study, we conducted QTL analysis for smut disease resistance using a mapping population derived from a resistant variety 'Yaenoushie', in which resistance is inherited from 'Iriomote8'. We identified 4813 non-redundant markers using GRAS-Di technology and developed a linkage map of mapping parents. We evaluated smut disease resistance of the mapping population by the inoculation test. Consequently, a large number of clones did not show the disease symptoms and the distribution of smut disease incidence tended to be "L shaped". Composite interval mapping detected an identical QTL for indices of smut disease incidence with a markedly high LOD score (26.6~45.6) at the end of linkage group 8 of 'Yaenoushie'. This QTL explained approximately 50% of the cases of smut disease incidence. In the mapping population, there were no correlations between the indices of smut disease incidence and other agronomic traits. In conclusion, this QTL could be used for marker-assisted selection to significantly improve smut disease resistance without negative effects on other agronomic traits.
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Affiliation(s)
- Makoto Umeda
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Takeo Sakaigaichi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Miyakonojo Research Station, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Minoru Tanaka
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Central Region Agricultural Research Center, Tsukuba Headquarters, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Yusuke Tarumoto
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Katsuki Adachi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- Kubota Corporation, Agri-Solution Department, 1-2-47 Shikitsuhigashi, Naniwa-ku, Osaka 556-8601, Japan
| | - Taiichiro Hattori
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Headquarters, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Michiko Hayano
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Institute for Agro-Environmental Science, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Hiroyuki Takahashi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Yasuaki Tamura
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Tatsuro Kimura
- Toyota Motor Corporation, Agriculture & Biotechnology Business Division, 1 Toyota-cho, Toyota, Aichi 471-8571, Japan
| | - Masaaki Mori
- Toyota Motor Corporation, Environmental Affairs Division, 1-4-18 Koraku, Bunkyo-ku, Tokyo 112-8701, Japan
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Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). Front Plant Sci 2021; 12:615749. [PMID: 34093602 PMCID: PMC8170412 DOI: 10.3389/fpls.2021.615749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
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Affiliation(s)
- Christopher R. Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H. Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E. Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M. Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M. Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). Front Plant Sci 2021; 12:615749. [PMID: 34093602 DOI: 10.1101/2020.10.07.330001v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
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Affiliation(s)
- Christopher R Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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Lian Q, Fu Q, Xu Y, Hu Z, Zheng J, Zhang A, He Y, Wang C, Xu C, Chen B, Garcia-Mas J, Zhao G, Wang H. QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps. BMC Plant Biol 2021; 21:126. [PMID: 33658004 PMCID: PMC7931605 DOI: 10.1186/s12870-021-02904-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown. RESULTS Two high-density genetic maps were constructed by whole-genome resequencing with two F2 segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci. CONCLUSION The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.
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Affiliation(s)
- Qun Lian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yongyang Xu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yuhua He
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200000, China
| | - Chuanqiang Xu
- Shenyang Agricultural University, College of Horticulture, Shenyang, 110866, China
| | - Benxue Chen
- Design Gollege, Zhoukou Normal University, Zhoukou, 466000, China
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Guangwei Zhao
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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Chen S, Zhang Z, Sun Y, Li D, Gao D, Zhan K, Cheng S. Identification of quantitative trait loci for Fusarium head blight (FHB) resistance in the cross between wheat landrace N553 and elite cultivar Yangmai 13. Mol Breed 2021; 41:24. [PMID: 37309419 PMCID: PMC10236037 DOI: 10.1007/s11032-021-01220-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/28/2021] [Indexed: 06/14/2023]
Abstract
Fusarium head blight (FHB) of wheat poses a serious threat to food security in the Yellow-Huai River Valley Winter Wheat Region (YHW) of China. Discovery of new resistant quantitative trait loci (QTLs) or genes and application of them to highly susceptible varieties in the YHW are of great significance for ensuring the grain yield. Here, 160 recombinant inbred lines (RILs) from the cross between N553 (resistant) and Yangmai 13 (moderately susceptible) were used to evaluate FHB resistance by point inoculation, spray inoculation, and natural infection. A high-density genetic map was constructed by using a 15K SNP array and 128 polymorphism SSR markers. A total of 1452 polymorphic markers were identified, which formed 21 linkage groups and covered a total of 3555.1 cM in length. Two and four QTLs respectively related to type I and type II resistance were detected, among which QFhb-hnau.3BS.1 and QFhb-hnau.2DL were stably identified in most environments in Yangzhou and Zhengzhou, whereas QFhbn-hnau.5AL was only identified under natural infection in Jianyang. Based on the physical position (IWGSC RefSeq v1.0), QFhb-hnau.3BS.1 from the landrace N553 is likely to be Fhb1, while QFhb-hnau.2DL from Yangmai 13 may be a novel QTL. Significantly higher FHB resistance was observed in the lines with both QFhb-hnau.3BS.1 and QFhb-hnau.2DL, indicating that these two QTLs have apparent additive effects, and the RILs harboring both the two QTLs may have great application potential for the improvement of FHB resistance in wheat breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01220-5.
