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Wen T, Zhang X, Zhu J, Zhang S, Rhaman MS, Zeng W. A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1338086. [PMID: 38384753 PMCID: PMC10880447 DOI: 10.3389/fpls.2024.1338086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.
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Affiliation(s)
- Tingting Wen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- Seed Administration Station of Shandong Province, Jinan, China
| | - Xuefei Zhang
- Taian Daiyue District Bureau of Agriculture and Rural Affairs, Taian, China
| | - Jiaojiao Zhu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Susu Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Wei Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
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Che Y, Yang Y, Yang Y, Wei L, Guo J, Yang X, Li X, Liu W, Li L. Construction of a high-density genetic map and mapping of a spike length locus for rye. PLoS One 2023; 18:e0293604. [PMID: 37903124 PMCID: PMC10615298 DOI: 10.1371/journal.pone.0293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yunjie Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Juan Guo
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Gubaev R, Boldyrev S, Martynova E, Chernova A, Kovalenko T, Chebanova Y, Peretyagina T, Goryunova S, Goryunov D, Mukhina Z, Ben C, Gentzbittel L, Khaitovich P, Demurin Y. QTL mapping of oleic acid content in modern VNIIMK sunflower (Helianthus annuus L.) lines by using GBS-based SNP map. PLoS One 2023; 18:e0288772. [PMID: 37792750 PMCID: PMC10550128 DOI: 10.1371/journal.pone.0288772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/05/2023] [Indexed: 10/06/2023] Open
Abstract
Oleic acid is a monounsaturated fatty acid increasing oil oxidative stability. High content of oleic acid is thus a valuable trait in oilseed crops. Sunflower (Helianthus annuus L.) normally accumulates linoleic acid as a major fatty acid, but a mutant expressing a high oleic phenotype form was previously obtained by chemical mutagenesis and mapped on the sunflower genome. Several studies suggest the presence of additional genes involved in the control of the high content of oleic acid, with their expression possibly depending on the genetic background. To test this hypothesis, we performed a QTL mapping of the high oleic acid trait within two independent F2 crosses involving lines with contrasting oleic acid content from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We applied genotyping-by-sequencing (GBS) to construct single nucleotide polymorphism-based genetic maps and performed QTL mapping using quantitative and qualitative encoding for oleic acid content. Our results support the finding that the oleic acid content in the assessed crosses is controlled by one major effect locus. However, different dominant/recessive effects of the major locus were reported for both crosses. Additionally, a possible translocation between chromosome 7 and 14 was reported in one assessed cross. We defined a set of single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.
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Affiliation(s)
- Rim Gubaev
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- LLC "Oil Gene", Moscow, Russia
| | - Stepan Boldyrev
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- LLC "Oil Gene", Moscow, Russia
| | - Elena Martynova
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- LLC "Oil Gene", Moscow, Russia
| | - Alina Chernova
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- LLC "Oil Gene", Moscow, Russia
| | - Tatyana Kovalenko
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar, Russia
| | - Yuliya Chebanova
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar, Russia
| | | | - Svetlana Goryunova
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- FSBSI Lorch Potato Research Institute, Kraskovo, Russia
- Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Denis Goryunov
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Cecile Ben
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
| | | | | | - Yakov Demurin
- Skolkovo Institute of Science and Technology, Bolshoy Moscow, Russia
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar, Russia
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:840954. [PMID: 35665155 PMCID: PMC9158519 DOI: 10.3389/fpls.2022.840954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017-2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H 2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%-16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Gubaev R, Boldyrev S, Martynova E, Chernova A, Kovalenko T, Peretyagina T, Goryunova S, Goryunov D, Mukhina Z, Ben C, Gentzbittel L, Khaitovich P, Demurin Y. Genetic mapping of loci involved in oil tocopherol composition control in Russian sunflower ( Helianthus annuus L.) lines. G3 GENES|GENOMES|GENETICS 2022; 12:6527637. [PMID: 35150257 PMCID: PMC8982403 DOI: 10.1093/g3journal/jkac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Tocopherols are antioxidants that preserve oil lipids against oxidation and serve as a natural source of vitamin E in the human diet. Compared with other major oilseeds like rapeseed and soybean, sunflower (Helianthus annuus L.) exhibits low phenotypic diversity of tocopherol composition, both in wild and cultivated accessions from germplasm collections. Two major mutations that alter tocopherol composition were identified in genetic collections, and several studies suggested additional loci controlling tocopherol composition, with their expression possibly depending on the genetic background. In the present study, we performed QTL mapping of tocopherol composition in two independent F2 crosses between lines with contrasting tocopherol composition from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We used genotyping-bysequencing (GBS) to construct single nucleotide polymorphism-based genetic maps, and performed QTL mapping using quantitative and qualitative encoding for phenotypic traits. Our results support the notion that the tocopherol composition in the assessed crosses is controlled by two loci. We additionally selected and validated two single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.
