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Zhou C, Wang P, Zeng Q, Zeng R, Hu W, Sun L, Liu S, Luan F, Zhu Q. Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure. Sci Rep 2023; 13:6779. [PMID: 37185306 PMCID: PMC10130142 DOI: 10.1038/s41598-023-34046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023] Open
Abstract
Citrullus ecirrhosus, Citrullus rehmii, and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus, and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus, C. rehmii, and C. naudinianus. A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130-133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85-88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ) could be used for taxonomy in Citrullus. Three genes (atpB, clpP1, and rpoC2) were identified to undergo selection and would promote the environmental adaptation of Citrullus.
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Affiliation(s)
- Cong Zhou
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Putao Wang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Qun Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Rongbin Zeng
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Wei Hu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China
| | - Lei Sun
- Department of Agronomy and Horticulture, Liaoning Agricultural Technical College, Yingkou, 115009, People's Republic of China
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Qianglong Zhu
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, NO. 1101 Zhimin Street, Qingshanhu District, Nanchang, 330045, People's Republic of China.
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De Smet I, Vergauwen D. The Collaboration Between Art History and Genetics - An Unlikely Marriage of Disciplines. FRONTIERS IN PLANT SCIENCE 2021; 12:757439. [PMID: 34790214 PMCID: PMC8591120 DOI: 10.3389/fpls.2021.757439] [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: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Our fruits, vegetables, and cereal crops stem from a wild ancestor and have undergone major changes through millennia of domestication and selection. There are various ways to reveal plant diversity over time, and one of these is through the combination of art history and genetics (also known as #ArtGenetics). Here, we discuss this approach from the art historian's point of view and flag the advantages and caveats of such an approach. We also advocate for the development of an integrated, global art database to facilitate such analyses.
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Affiliation(s)
- Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Enhancement of a Landrace of Carosello (Unripe Melon) through the Use of Light-Emitting Diodes (LED) and Nutritional Characterization of the Fruit Placenta. SUSTAINABILITY 2021. [DOI: 10.3390/su132011464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Landraces of ‘Carosello’ (Cucumis melo L.) are a typical expression of Apulia’s agro-biodiversity and are consumed in the same way as cucumbers. The aim of this research was to valorize the cultivation of a local variety of ‘Carosello’, extending the cultivation period and valorizing a part of the fruits that are generally wasted (endosperm). To accomplish this, a local variety called ‘Carosello leccese’ was grown in a greenhouse during the fall season under red + blue and red + blue + far red light-emitting diodes (LED) interlight. Yield, morphology, color and biochemical composition of the external and internal part of the fruit were evaluated. Although yield increased by 26% under supplemental light, the fruit quality was not influenced by LED application. However, the exocarp was greener (chlorophylls) and more yellow (carotenoids) than the mesocarp. Finally, the endosperm, which is the part of the fruit that is generally wasted, showed the highest polyphenols content, proving to be an important source of nutraceutical compounds. Therefore, it was demonstrated that the nutritional value of the endosperm is comparable or higher than the external part of the fruit, but further studies will be necessary to valorize it from a culinary perspective.
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Vergauwen D, De Smet I. Genomes on Canvas: Artist's Perspective on Evolution of Plant-Based Foods. TRENDS IN PLANT SCIENCE 2020; 25:717-719. [PMID: 32673578 DOI: 10.1016/j.tplants.2020.05.010] [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: 03/24/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
How can we trace the evolution of our plant-based food through time? Here, we will discuss the advantages and disadvantages of using historical paintings to map the history of modern fruits, vegetables, legumes, grains, nuts, and seeds, and explain how the general public can contribute to such studies.
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Affiliation(s)
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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5
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Chomicki G, Schaefer H, Renner SS. Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology. THE NEW PHYTOLOGIST 2020; 226:1240-1255. [PMID: 31230355 DOI: 10.1111/nph.16015] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/17/2019] [Indexed: 05/10/2023]
Abstract
Some of the World's most valuable crops, including watermelon, honey melon, cucumber, squash, zucchini and pumpkin, belong to the family Cucurbitaceae. We review insights on their domestication from new phylogenies, archaeology and genomic studies. Ancestral state estimation on the most complete Cucurbitaceae phylogeny to date suggests that an annual life cycle may have contributed to domestication. Domestication started c. 11 000 years ago in the New World and Asia, and apparently more recently in Africa. Some cucurbit crops were domesticated only once, others multiple times (e.g. melon from different Asian and African populations). Most wild cucurbit fruits are bitter and nonpalatable to humans, and nonbitterness of the pulp apparently was a trait favoured early during domestication, with genomic data showing how bitterness loss was achieved convergently. The genetic pathways underlying lycopene accumulation, red or orange pulp colour, and fruit size and shape are only just beginning to be understood. The study of cucurbit domestication in recent years has benefitted from the increasing integration of archaeological and genomic data with insights from herbarium collections, the most efficient way to understand species' natural geographic ranges and climate adaptations.
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Affiliation(s)
- Guillaume Chomicki
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
- The Queen's College, University of Oxford, High St, Oxford, OX1 4AW, UK
| | - Hanno Schaefer
- Plant Biodiversity Research, Technical University of Munich, Emil-Ramann Str. 2, Freising, 85354, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, Munich, 80638, Germany
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Vergauwen D, De Smet I. Watermelons versus Melons: A Matter of Taste. TRENDS IN PLANT SCIENCE 2019; 24:973-976. [PMID: 31629665 DOI: 10.1016/j.tplants.2019.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/03/2023]
Affiliation(s)
- David Vergauwen
- Amarant vzw, Zebrastraat 30-001, B-9000 Ghent, Belgium; Royal Conservatoire Antwerp, Artesis Plantijn University College Antwerp, 2000 Antwerp, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.
