1
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Kim M, Kim J, Lee S, Khanh N, Li Z, Polle JEW, Jin E. Deciphering the β-carotene hyperaccumulation in Dunaliella by the comprehensive analysis of Dunaliella salina and Dunaliella tertiolecta under high light conditions. PLANT, CELL & ENVIRONMENT 2024; 47:213-229. [PMID: 37727131 DOI: 10.1111/pce.14724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023]
Abstract
The green microalga Dunaliella salina hyperaccumulates β-carotene in the chloroplast, which turns its cells orange. This does not occur in the sister species Dunaliella tertiolecta. However, the molecular mechanisms of β-carotene hyperaccumulation were still unclear. Here, we discovered the reasons for β-carotene hyperaccumulation by comparing the morphology, physiology, genome, and transcriptome between the carotenogenic D. salina and the noncarotenogenic D. tertiolecta after transfer to high light. The differences in photosynthetic capacity, cell growth, and the concentration of stored carbon suggest that these species regulate the supply and utilization of carbon differently. The number of β-carotene-containing plastid lipid globules increased in both species, but much faster and to a greater extent in D. salina than in D. tertiolecta. Consistent with the accumulation of plastid lipid globules, the expression of the methyl-erythritol-phosphate and carotenoid biosynthetic pathways increased only in D. salina, which explains the de novo synthesis of β-carotene. In D. salina, the concomitantly upregulated expression of the carotene globule proteins suggests that hyperaccumulation of β-carotene also requires a simultaneous increase in its sink capacity. Based on genomic analysis, we propose that D. salina has genetic advantages for routing carbon from growth to carotenoid metabolism.
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Affiliation(s)
- Minjae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Sangmuk Lee
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Nguyen Khanh
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Juergen E W Polle
- Department of Biology, Brooklyn College of the City University of New York, New York, Brooklyn, USA
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
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2
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Yu X, Qin M, Qu M, Jiang Q, Guo S, Chen Z, Shen Y, Fu G, Fei Z, Huang H, Gao L, Yao X. Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1528-1543. [PMID: 37258460 DOI: 10.1111/tpj.16336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead-end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome-scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A. zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit.
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Affiliation(s)
- Xiaofen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Mengyun Qin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sumin Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zhenghai Chen
- Forest Resources Monitoring Center of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Yufang Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Guodong Fu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853, USA
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
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4
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Peters SA, Underwood CJ. Technology-driven approaches for meiosis research in tomato and wild relatives. PLANT REPRODUCTION 2023; 36:97-106. [PMID: 36149478 PMCID: PMC9957858 DOI: 10.1007/s00497-022-00450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Meiosis is a specialized cell division during reproduction where one round of chromosomal replication is followed by genetic recombination and two rounds of segregation to generate recombined, ploidy-reduced spores. Meiosis is crucial to the generation of new allelic combinations in natural populations and artificial breeding programs. Several plant species are used in meiosis research including the cultivated tomato (Solanum lycopersicum) which is a globally important crop species. Here we outline the unique combination of attributes that make tomato a powerful model system for meiosis research. These include the well-characterized behavior of chromosomes during tomato meiosis, readily available genomics resources, capacity for genome editing, clonal propagation techniques, lack of recent polyploidy and the possibility to generate hybrids with twelve related wild species. We propose that further exploitation of genome bioinformatics, genome editing and artificial intelligence in tomato will help advance the field of plant meiosis research. Ultimately this will help address emerging themes including the evolution of meiosis, how recombination landscapes are determined, and the effect of temperature on meiosis.
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Affiliation(s)
- Sander A Peters
- Business Unit Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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5
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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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Next generation sequencing technologies to explore the diversity of germplasm resources: achievements and trends in tomato. Comput Struct Biotechnol J 2022; 20:6250-6258. [PMID: 36420160 PMCID: PMC9676195 DOI: 10.1016/j.csbj.2022.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022] Open
Abstract
Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, de novo sequencing, and whole genome resequencing. Significant findings in evolutionary history are outlined, thus discussing how genomics has provided new hints about the processes behind domestication. Finally, achievement and perspectives on pan-genome construction and graphical pan-genome development toward precise mining of the natural variation to be exploited for breeding purposes are presented.
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7
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Martina M, Acquadro A, Gulino D, Brusco F, Rabaglio M, Portis E, Lanteri S. First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq. FRONTIERS IN PLANT SCIENCE 2022; 13:1009206. [PMID: 36212343 PMCID: PMC9539318 DOI: 10.3389/fpls.2022.1009206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.
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Affiliation(s)
- Matteo Martina
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Davide Gulino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | | | | | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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8
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Salem KFM, Alghuthaymi MA, Elabd AB, Elabsawy EA, Mierah HH. Prediction of Heterosis for Agronomic Traits in Half-Diallel Cross of Rice ( Oryza sativa L.) under Drought Stress Using Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2022; 11:1532. [PMID: 35736683 PMCID: PMC9229443 DOI: 10.3390/plants11121532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Rice breeders are encouraged to classify potential F1-hybrids without crossing all viable mixtures by testing depending on genetic distance due to lack of labor and time in yield trials. The goals of this research were to establish heterosis and investigate the relationship between genomic distance and agronomic attributes under drought. Half-diallel mating design, 28 F1′s and 8 parents were evaluated under drought and genotyped using 11 microsatellite markers. In total, 39 alleles were detected. Results indicated that the greatest heterotic effects for grain yield were observed in Sakha 103 × Sakha 104 and GZ7576-10-3-2-1 × Giza 179, which gave 29.32−22.57% heterosis, respectively. Heterosis for grain yield in these crosses occurred as a rise in panicle weight, filled grains per panicle, low sterility and 100-grain weight. Correlations of marker-based genetic distance with mid-parent heterosis were positively and significantly correlated with sterility percentage (r = 0.390 *, p < 0.05). However, better-parent heterosis was positively and significantly correlated with sterility percentage (r = 0.352 *, p < 0.05) and grain yield per plant (r = 0.345 *, p < 0.05). Associations indicate that high grain yield and low sterility of rice crosses can be expected from microsatellite marker-defined distances of parents. This study indicated that genetic distance is very effective for heterosis prediction in breeding programs.
