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

Abstract

BackgroundA 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.ResultsWe 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.ConclusionsInformation 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 materialThe online version of this article (doi:10.1186/1471-2164-15-767) contains supplementary material, which is available to authorized users.

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…The number of SNPs per chromosome varied according to chromosome with the least on chromosome 10 (416 SNPs; 3%) and the most on chromosome 2 (2561 SNPs; 16%); the average was 1487 SNPs (Figure 1). Similar distributions have been detected in the germplasm of different crops using SNPs, including maize (Romay et al, 2013), chickpea (Bajaj et al, 2014), and watermelon (Nimmakayala et al, 2014). Schröder et al (2016), reported that the most SNPs were located on chromosome 8 using ApeKI and MseI/ TaqαI restriction enzymes.…”

“…This SNP number was similar to other diversity studies. For example, Jarquín et al (2014) detected 52,349 SNPs and after filtering used 16,502 SNPs obtained from 301 elite soybean breeding lines, and Nimmakayala et al (2014) detected 23,693 SNPs and after filtering used 11,485 in a genetic analysis of watermelon germplasm. Likewise, Phuong Phung et al (2014) characterized 182 rice accessions with 25,971 markers after a data-cleaning step.…”

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

“…have been estimated by different approaches, including the use of biochemical, morphological and molecular markers [11–15]. Molecular markers permit in-depth characterization of germplasm [16] and improve the efficiency and precision of conventional plant breeding schemes through marked-assisted selection. Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers proved useful in detecting genetic diversity and determining genetic relationships in pepper germplasm [13–15].…”

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

“…SNPs generated by GBS have been successfully deployed for genetic diversity analysis and Genome-wide association studies (GWAS) in several crops (Poland and Rife, 2012; Narum et al, 2013; Liu et al, 2014; Nimmakayala et al, 2014, 2016; Guajardo et al, 2015; Otto et al, 2016). Increased marker density across the chromosomes facilitates to estimate genome-wide non-random association of allelic states across the chromosomes, which is known as Linkage disequilibrium (LD; Mackay and Powell, 2007; Reddy et al, 2014; Baird, 2015; Wang et al, 2015; Zanke et al, 2015).…”