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Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon. Int J Mol Sci 2019; 20:ijms20215392. [PMID: 31671884 PMCID: PMC6862219 DOI: 10.3390/ijms20215392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/30/2022] Open
Abstract
Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.
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Jang YJ, Seo M, Hersh CP, Rhee SJ, Kim Y, Lee GP. An evolutionarily conserved non-synonymous SNP in a leucine-rich repeat domain determines anthracnose resistance in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:473-488. [PMID: 30446794 DOI: 10.1007/s00122-018-3235-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
A non-synonymous SNP of CC-NBS-LRR was firstly mapped to confer resistance to anthracnose in watermelon. Newly proposed LRR domain harboring the SNP is evolutionary conserved in the Cucurbitaceae and Fabaceae. Anthracnose disease caused by Colletotrichum devastates many plants. Despite the importance of the disease, the mechanisms of resistance against it are poorly understood. Here, we identified a non-synonymous single-nucleotide polymorphism (SNP) located in a leucine-rich repeat domain as a marker for resistance to anthracnose race 1 in watermelon, using a combination of genetic analyses. We validated this SNP in segregating populations and 59 watermelon accessions using high-resolution melting assays and Sanger sequencing. We demonstrated that the resulting arginine-to-lysine substitution is particularly conserved among the Cucurbitaceae and Fabaceae. We identified a conserved motif, IxxLPxSxxxLYNLQTLxL, found in 1007 orthologues/paralogues from 89 plant species, and discovered that residue 18 of this motif could determine resistance to disease caused by external invaders. This study provides a step forward in understanding anthracnose resistance in watermelon, as well as functional and evolutionary insight into leucine-rich repeat proteins.
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Affiliation(s)
- Yoon Jeong Jang
- Department of Integrative Plant Science, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Minseok Seo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sun-Ju Rhee
- Department of Plant Sciences, The University of Cambridge, Cambridge, CB2 3EA, UK
| | - Yongjae Kim
- Partner Seeds Co., Ltd., Anseong, 17601, Republic of Korea
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Li B, Lu X, Dou J, Aslam A, Gao L, Zhao S, He N, Liu W. Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon ( Citrullus Lanatus L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2018; 19:ijms19103268. [PMID: 30347873 PMCID: PMC6214002 DOI: 10.3390/ijms19103268] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022] Open
Abstract
Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.
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Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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10
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Paris HS. Origin and emergence of the sweet dessert watermelon, Citrullus lanatus. ANNALS OF BOTANY 2015; 116:133-48. [PMID: 26141130 PMCID: PMC4512189 DOI: 10.1093/aob/mcv077] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Watermelons, Citrullus species (Cucurbitaceae), are native to Africa and have been cultivated since ancient times. The fruit flesh of wild watermelons is watery, but typically hard-textured, pale-coloured and bland or bitter. The familiar sweet dessert watermelons, C. lanatus, featuring non-bitter, tender, well-coloured flesh, have a narrow genetic base, suggesting that they originated from a series of selection events in a single ancestral population. The objective of the present investigation was to determine where dessert watermelons originated and the time frame during which sweet dessert watermelons emerged. KEY FINDINGS Archaeological remains of watermelons, mostly seeds, that date from 5000 years ago have been found in northeastern Africa. An image of a large, striped, oblong fruit on a tray has been found in an Egyptian tomb that dates to at least 4000 years ago. The Greek word pepon, Latin pepo and Hebrew avattiah of the first centuries CE were used for the same large, thick-rinded, wet fruit which, evidently, was the watermelon. Hebrew literature from the end of the second century CE and Latin literature from the beginning of the sixth century CE present watermelons together with three sweet fruits: figs, table grapes and pomegranates. Wild and primitive watermelons have been observed repeatedly in Sudan and neighbouring countries of northeastern Africa. CONCLUSIONS The diverse evidence, combined, indicates that northeastern Africa is the centre of origin of the dessert watermelon, that watermelons were domesticated for water and food there over 4000 years ago, and that sweet dessert watermelons emerged in Mediterranean lands by approximately 2000 years ago. Next-generation ancient-DNA sequencing and state-of-the-art genomic analysis offer opportunities to rigorously assess the relationships among ancient and living wild and primitive watermelons from northeastern Africa, modern sweet dessert watermelons and other Citrullus taxa.
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Affiliation(s)
- Harry S Paris
- Institute of Plant Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, P. O. Box 1021, Ramat Yishay 30-095, Israel
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11
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Reddy UK, Abburi L, Abburi VL, Saminathan T, Cantrell R, Vajja VG, Reddy R, Tomason YR, Levi A, Wehner TC, Nimmakayala P. A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon. J Hered 2014; 106:166-76. [PMID: 25425675 DOI: 10.1093/jhered/esu077] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness.
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Affiliation(s)
- Umesh K Reddy
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Lavanya Abburi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Venkata Lakshmi Abburi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Thangasamy Saminathan
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Robert Cantrell
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Venkata Gopinath Vajja
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Rishi Reddy
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Yan R Tomason
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Amnon Levi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Todd C Wehner
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Padma Nimmakayala
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
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Nimmakayala P, Levi A, Abburi L, Abburi VL, Tomason YR, Saminathan T, Vajja VG, Malkaram S, Reddy R, Wehner TC, Mitchell SE, Reddy UK. Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics 2014; 15:767. [PMID: 25196513 PMCID: PMC4246513 DOI: 10.1186/1471-2164-15-767] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/29/2014] [Indexed: 02/08/2023] Open
Abstract
Background A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication. Results We examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of ≥ 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise FST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model. Conclusions Information concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-767) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Umesh K Reddy
- Gus R, Douglass Institute, Department of Biology, West Virginia State University, Dunbar, WV 25112-1000, USA.
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