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Affiliation(s)
- Khaled F. M. Salem
- Plant Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 22857, Egypt;
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia
| | - Mousa A. Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia
| | - Abdelmoaty B. Elabd
- Field Crops Research Institute, Agricultural Research Center (ARC), Giza 33717, Egypt;
| | - Elsayed A. Elabsawy
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 22857, Egypt;
| | - Hossam H. Mierah
- Plant Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 22857, Egypt;
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9
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Barchenger DW, Hsu YM, Ou JY, Lin YP, Lin YC, Balendres MAO, Hsu YC, Schafleitner R, Hanson P. Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomato. Sci Rep 2022; 12:8374. [PMID: 35589778 PMCID: PMC9120091 DOI: 10.1038/s41598-022-12326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/07/2022] [Indexed: 01/19/2023] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops worldwide. Bacterial wilt (BW), caused by the Ralstonia solanacearum species complex, has been reported as the second most important plant pathogenic bacteria worldwide, and likely the most destructive. Extensive research has identified two major loci, Bwr-6 and Bwr-12, that contribute to resistance to BW in tomato; however, these loci do not completely explain resistance. Segregation of resistance in two populations that were homozygous dominant or heterozygous for all Bwr-6 and Bwr-12 associated molecular markers suggested the action of one or two resistance loci in addition to these two major QTLs. We utilized whole genome sequence data analysis and pairwise comparison of six BW resistant and nine BW susceptible tomato lines to identify candidate genes that, in addition to Bwr-6 and Bwr-12, contributed to resistance. Through this approach we found 27,046 SNPs and 5975 indels specific to the six resistant lines, affecting 385 genes. One sequence variant on chromosome 3 captured by marker Bwr3.2dCAPS located in the Asc (Solyc03g114600.4.1) gene had significant association with resistance, but it did not completely explain the resistance phenotype. The SNP associated with Bwr3.2dCAPS was located within the resistance gene Asc which was inside the previously identified Bwr-3 locus. This study provides a foundation for further investigations into new loci distributed throughout the tomato genome that could contribute to BW resistance and into the role of resistance genes that may act against multiple pathogens.
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Affiliation(s)
| | - Yu-Ming Hsu
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | | | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Mark Angelo O Balendres
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Laguna, Philippines
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10
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iTRAQ and PRM -based proteomics analysis for the identification of differentially abundant proteins related to male sterility in ms-7 mutant tomato (Solanum lycoperscium) plants. J Proteomics 2022; 261:104557. [DOI: 10.1016/j.jprot.2022.104557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/20/2022]
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11
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Deanna R, Acosta MC, Scaldaferro M, Chiarini F. Chromosome Evolution in the Family Solanaceae. FRONTIERS IN PLANT SCIENCE 2022; 12:787590. [PMID: 35154179 PMCID: PMC8832121 DOI: 10.3389/fpls.2021.787590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
This review summarizes and discusses the knowledge of cytogenetics in Solanaceae, the tomato family, its current applications, and prospects for making progress in fundamental systematic botany and plant evolution. We compile information on basic chromosome features (number, size, morphology) and molecular cytogenetics (chromosome banding and rDNA patterns). These data were mapped onto the Solanaceae family tree to better visualize the changes in chromosome features and evaluate them in a phylogenetic context. We conclude that chromosomal features are important in understanding the evolution of the family, especially in delimiting clades, and therefore it is necessary to continue producing this type of data. The potential for future applications in plant biology is outlined. Finally, we provide insights into understanding the mechanisms underlying Solanaceae's diversification that could substantially contribute to developing new approaches for future research.
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Affiliation(s)
- Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Córdoba, Argentina
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | | | - Marisel Scaldaferro
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Córdoba, Argentina
| | - Franco Chiarini
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Córdoba, Argentina
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12
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Breeding for Resistance to Fusarium Wilt of Tomato: A Review. Genes (Basel) 2021; 12:genes12111673. [PMID: 34828278 PMCID: PMC8624629 DOI: 10.3390/genes12111673] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023] Open
Abstract
For over a century, breeders have worked to develop tomato (Solanum lycopersicum) cultivars with resistance to Fusarium wilt (Fol) caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici. Host resistance is the most effective strategy for the management of this disease. For each of the three Fol races, resistance has been introgressed from wild tomato species, predominately in the form of R genes. The I, I-2, I-3, and I-7 R genes have each been identified, as well as the corresponding Avr effectors in the fungus with the exception of Avr7. The mechanisms by which the R gene protein products recognize these effectors, however, has not been elucidated. Extensive genetic mapping, gene cloning, and genome sequencing efforts support the development of tightly-linked molecular markers, which greatly expedite tomato breeding and the development of elite, Fol resistant cultivars. These resources also provide important tools for pyramiding resistance genes and should support the durability of host resistance.
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13
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Qi S, Zhang S, Islam MM, El-Sappah AH, Zhang F, Liang Y. Natural Resources Resistance to Tomato Spotted Wilt Virus (TSWV) in Tomato ( Solanum lycopersicum). Int J Mol Sci 2021; 22:ijms222010978. [PMID: 34681638 PMCID: PMC8538096 DOI: 10.3390/ijms222010978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) is one of the most destructive diseases affecting tomato (Solanum lycopersicum) cultivation and production worldwide. As defenses against TSWV, natural resistance genes have been identified in tomato, including Sw-1a, Sw-1b, sw-2, sw-3, sw-4, Sw-5, Sw-6, and Sw-7. However, only Sw-5 exhibits a high level of resistance to the TSWV. Thus, it has been cloned and widely used in the breeding of tomato with resistance to the disease. Due to the global spread of TSWV, resistance induced by Sw-5 decreases over time and can be overcome or broken by a high concentration of TSWV. How to utilize other resistance genes and identify novel resistance resources are key approaches for breeding tomato with resistance to TSWV. In this review, the characteristics of natural resistance genes, natural resistance resources, molecular markers for assisted selection, and methods for evaluating resistance to TSWV are summarized. The aim is to provide a theoretical basis for identifying, utilizing resistance genes, and developing tomato varieties that are resistant to TSWV.
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Affiliation(s)
- Shiming Qi
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Shijie Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Md. Monirul Islam
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Ahmed H. El-Sappah
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Fei Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Yan Liang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Correspondence: ; Tel.: +86-29-8708-2613
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Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize. Genes Genomics 2021; 43:1403-1411. [PMID: 34591233 DOI: 10.1007/s13258-021-01169-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers. OBJECTIVES High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population. METHODS In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software. RESULTS This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7 cm, with an average interval of 1.22 cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance. CONCLUSIONS The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.