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Affiliation(s)
- Shulin Chen
- College of Agronomy, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops, Zhengzhou, 450002 China
| | - Ziliang Zhang
- College of Agronomy, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops, Zhengzhou, 450002 China
| | - Yangyang Sun
- College of Agronomy, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops, Zhengzhou, 450002 China
| | - Dongsheng Li
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Kehui Zhan
- College of Agronomy, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops, Zhengzhou, 450002 China
| | - Shunhe Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
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Gad M, Chao H, Li H, Zhao W, Lu G, Li M. QTL Mapping for Seed Germination Response to Drought Stress in Brassica napus. Front Plant Sci 2021; 11:629970. [PMID: 33633753 PMCID: PMC7900748 DOI: 10.3389/fpls.2020.629970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/22/2020] [Indexed: 05/25/2023]
Abstract
Drought stress is one of the most environmental abiotic stresses affecting seed germination and crop growth. In the present study, the genetic characteristics of seed germination under drought stress in a Brassica napus double haploid population were analyzed. Five germination-related indexes, including germination percentage (GP), root length (RL), shoot length (SL), fresh weight (FW), and root-to-shoot length ratio (R/S) under control and drought stress, were calculated, and the drought stress index (DSI), including DSI-GP, DSI-RL, DSI-SL, DSI-FW, and DSI-R/S, was determined using the quantitative trait loci (QTLs) analysis based on high-density genetic linkage map. The phenotypic analysis indicated that the R/S is an effective morphological trait in the determination of drought tolerance in the seedling stage. Thirty-nine identified QTLs were observed for these traits and then integrated into 36 consensus QTLs, in which 18 QTLs were found to affect the DSI of four traits (GP, RL, SL, and R/S). Based on the co-linearity between genetic and physical maps of B. napus, 256 candidate genes were detected, and 128 genes have single-nucleotidepolymorphisms/insertion-deletion (SNP/InDel) variations between two parents, some of which were associated with the drought stress tolerance (for example, BnaC03g32780D, BnaC03g37030D, and BnaC09g27300D). The present results laid insights into drought tolerance and its genetic bases in B. napus.
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Affiliation(s)
- Mahmoud Gad
- Department of Biotechnology, Collage of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, Collage of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huaixin Li
- Department of Biotechnology, Collage of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Weiguo Zhao
- Department of Biotechnology, Collage of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangyuan Lu
- Faculty of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Maoteng Li
- Department of Biotechnology, Collage of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Pačnik K, Ogrizović M, Diepold M, Eisenberg T, Žganjar M, Žun G, Kužnik B, Gostinčar C, Curk T, Petrovič U, Natter K. Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae. BMC Genomics 2021; 22:110. [PMID: 33563210 PMCID: PMC7871550 DOI: 10.1186/s12864-021-07417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/31/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantitative trait loci analysis can be used to identify those genetic differences between two strains of the same species that are responsible for the differences in a given phenotype. We used this method and complementary approaches to identify genes in the yeast Saccharomyces cerevisiae that are involved in neutral lipid storage. RESULTS We selected two yeast strains, the laboratory strain BY4741 and the wine yeast AWRI1631, with a more than two-fold difference in neutral lipid content. After crossing, sporulation and germination, we used fluorescence activated cell sorting to isolate a subpopulation of cells with the highest neutral lipid content from the pool of segregants. Whole genome sequencing of this subpopulation and of the unsorted pool of segregants implicated several loci that are involved in lipid accumulation. Three of the identified genes, PIG1, PHO23 and RML2, were investigated in more detail. Deletions of these genes and the exchange of the alleles between the two parental strains confirmed that the encoded proteins contribute to neutral lipid storage in S. cerevisiae and that PIG1, PHO23 and RML2 are the major causative genes. Backcrossing of one of the segregants with the parental strains for seven generations revealed additional regions in the genomes of both strains with potential causative genes for the high lipid accumulation phenotype. CONCLUSIONS We identified several genes that contribute to the phenotype of lipid accumulation in an allele-specific manner. Surprisingly, no allelic variations of genes with known functions in lipid metabolism were found, indicating that the level of storage lipid accumulation is determined by many cellular processes that are not directly related to lipid metabolism.
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Affiliation(s)
- Klavdija Pačnik
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mojca Ogrizović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matthias Diepold
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Mia Žganjar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Žun
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Beti Kužnik
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.
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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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