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Affiliation(s)
- Rim Gubaev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Stepan Boldyrev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Elena Martynova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alina Chernova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Tatyana Kovalenko
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Tatyana Peretyagina
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Svetlana Goryunova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Russian Potato Research Center, Kraskovo 140051, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Denis Goryunov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zhanna Mukhina
- All-Russia Rice Research Institute, Krasnodar 350921, Russia
| | - Cecile Ben
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | | | - Yakov Demurin
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
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Yol E, Basak M, Kızıl S, Lucas SJ, Uzun B. A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame. FRONTIERS IN PLANT SCIENCE 2021; 12:679659. [PMID: 34140967 PMCID: PMC8204047 DOI: 10.3389/fpls.2021.679659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/23/2021] [Indexed: 05/05/2023]
Abstract
The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. In the present study, we generated a sesame F2 population derived from a cross between a capsule shattering cultivar (Muganli-57) and a non-shattering mutant (PI 599446), which was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing. The resulting high-density genetic map contained 782 single-nucleotide polymorphisms (SNPs) and spanned a length of 697.3 cM, with an average marker interval of 0.89 cM. Based on the reference genome, the capsule shattering trait was mapped onto SNP marker S8_5062843 (78.9 cM) near the distal end of LG8 (chromosome 8). In order to reveal genes potentially controlling the shattering trait, the marker region (S8_5062843) was examined, and a candidate gene including six CDSs was identified. Annotation showed that the gene encodes a protein with 440 amino acids, sharing ∼99% homology with transcription repressor KAN1. Compared with the capsule shattering allele, the SNP change and altered splicing in the flanking region of S8_5062843 caused a frameshift mutation in the mRNA, resulting in the loss of function of this gene in the mutant parent and thus in non-shattering capsules and leaf curling. With the use of genomic data, InDel and CAPS markers were developed to differentiate shattering and non-shattering capsule genotypes in marker-assisted selection studies. The obtained results in the study can be beneficial in breeding programs to improve the shattering trait and enhance sesame productivity.
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Affiliation(s)
- Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
- *Correspondence: Engin Yol,
| | - Merve Basak
- Department of Medicinal and Aromatic Plants, Akev University, Antalya, Turkey
| | - Sibel Kızıl
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Istanbul, Turkey
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
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Wu X, Feng F, Zhu Y, Xie F, Yang J, Gong J, Liu Y, Zhu W, Gao T, Chen D, Li X, Huang J. Construction of High-Density Genetic Map and Identification of QTLs Associated with Seed Vigor after Exposure to Artificial Aging Conditions in Sweet Corn Using SLAF-seq. Genes (Basel) 2019; 11:genes11010037. [PMID: 31905667 PMCID: PMC7016829 DOI: 10.3390/genes11010037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 01/23/2023] Open
Abstract
Seed vigor is a key factor that determines the quality of seeds, which is of great significance for agricultural production, with the potential to promote growth and productivity. However, the underlying molecular mechanisms and genetic basis for seed vigor remain unknown. High-density genetic linkage mapping is an effective method for genomic study and quantitative trait loci (QTL) mapping. In this study, a high-density genetic map was constructed from a 148 BC4F3 population cross between ‘M03’ and ‘M08’ strains based on specific-locus amplified fragment (SLAF) sequencing. The constructed high-density genetic linkage map (HDGM) included 3876 SNP markers on ten chromosomes covering 2413.25 cM in length, with a mean distance between markers of 0.62 cM. QTL analysis was performed on four sweet corn germination traits that are related to seed vigor under artificial aging conditions. A total of 18 QTLs were identified in two seasons. Interestingly, a stable QTL was detected in two seasons on chromosome 10—termed qGR10—within an interval of 1.37 Mb. Within this interval, combined with gene annotation, we found four candidate genes (GRMZM2G074309, GRMZM2G117319, GRMZM2G465812, and GRMZM2G343519) which may be related to seed vigor after artificial aging.
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Affiliation(s)
- Xiaming Wu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Faqiang Feng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Yuzhong Zhu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Fugui Xie
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China;
| | - Jie Gong
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Yu Liu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Wei Zhu
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Tianle Gao
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Danyi Chen
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Xiaoqin Li
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
| | - Jun Huang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (F.F.); (Y.Z.); (F.X.); (J.G.); (Y.L.); (W.Z.); (T.G.); (D.C.); (X.L.)
- Correspondence: ; Tel.: +86-020-85288311
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Su J, Jiang J, Zhang F, Liu Y, Ding L, Chen S, Chen F. Current achievements and future prospects in the genetic breeding of chrysanthemum: a review. HORTICULTURE RESEARCH 2019; 6:109. [PMID: 31666962 PMCID: PMC6804895 DOI: 10.1038/s41438-019-0193-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat.) is a leading flower with applied value worldwide. Developing new chrysanthemum cultivars with novel characteristics such as new flower colors and shapes, plant architectures, flowering times, postharvest quality, and biotic and abiotic stress tolerance in a time- and cost-efficient manner is the ultimate goal for breeders. Various breeding strategies have been employed to improve the aforementioned traits, ranging from conventional techniques, including crossbreeding and mutation breeding, to a series of molecular breeding methods, including transgenic technology, genome editing, and marker-assisted selection (MAS). In addition, the recent extensive advances in high-throughput technologies, especially genomics, transcriptomics, proteomics, metabolomics, and microbiomics, which are collectively referred to as omics platforms, have led to the collection of substantial amounts of data. Integration of these omics data with phenotypic information will enable the identification of genes/pathways responsible for important traits. Several attempts have been made to use emerging molecular and omics methods with the aim of accelerating the breeding of chrysanthemum. However, applying the findings of such studies to practical chrysanthemum breeding remains a considerable challenge, primarily due to the high heterozygosity and polyploidy of the species. This review summarizes the recent achievements in conventional and modern molecular breeding methods and emerging omics technologies and discusses their future applications for improving the agronomic and horticultural characteristics of chrysanthemum.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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