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Bhattarai R, Liu H, Siddique KHM, Yan G. Characterisation of a 4A QTL for Metribuzin Resistance in Wheat by Developing Near-Isogenic Lines. PLANTS (BASEL, SWITZERLAND) 2021; 10:1856. [PMID: 34579389 PMCID: PMC8466451 DOI: 10.3390/plants10091856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/26/2021] [Accepted: 09/05/2021] [Indexed: 11/17/2022]
Abstract
Wheat (Triticum aestivum L.) production is constantly affected by weeds in the farming system. Chemical-based weed management is widely practiced; broad-spectrum herbicides such as metribuzin have been successfully used to control weeds in Australia and elsewhere of the world. Breeding metribuzin-resistant wheat through genetic improvement is needed for effective control of weeds. Quantitative trait loci (QTLs) mapping efforts identified a major QTL on wheat chromosome 4A, explaining up to 20% of the phenotypic variance for metribuzin resistance. The quantitative nature of inheritance of this QTL signifies the importance of near-isogenic lines (NILs), which can convert a quantitative trait into a Mendelian factor for better resolution of the QTL. In the current study, NILs were developed using a heterogeneous inbred family method combined with a fast generation-cycling system in a population of Chuan Mai 25 (resistant) and Ritchie (susceptible). Seven pairs of NILs targeting the 4A QTL for metribuzin resistance were confirmed with a molecular marker and phenotyping. The resistant allele from the resistant parent increased metribuzin resistance by 63-85% (average 69%) compared with the susceptible allele from the susceptible parent. Segregation analysis in the NIL pairs for thousand grain weight (TGW) (g), biomass per plant (kg), tillers per plant, plant height (cm), yield per plant, and powdery mildew visual score (0-9) indicated that these traits were linked with metribuzin resistance. Similarly, TGW was observed to co-segregate with metribuzin resistance in most confirmed NILs, signifying that the two traits are controlled by closely linked genes. The most contrasting NILs can be further characterised by transcriptomic and proteomic analyses to identify the candidate genes responsible for metribuzin resistance.
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Affiliation(s)
- Rudra Bhattarai
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H. M. Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (R.B.); (K.H.M.S.)
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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Li WX, Wang P, Zhao H, Sun X, Yang T, Li H, Hou Y, Liu C, Siyal M, Raja veesar R, Hu B, Ning H. QTL for Main Stem Node Number and Its Response to Plant Densities in 144 Soybean FW-RILs. FRONTIERS IN PLANT SCIENCE 2021; 12:666796. [PMID: 34489989 PMCID: PMC8417731 DOI: 10.3389/fpls.2021.666796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Although the main stem node number of soybean [Glycine max (L.) Merr. ] is an important yield-related trait, there have been limited studies on the effect of plant density on the identification of quantitative trait loci (QTL) for main stem node number (MSNN). To address this issue, here, 144 four-way recombinant inbred lines (FW-RILs) derived from Kenfeng 14, Kenfeng 15, Heinong 48, and Kenfeng 19 were used to identify QTL for MSNN with densities of 2.2 × 105 (D1) and 3 × 105 (D2) plants/ha in five environments by linkage and association studies. As a result, the linkage and association studies identified 40 and 28 QTL in D1 and D2, respectively, indicating the difference in QTL in various densities. Among these QTL, five were common in the two densities; 36 were singly identified for response to density; 12 were repeatedly identified by both response to density and phenotype of two densities. Thirty-one were repeatedly detected across various methods, densities, and environments in the linkage and association studies. Among the 24 common QTL in the linkage and association studies, 15 explained a phenotypic variation of more than 10%. Finally, Glyma.06G094400, Glyma.06G147600, Glyma.19G160800.1, and Glyma.19G161100 were predicted to be associated with MSNN. These findings will help to elucidate the genetic basis of MSNN and improve molecular assistant selection in high-yield soybean breeding.
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Affiliation(s)
- Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Ping Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
- High Education Institute, Huaiyin Institute of Technology, Huai'an, China
| | - Hengxing Zhao
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xu Sun
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Tao Yang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Haoran Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yongqin Hou
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Cuiqiao Liu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Mahfishan Siyal
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rameez Raja veesar
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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López H, Schmitz G, Thoma R, Theres K. Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato. THE PLANT CELL 2021; 33:2412-2430. [PMID: 34009392 PMCID: PMC8364250 DOI: 10.1093/plcell/koab121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/22/2021] [Indexed: 05/28/2023]
Abstract
Shoot branching and complex leaf development relies on the establishment of boundaries that precedes the formation of axillary meristems (AMs) and leaflets. The tomato (Solanum lycopersicum) super determinant mutant is compromised in both processes, due to a mutation in Sde1A. Sde1A encodes a protein with a RAWUL domain, which is also present in Polycomb Group Repressive Complex 1 (PRC1) RING finger proteins and WD Repeat Domain 48 proteins. Genetic analysis revealed that Sde1A and Bmi1A cooperate, whereas Bmi1C antagonizes both activities, indicating the existence of functionally opposing PRC1 complexes that interact with Sde1A. Sde1A is expressed at early stages of boundary development in a small group of cells in the center of the leaf-axil boundary, but its activity is required for meristem formation at later stages. This suggests that Sde1A and Bmi1A promote AM formation and complex leaf development by safeguarding a pool of cells in the developing boundary zones. Genetic and protein interaction analyses showed that Sde1A and Lateral suppressor (Ls) are components of the same genetic pathway. In contrast to ls, sde1a mutants are not compromised in inflorescence branching, suggesting that Sde1A is a potential target for breeding tomato cultivars with reduced side-shoot formation during vegetative development.
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Affiliation(s)
- Hernán López
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Gregor Schmitz
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Rahere Thoma
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
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Shukla RP, Tiwari GJ, Joshi B, Song-Beng K, Tamta S, Boopathi NM, Jena SN. GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1731-1745. [PMID: 34539113 PMCID: PMC8405779 DOI: 10.1007/s12298-021-01041-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 05/16/2023]
Abstract
UNLABELLED A recombinant inbred line mapping population of intra-species upland cotton was generated from a cross between the drought-tolerant female parent (AS2) and the susceptible male parent (MCU13). A linkage map was constructed deploying 1,116 GBS-based SNPs and public domain-based 782 SSRs spanning a total genetic distance of 28,083.03 cM with an average chromosomal span length of 1,080.12 cM with inter-marker distance of 10.19 cM.A total of 19 quantitative trait loci (QTLs) were identified in nine chromosomes for field drought tolerance traits. Chromosomes 3 and 8 harbored important drought tolerant QTLs for chlorophyll stability index trait while for relative water content trait, three QTLs on chromosome 8 and one QTL each on chromosome 4, 12 were identified. One QTL on each chromosome 8, 5, and 7, and two QTLs on chromosome 15 linking to proline content were identified. For the nitrate reductase activity trait, two QTLs were identified on chromosome 3 and one on each chromosome 8, 13, and 26. To complement our QTL study, a meta-analysis was conducted along with the public domain database and resulted in a consensus map for chromosome 8. Under field drought stress, chromosome 8 harbored a drought tolerance QTL hotspot with two in-house QTLs for chlorophyll stability index (qCSI01, qCSI02) and three public domain QTLs (qLP.FDT_1, qLP.FDT_2, qCC.ST_3). Identified QTL hotspot on chromosome 8 could play a crucial role in exploring abiotic stress-associated genes/alleles for drought trait improvement. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01041-y.
