Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon

BMC Genomics

Umesh K Reddy³  Sharon E Mitchell⁴  Todd C Wehner¹  Rishi Reddy³  Sridhar Malkaram³  Venkata Gopinath Vajja³  Thangasamy Saminathan³  Yan R Tomason³  Venkata Lakshmi Abburi³  Lavanya Abburi³  Amnon Levi²  Padma Nimmakayala³ 

[1] Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA;U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414, USA;Gus R. Douglass Institute, Department of Biology, West Virginia State University, Dunbar, WV 25112-1000, USA;Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA

关键词: Citrullus lanatus var. lanatus;    Watermelon;    Genotyping by sequencing;    Population structure;    Selective sweep;    GWAS;    Linkage disequilibrium;   

Others  :  1140805
DOI  :  10.1186/1471-2164-15-767

 received in 2014-06-10, accepted in 2014-08-29,  发布年份 2014

【 摘 要 】

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 F_ST 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 F_ST 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.

【 授权许可】

   
2014 Nimmakayala et al.; licensee BioMed Central Ltd.

【 图 表 】

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