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Affiliation(s)
- Ravi Prakash Shukla
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.) 226001 India
- Aakash Institute, Bhopal, Madhya Pradesh 462011 India
| | - Gopal Ji Tiwari
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.) 226001 India
| | - Babita Joshi
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.) 226001 India
- Acamedy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Kah Song-Beng
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor Malaysia
| | - Sushma Tamta
- Department of Botany, D.S.B. Campus, Kumaun University, Nainital, Uttarakhand 263002 India
| | - N. Manikanda Boopathi
- Department of Plant Biotechnology, CPMP & B, Tamil Nadu Agricultural University, Coimbatore, India
| | - Satya Narayan Jena
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.) 226001 India
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20
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Therezan R, Kortbeek R, Vendemiatti E, Legarrea S, de Alencar SM, Schuurink RC, Bleeker P, Peres LEP. Introgression of the sesquiterpene biosynthesis from Solanum habrochaites to cultivated tomato offers insights into trichome morphology and arthropod resistance. PLANTA 2021; 254:11. [PMID: 34160697 PMCID: PMC8222033 DOI: 10.1007/s00425-021-03651-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/29/2021] [Indexed: 05/13/2023]
Abstract
Cultivated tomatoes harboring the plastid-derived sesquiterpenes from S. habrochaites have altered type-VI trichome morphology and unveil additional genetic components necessary for piercing-sucking pest resistance. Arthropod resistance in the tomato wild relative Solanum habrochaites LA1777 is linked to specific sesquiterpene biosynthesis. The Sesquiterpene synthase 2 (SsT2) gene cluster on LA1777 chromosome 8 controls plastid-derived sesquiterpene synthesis. The main genes at SsT2 are Z-prenyltransferase (zFPS) and Santalene and Bergamotene Synthase (SBS), which produce α-santalene, β-bergamotene, and α-bergamotene in LA1777 round-shaped type-VI glandular trichomes. Cultivated tomatoes have mushroom-shaped type-VI trichomes with much smaller glands that contain low levels of monoterpenes and cytosolic-derived sesquiterpenes, not presenting the same pest resistance as in LA1777. We successfully transferred zFPS and SBS from LA1777 to cultivated tomato (cv. Micro-Tom, MT) by a backcrossing approach. The trichomes of the MT-Sst2 introgressed line produced high levels of the plastid-derived sesquiterpenes. The type-VI trichome internal storage-cavity size increased in MT-Sst2, probably as an effect of the increased amount of sesquiterpenes, although it was not enough to mimic the round-shaped LA1777 trichomes. The presence of high amounts of plastid-derived sesquiterpenes was also not sufficient to confer resistance to various tomato piercing-sucking pests, indicating that the effect of the sesquiterpenes found in the wild S. habrochaites can be insect specific. Our results provide for a better understanding of the morphology of S. habrochaites type-VI trichomes and paves the way to obtain insect-resistant tomatoes.
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Affiliation(s)
- Rodrigo Therezan
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Ruy Kortbeek
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Eloisa Vendemiatti
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Saioa Legarrea
- Molecular and Chemical Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Severino M de Alencar
- Department of Agri-Food Industry, Food and Nutrition, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Robert C Schuurink
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Petra Bleeker
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Lázaro E P Peres
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil.
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Liu G, Yu H, Yuan L, Li C, Ye J, Chen W, Wang Y, Ge P, Zhang J, Ye Z, Zhang Y. SlRCM1, which encodes tomato Lutescent1, is required for chlorophyll synthesis and chloroplast development in fruits. HORTICULTURE RESEARCH 2021; 8:128. [PMID: 34059638 PMCID: PMC8166902 DOI: 10.1038/s41438-021-00563-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 05/12/2023]
Abstract
In plants, chloroplasts are the sites at which photosynthesis occurs, and an increased abundance of chloroplasts increases the nutritional quality of plants and the resultant color of fruits. However, the molecular mechanisms underlying chlorophyll synthesis and chloroplast development in tomato fruits remain unknown. In this study, we isolated a chlorophyll-deficient mutant, reduced chlorophyll mutant 1 (rcm1), by ethylmethanesulfonate mutagenesis; this mutant produced yellowish fruits with altered chloroplast development. MutMap revealed that Solyc08g005010 is the causal gene underlying the rcm1 mutant phenotype. A single-nucleotide base substitution in the second exon of SlRCM1 results in premature termination of its translated protein. SlRCM1 encodes a chloroplast-targeted metalloendopeptidase that is orthologous to the BCM1 protein of Arabidopsis and the stay-green G protein of soybean (Glycine max L. Merr.). Notably, the yellowish phenotype of the lutescent1 mutant can be restored with the allele of SlRCM1 from wild-type tomato. In contrast, knockout of SlRCM1 by the CRISPR/Cas9 system in Alisa Craig yielded yellowish fruits at the mature green stage, as was the case for lutescent1. Amino acid sequence alignment and functional complementation assays showed that SlRCM1 is indeed Lutescent1. These findings provide new insights into the regulation of chloroplast development in tomato fruits.
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Affiliation(s)
- Genzhong Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Lei Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jie Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Weifang Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ying Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Pingfei Ge
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
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Xu W, Gao S, Song J, Yang Q, Wang T, Zhang Y, Zhang J, Li H, Yang C, Ye Z. NDW, encoding a receptor-like protein kinase, regulates plant growth, cold tolerance and susceptibility to Botrytis cinerea in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110684. [PMID: 33218645 DOI: 10.1016/j.plantsci.2020.110684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 05/29/2023]
Abstract
Plants utilize different mechanisms to respond and adapt to continuously changing environmental factors. Receptor-like protein kinases (RLKs) comprise one of the largest families of plant transmembrane signaling proteins, which play critical and diverse roles in plant growth, development, and stress response. Here, we identified the necrotic dwarf (ndw) mutant introgression line (IL) 6-2, which demonstrated stunting, leaf curl, and progressive necrosis at low temperatures. Based on map-based cloning and transgenic analysis, we determined that the phenotype of ndw mutant is caused by decreased expression of NDW, which encodes an RLK. NDW is a plasma membrane and cytoplasmic located protein. Overexpression of NDW can restore both of the semi-dwarf and necrotic phenotype in IL6-2 at low temperatures, further we found that NDW could significantly reduce susceptibility to Botrytis cinerea. On the contrary, knockdown NDW in M82 plants could increase the sensitivity to B. cinerea. Furthermore, transcriptional expression analysis showed that NDW affects the expression of genes related to the abscisic acid (ABA) signaling pathway. Taken together, these results indicate that NDW plays an important role in regulating plant growth, cold tolerance and mitigating susceptibility to Botrytis cinerea.
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Affiliation(s)
- Wei Xu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization (Xinjiang Production and Construction Crops), College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Shenghua Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Vegetable Germplasm Innovation and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, Hubei, China
| | - Jianwen Song
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qihong Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Mangat PK, Gannaban RB, Singleton JJ, Angeles-Shim RB. Development of a PCR-based, genetic marker resource for the tomato-like nightshade relative, Solanum lycopersicoides using whole genome sequence analysis. PLoS One 2020; 15:e0242882. [PMID: 33227039 PMCID: PMC7682897 DOI: 10.1371/journal.pone.0242882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022] Open
Abstract
Solanum lycopersicoides is a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilize S. lycopersicoides as a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific to S. lycopersicoides are limited in number, distribution and polymorphism rate. In this study, we developed a suite of S. lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb of S. lycopersicoides contigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci in S. lycopersicoides for which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments between S. lycopersicoides and tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets in S. lycopersicoides and polymorphic loci between S. lycopersicoides and tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource for S. lycopersicoides, as well as for related Solanum spp. for applications in genetics and breeding studies.
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Affiliation(s)
- Puneet Kaur Mangat
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Ritchel B. Gannaban
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Joshua J. Singleton
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
| | - Rosalyn B. Angeles-Shim
- Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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Acharya B, Ingram TW, Oh Y, Adhikari TB, Dean RA, Louws FJ. Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1622. [PMID: 33266395 PMCID: PMC7700276 DOI: 10.3390/plants9111622] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.
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Affiliation(s)
- Bhupendra Acharya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Thomas W. Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - YeonYee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Ralph A. Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
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25
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Rehman F, Gong H, Li Z, Zeng S, Yang T, Ai P, Pan L, Huang H, Wang Y. Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). BMC PLANT BIOLOGY 2020; 20:474. [PMID: 33059596 PMCID: PMC7565837 DOI: 10.1186/s12870-020-02567-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/22/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. RESULTS In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. CONCLUSIONS This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.
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Affiliation(s)
- Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhong Li
- Bairuiyuan Company, Yinchuan, 750000, Ningxia, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Peiyan Ai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lizhu Pan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hongwen Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
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Hao N, Han D, Huang K, Du Y, Yang J, Zhang J, Wen C, Wu T. Genome-based breeding approaches in major vegetable crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1739-1752. [PMID: 31728564 DOI: 10.1007/s00122-019-03477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/09/2019] [Indexed: 05/09/2023]
Abstract
Vegetable crops are major nutrient sources for humanity and have been well-cultivated since thousands of years of domestication. With the rapid development of next-generation sequencing and high-throughput genotyping technologies, the reference genome of more than 20 vegetables have been well-assembled and published. Resequencing approaches on large-scale germplasm resources have clarified the domestication and improvement of vegetable crops by human selection; its application on genetic mapping and quantitative trait locus analysis has led to the discovery of key genes and molecular markers linked to important traits in vegetables. Moreover, genome-based breeding has been utilized in many vegetable crops, including Solanaceae, Cucurbitaceae, Cruciferae, and other families, thereby promoting molecular breeding at a single-nucleotide level. Thus, genome-wide SNP markers have been widely used, and high-throughput genotyping techniques have become one of the most essential methods in vegetable breeding. With the popularization of gene editing technology research on vegetable crops, breeding efficiency can be rapidly increased, especially by combining the genomic and variomic information of vegetable crops. This review outlines the present genome-based breeding approaches used for major vegetable crops to provide insights into next-generation molecular breeding for the increasing global population.
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Affiliation(s)
- Ning Hao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Deguo Han
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Ke Huang
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Yalin Du
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Tao Wu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China.
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China.
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 DOI: 10.3389/fpls.2020.00296/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/24/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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28
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 PMCID: PMC7093584 DOI: 10.3389/fpls.2020.00296] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/11/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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Cazzaniga S, Kim M, Bellamoli F, Jeong J, Lee S, Perozeni F, Pompa A, Jin E, Ballottari M. Photosystem II antenna complexes CP26 and CP29 are essential for nonphotochemical quenching in Chlamydomonas reinhardtii. PLANT, CELL & ENVIRONMENT 2020; 43:496-509. [PMID: 31724187 PMCID: PMC7004014 DOI: 10.1111/pce.13680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 05/08/2023]
Abstract
Photosystems must balance between light harvesting to fuel the photosynthetic process for CO2 fixation and mitigating the risk of photodamage due to absorption of light energy in excess. Eukaryotic photosynthetic organisms evolved an array of pigment-binding proteins called light harvesting complexes constituting the external antenna system in the photosystems, where both light harvesting and activation of photoprotective mechanisms occur. In this work, the balancing role of CP29 and CP26 photosystem II antenna subunits was investigated in Chlamydomonas reinhardtii using CRISPR-Cas9 technology to obtain single and double mutants depleted of monomeric antennas. Absence of CP26 and CP29 impaired both photosynthetic efficiency and photoprotection: Excitation energy transfer from external antenna to reaction centre was reduced, and state transitions were completely impaired. Moreover, differently from higher plants, photosystem II monomeric antenna proteins resulted to be essential for photoprotective thermal dissipation of excitation energy by nonphotochemical quenching.
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Affiliation(s)
| | - Minjae Kim
- Department of Life ScienceHanyang UniversitySeoulSouth Korea
| | | | - Jooyoen Jeong
- Department of Life ScienceHanyang UniversitySeoulSouth Korea
| | - Sangmuk Lee
- Department of Life ScienceHanyang UniversitySeoulSouth Korea
| | | | - Andrea Pompa
- Dipartimento di Scienze BiomolecolariUniversità degli Studi di UrbinoUrbinoItaly
- Istituto di Bioscienze e BiorisorseConsiglio Nazionale delle RicerchePerugiaItaly
| | - EonSeon Jin
- Department of Life ScienceHanyang UniversitySeoulSouth Korea
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An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10010114] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.
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31
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Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:253-264. [PMID: 31529535 DOI: 10.1111/tpj.14536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/25/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
The karyotype represents the basic genetic make-up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.
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Affiliation(s)
- Haoyang Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yufeng Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenli Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species. G3-GENES GENOMES GENETICS 2019; 9:3933-3941. [PMID: 31604826 PMCID: PMC6893187 DOI: 10.1534/g3.119.400529] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved. We generated ∼134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to S. chilense. Synteny analysis suggests significant degree of the gene order conservation between the S. chilense, S. lycopersicum and S. pennellii genomes. We generated the first genome and transcriptome sequence assemblies for the wild tomato species Solanum chilense and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility and for tomato breeding.
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Habe I, Miyatake K, Nunome T, Yamasaki M, Hayashi T. QTL analysis of resistance to bacterial wilt caused by Ralstonia solanacearum in potato. BREEDING SCIENCE 2019; 69:592-600. [PMID: 31988623 PMCID: PMC6977455 DOI: 10.1270/jsbbs.19059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F1-1 to generate a diploid, two-way pseudo-testcross F1 population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to -5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.
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Affiliation(s)
- Ippei Habe
- Nagasaki Agricultural and Forestry Technical Development Center,
3118 Kaizu-cho, Isahaya, Nagasaki 854-0063,
Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa 360, Tsu, Mie 514-2392,
Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa 360, Tsu, Mie 514-2392,
Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
1348 Uzurano, Kasai, Hyogo 675-2103,
Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO,
Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602,
Japan
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Benoit M, Drost HG, Catoni M, Gouil Q, Lopez-Gomollon S, Baulcombe D, Paszkowski J. Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet 2019; 15:e1008370. [PMID: 31525177 PMCID: PMC6762207 DOI: 10.1371/journal.pgen.1008370] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/26/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022] Open
Abstract
Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants. Transposons are major constituents of plant genomes and represent a powerful source of internal genetic and epigenetic variation. For example, domestication of maize has been facilitated by a dramatic change in plant architecture, the consequence of a transposition event. Insertion of transposons near genes often confers quantitative phenotypic variation linked to changes in transcriptional patterns, as documented for blood oranges and grapes. In tomato, the most widely grown fruit crop and model for fleshy fruit biology, occurrences of several beneficial traits related to fruit shape and plant architecture are due to the activity of the transposon family Rider. While Rider represents a unique endogenous source of genetic and epigenetic variation, mechanisms regulating Rider activity remain unexplored. By achieving experimentally-controlled activation of the Rider family, we shed light on the regulation of these transposons by drought stress, signalling by phytohormones, as well as epigenetic pathways. Furthermore, we reveal the presence of Rider-like elements in other economically important crops such as rapeseed, beetroot and quinoa. This suggests that drought-inducible Rider activation could be further harnessed to generate genetic and epigenetic variation for crop breeding, and highlights the potential of transposon-directed mutagenesis for crop improvement.
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Affiliation(s)
- Matthias Benoit
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Quentin Gouil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sara Lopez-Gomollon
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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35
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Anisimova IN, Alpatieva NV, Karabitsina YI, Gavrilenko TA. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J Genet 2019; 98:87. [PMID: 31544787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cytoplasmic male sterility (CMS) is widely used for hybrid seed production in cultivated Solanaceae species. However, there is very limited information about CMS-Rf genetic systems in potato (Solanum tuberosum). Studying the CMS-Rf systems in potato is both of theoretical and practical significance due to the emergence of a new revolutionary strategy of reinventing potato as adiploid inbred line-based crop to develop F1 hybrid seed potato breeding (Lindhout et al. 2011; Jansky et al. 2016). To search for potato Rf gene candidates, the comparative genetic approach was applied. Based on similarity to petunia Rf-PPR592 gene, 38 fragments were identified in five loci of the whole-genome nucleotide sequence of the accession DM 1-3 516 R44 S. tuberosum Phureja group (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The putative encoded mitochondrial proteins have 589-597 amino acid residues, similarto RF-PPR proteins of petunia and chili pepper and contain 14 or 15 PPR motifs. Primers have been developed flanking the most variable 782-865 bp regions of the selected loci, and polymorphism of the cloned fragments has been investigated in a subset of nine potato genotypes. The amplified fragments included seven or eight PPR motifs and lacked introns. The SNP frequencies ranged from 7.0 to 19.8% depending on the locus, while the ratio of nonsynonymous to synonymous substitutions varied between 0.9 and 2.1. Positions 1, 3 and 6 were the most variable in the studied PPR motifs. Our results demonstrated that the analysed sequences belong to the RFL-PPR gene subfamily and may be considered as Rf gene candidates in potato.
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Affiliation(s)
- Irina N Anisimova
- Federal Research Centre, The N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg 190000, Russia.
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36
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Anisimova IN, Alpatieva NV, Karabitsina YI, Gavrilenko TA. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J Genet 2019. [DOI: 10.1007/s12041-019-1130-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Shcherban AB. Prospects for marker-associated selection in tomato <i>Solanum lycopersicum</i> L. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The review gives a brief description of tomato, one of the main objects of olericulture for Siberia. The data on the main directions in the breeding of this culture, such as resistance to various pathogens, the nutritional properties of fruits, the timing of their maturation and storage are generalized. A separate chapter is devoted to the use of various types of DNA markers for constructing detailed genetic maps of the specified object, which, along with full-genome sequencing data, can be used to screen for genes responsible for breeding traits. Most of these traits, especially specific resistance to one or another pathogen, were transferred to the cultivated tomato by crossing with wild species, therefore, special attention was paid in the article to identifying and marking resistance genes to a variety of viral, fungal and bacterial pathogens occurring in Western Siberia and adjacent areas. Another important aspect for breeding is the nutrient content of tomato fruits, including carotenoids, vitamins, sugars, organic acids, etc. Recently, due to modern technologies of sequencing, SNP-genotyping, the development of new bioinformatic approaches, it has become possible to establish genetic cascades determining the biochemical composition of tomato fruits, to identify key genes that can be used in the future for marker-associated selection of nutritional value. And, finally, genetic works devoted to the problem of the optimal dates of fruit ripening in certain climatic conditions and their prolonged storage without loss of quality are discussed.
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Gao S, Gao W, Liao X, Xiong C, Yu G, Yang Q, Yang C, Ye Z. The tomato WV gene encoding a thioredoxin protein is essential for chloroplast development at low temperature and high light intensity. BMC PLANT BIOLOGY 2019; 19:265. [PMID: 31221088 PMCID: PMC6585109 DOI: 10.1186/s12870-019-1829-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 05/13/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Chloroplast biogenesis, a complex process in higher plants, is the key to photoautotrophic growth in plants. White virescent (wv) mutants have been used to unfold the molecular mechanisms underlying the regulation of chloroplast development and chloroplast gene expression in plants. However, most of genes controlling white virescent phenotype still remain unknown. RESULTS In this study, we identified a temperature- and light intensity-sensitive mutant, named as wv. The content of chlorophyll was dramatically decreased in the immature leaves of wv mutant under the conditions of low temperature and high-light intensity. TEM observation showed that the chloroplasts in the young leaves of wv mutant lacked an organized thylakoid membrane, whereas crescent-shaped chloroplasts with well-developed stromal and stacked grana thylakoids in the mature leaves were developed. Immunoblot analyses suggested that proteins of photosynthetic complexes were decreased substantially in wv mutants. Based on map-based cloning and transgenic analysis, we determined that the wv phenotype was caused by single base mutation in the first intron of WV gene, which encoded a thioredoxin protein with 365 amino acids. qRT-PCR analysis revealed that the expression of WV gene was significantly down-regulated in wv mutant. In addition, knockdown of WV gene through RNAi also resulted in white virescent young leaves, suggesting that the mutation possibly blocks the differentiation of chloroplasts through inhibiting the expression of WV gene. Furthermore, the expression of WV peaked in apical buds and gradually decreased along with the developmental stage, which was consistent with the wv mutant phenotype. Expression analysis of chloroplast-encoded genes by qRT-PCR showed that the wv mutation affected the expression pattern of chloroplast-encoded PEP dependent genes. CONCLUSION Our results suggested that wv mutant was sensitive to low temperature and light intensity. WV gene was essential for chloroplast differentiation. A single base mutation in the first intron resulted in down-regulation of WV gene expression, which inhibited the expression of chloroplast-encoded genes, thereby blocking chloroplast formation and chlorophyll synthesis.
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Affiliation(s)
- Shenghua Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430070, Hubei, China
| | - Wenjing Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cheng Xiong
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Gang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qihong Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Padmanabhan C, Ma Q, Shekasteband R, Stewart KS, Hutton SF, Scott JW, Fei Z, Ling KS. Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus. Sci Rep 2019; 9:7673. [PMID: 31114006 PMCID: PMC6529424 DOI: 10.1038/s41598-019-44100-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
Tomato spotted wilt tospovirus (TSWV), one of the most important plant viruses, causes yield losses to many crops including tomato. The current disease management for TSWV is based mainly on breeding tomato cultivars containing the Sw-5 locus. Unfortunately, several Sw-5 resistance-breaking strains of TSWV have been identified. Sw-7 is an alternative locus conferring resistance to a broad range of TSWV strains. In an effort to uncover gene networks that are associated with the Sw-7 resistance, we performed a comparative transcriptome profiling and gene expression analysis between a nearly-isogenic Sw-7 line and its susceptible recurrent parent (Fla. 8059) upon infection by TSWV. A total of 1,244 differentially expressed genes were identified throughout a disease progression process involving networks of host resistance genes, RNA silencing/antiviral defense genes, and crucial transcriptional and translational regulators. Notable induced genes in Sw-7 include those involved in callose accumulation, lignin deposition, proteolysis process, transcriptional activation/repression, and phosphorylation. Finally, we investigated potential involvement of PR-5 in the Sw-7 resistance. Interestingly, PR-5 overexpressed plants conferred enhanced resistance, resulting in delay in virus accumulation and symptom expression. These findings will facilitate breeding and genetic engineering efforts to incorporate this new source of resistance in tomato for protection against TSWV.
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Affiliation(s)
- Chellappan Padmanabhan
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - Qiyue Ma
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Reza Shekasteband
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - Kevin S Stewart
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - Samuel F Hutton
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - John W Scott
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA.
- USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA.
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA.
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40
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Komakhin RA, Strelnikova SR, Zhuchenko AA. Genetic Features of the Tomato Marker Line Мо938. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419010083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Li S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose. Sci Rep 2019; 9:5985. [PMID: 30979937 PMCID: PMC6461668 DOI: 10.1038/s41598-019-42428-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/07/2019] [Indexed: 01/11/2023] Open
Abstract
Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis ‘Old Blush’ (OB) and R. wichuraiana ‘Basyes’ Thornless’ (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
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Affiliation(s)
- Shubin Li
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Guoqian Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Huijun Yan
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Ningning Zhou
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hongying Jian
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Qigang Wang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Min Chen
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xianqin Qiu
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hao Zhang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaodong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Yibo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Micai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ge
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Kaixue Tang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
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Wang L, Cheng Y, Ma Q, Mu Y, Huang Z, Xia Q, Zhang G, Nian H. QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations. BMC Genomics 2019; 20:260. [PMID: 30940069 PMCID: PMC6444683 DOI: 10.1186/s12864-019-5610-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping. RESULTS Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89-23.13% were highlighted. Furthermore, Glyma04g05840, Glyma19g37820, Glyma14g07140 and Glyma19g39340 were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis. CONCLUSIONS Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.
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Affiliation(s)
- Liang Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Yinghui Mu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Zhifeng Huang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086 People’s Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086 People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
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Egan AN, Moore S, Stellari GM, Kang BC, Jahn MM. Tandem gene duplication and recombination at the AT3 locus in the Solanaceae, a gene essential for capsaicinoid biosynthesis in Capsicum. PLoS One 2019; 14:e0210510. [PMID: 30673734 PMCID: PMC6343889 DOI: 10.1371/journal.pone.0210510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/23/2018] [Indexed: 01/18/2023] Open
Abstract
Capsaicinoids are compounds synthesized exclusively in the genus Capsicum and are responsible for the burning sensation experienced when consuming hot pepper fruits. To date, only one gene, AT3, a member of the BAHD family of acyltransferases, is currently known to have a measurable quantitative effect on capsaicinoid biosynthesis. Multiple AT3 paralogs exist in the Capsicum genome, but their evolutionary relationships have not been characterized well. Recessive alleles at this locus result in absence of capsaicinoids in pepper fruit. To explore the evolution of AT3 in Capsicum and the Solanaceae, we sequenced this gene from diverse Capsicum genotypes and species, along with a number of representative solanaceous taxa. Our results revealed that the coding region of AT3 is highly conserved throughout the family. Further, we uncovered a tandem duplication that predates the diversification of the Solanaceae taxa sampled in this study. This pair of tandem duplications were designated AT3-1 and AT3-2. Sequence alignments showed that the AT3-2 locus, a pseudogene, retains regions of amino acid conservation relative to AT3-1. Gene tree estimation demonstrated that AT3-1 and AT3-2 form well supported, distinct clades. In C. rhomboideum, a non-pungent basal Capsicum species, we describe a recombination event between AT3-1 and AT3-2 that modified the putative active site of AT3-1, also resulting in a frame-shift mutation in the second exon. Our data suggest that duplication of the original AT3 representative, in combination with divergence and pseudogene degeneration, may account for the patterns of sequence divergence and punctuated amino acid conservation observed in this study. Further, an early rearrangement in C. rhomboidium could account for the absence of pungency in this Capsicum species.
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Affiliation(s)
- Ashley N. Egan
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
| | - Shanna Moore
- Department of Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, New York, United States of America
| | - Giulia Marina Stellari
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Byoung-Cheorl Kang
- Department of Horticulture, Seoul National University, Seoul, Republic of Korea
| | - Molly M. Jahn
- Department of Agronomy, University of Wisconsin-Madison, USDA FPL, Madison, Wisconsin, United States of America
- * E-mail:
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Rothan C, Diouf I, Causse M. Trait discovery and editing in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:73-90. [PMID: 30417464 DOI: 10.1111/tpj.14152] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.
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Affiliation(s)
- Christophe Rothan
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Isidore Diouf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
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Pereira L, Ruggieri V, Pérez S, Alexiou KG, Fernández M, Jahrmann T, Pujol M, Garcia-Mas J. QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC PLANT BIOLOGY 2018; 18:324. [PMID: 30509167 PMCID: PMC6278158 DOI: 10.1186/s12870-018-1537-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/19/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. RESULTS In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: "Védrantais", from the cantalupensis group, and "Piel de Sapo", from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits. CONCLUSION Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.
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Affiliation(s)
- L. Pereira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - V. Ruggieri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - S. Pérez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - K. G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - M. Fernández
- Semillas Fitó S.A., 08348 Cabrera de Mar, Barcelona, Spain
| | - T. Jahrmann
- Semillas Fitó S.A., 08348 Cabrera de Mar, Barcelona, Spain
| | - M. Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - J. Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
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Pavani M, Sundaram RM, Ramesha MS, Kishore K, Kemparaju KB. Prediction of heterosis in rice based on divergence of morphological and molecular markers. J Genet 2018; 97:1263-1279. [PMID: 30555075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Identifying the best performing hybrid without a field test was essential to save resources and time. In this study, the genetic divergence was estimated using morphological and expressed sequence tag (EST)-derived simple sequence repeats (SSR) markers. Cluster analysis showed that APMS6A and RPHR 1005 belong to groups I and II, respectively, and the hybrid combination recorded the highest mean grain yield of 32.25 g among generated 40 F1s with standard heterosis of 8.4% over hybrid check, KRH2. The coefficient of marker polymorphism (CMP) value was calculated based on EST-SSRmarkers; it ranged from 0.40 to 0.80, and a higher CMP value of 0.80 was obtained for the parental combination APMS6A × RPHR1005. We predicted heterosis for 40 F1s based on correlation between CMP and standard heterosis in different traits with standard varietal and hybrid checks indicating positive correlation and significant value for grain yield per plant (r = 0.58**),productivity per day (r = 0.54**), productive tillers (r = 0.34*) and panicle weight (r = 0.42**). This study revealed that the relationship of molecular marker heterozygosity, along with the combining ability, high mean value of different traits,grouping of parental lines based on morphological and molecular characterization is helpful to identify heterotic patterns in rice.
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Affiliation(s)
- M Pavani
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
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Wang Y, Zhang N, Li T, Yang J, Zhu X, Fang C, Li S, Si H. Genome-wide identification and expression analysis of StTCP transcription factors of potato (Solanum tuberosum L.). Comput Biol Chem 2018; 78:53-63. [PMID: 30497020 DOI: 10.1016/j.compbiolchem.2018.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022]
Abstract
The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redundant TCP transcription factors of potato were identified and divided into two subfamilies including three distinct subclades. The various orthologous TCP genes in Arabidopsis, rice, potato and tomato were identified using synteny and phylogenetic analysis. Protein motif analysis demonstrated that StTCPs in the same subclade shared similar conserved motif structures. Gene structure analysis showed that almost all StTCPs displayed highly conserved exon-intron organization. The analysis of StTCP gene promoter regions revealed that multiple cis-acting elements were involved in plant growth, development, hormone responses as well as stress responses. The result of StTCP gene expression profiles showed they had tissue-specific expression patterns which implied their differentiated functions. According to the results of quantitative RT-PCR (qRT-PCR), 7 StTCP genes were dramatically up-regulated during the release of tuber dormancy and some specific StTCP genes were strongly responding to different abiotic stresses and multiple hormones, which suggested they had important roles in potato growth and development processes. The results of our findings could provide comprehensive insights in StTCP family genes of potato for further functional investigations.
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Affiliation(s)
- Yapeng Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Chenxi Fang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Shigui Li
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Loss of Function in Zeaxanthin Epoxidase of Dunaliella tertiolecta Caused by a Single Amino Acid Mutation within the Substrate-Binding Site. Mar Drugs 2018; 16:md16110418. [PMID: 30388729 PMCID: PMC6266236 DOI: 10.3390/md16110418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/21/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022] Open
Abstract
The zea1 mutant of marine microalga Dunaliella tertiolecta accumulates zeaxanthin under normal growth conditions, and its phenotype has been speculated to be related to zeaxanthin epoxidase (ZEP). In this study, we isolated the ZEP gene from both wild-type D. tertiolecta and the mutant. We found that the zea1 mutant has a point mutation of the 1337th nucleotide of the ZEP sequence (a change from guanine to adenine), resulting in a change of glycine to aspartate in a highly conserved region in the catalytic domain. Similar expression levels of ZEP mRNA and protein in both wild-type and zea1 were confirmed by using qRT-PCR and western blot analysis, respectively. Additionally, the enzyme activity analysis of ZEPs in the presence of cofactors showed that the inactivation of ZEP in zea1 was not caused by deficiency in the levels of cofactors. From the predicted three-dimensional ZEP structure of zea1, we observed a conformational change on the substrate-binding site in the ZEP. A comparative analysis of the ZEP structures suggested that the conformational change induced by a single amino acid mutation might impact the interaction between the substrate and substrate-binding site, resulting in loss of zeaxanthin epoxidase function.
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Chiarini F, Sazatornil F, Bernardello G. Data reassessment in a phylogenetic context gives insight into chromosome evolution in the giant genus Solanum (Solanaceae). SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1431320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Franco Chiarini
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - Federico Sazatornil
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - Gabriel Bernardello
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
- Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales, Casilla de Correo 495, 5000 Córdoba Argentina
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Bali S, Robinson BR, Sathuvalli V, Bamberg J, Goyer A. Single Nucleotide Polymorphism (SNP) markers associated with high folate content in wild potato species. PLoS One 2018; 13:e0193415. [PMID: 29474475 PMCID: PMC5825101 DOI: 10.1371/journal.pone.0193415] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/09/2018] [Indexed: 11/23/2022] Open
Abstract
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide micronutrient malnutrition. In the present study, we report on the identification of single nucleotide polymorphism (SNP) markers associated with folate, an essential micronutrient in the human diet. A high folate diploid clone Fol 1.6 from the wild potato relative Solanum boliviense (PI 597736) was crossed with a low/medium folate diploid S. tuberosum clone USW4self#3. The resulting F1 progeny was intermated to generate an F2 population, and tubers from 94 F2 individuals were harvested for folate analysis and SNP genotyping using a SolCap 12K Potato SNP array. Folate content in the progeny ranged from 304 to 2,952 ng g-1 dry weight. 6,759 high quality SNPs containing 4,174 (62%) polymorphic and 2,585 (38%) monomorphic SNPs were used to investigate marker-trait association. Association analysis was performed using two different approaches: survey SNP-trait association (SSTA) and SNP-trait association (STA). A total of 497 significant SNPs were identified, 489 by SSTA analysis and 43 by STA analysis. Markers identified by SSTA were located on all twelve chromosomes while those identified by STA were confined to chromosomes 2, 4, and 6. Eighteen of the significant SNPs were located within or in close proximity to folate metabolism-related genes. Forty two SNPs were identical between SSTA and STA analyses. These SNPs have potential to be used in marker-assisted selection for breeding high folate potato varieties.
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Affiliation(s)
- Sapinder Bali
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
| | - Bruce R. Robinson
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States of America
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States of America
| | - John Bamberg
- USDA/Agricultural Research Service, US Potato Genebank, Sturgeon Bay, WI, United States of America
| | - Aymeric Goyer
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
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