Assessment of population differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers

Abstract

1To mine new favorable alleles for tomato breeding, we investigated the 2 feasibility of utilizing Solanum pimpinellifolium as a diverse panel of 3 genome-wide association study through the restriction site-associated DNA 4 sequencing technique. Previous attempts to conduct genome-wide association 5 study using S. pimpinellifolium were impeded by an inability to correct for 6 population stratification and by lack of high-density markers to address the 7 issue of rapid linkage disequilibrium decay. In the current study, a set of 8 24,330 SNPs was identified using 99 S. pimpinellifolium accessions from the 9 Tomato Genetic Resource Center. Approximately 84% PstI site-associated 10 DNA sequencing regions were located in the euchromatic regions, resulting in 11 the tagging of most SNPs on or near genes. Our genotypic data suggested 12 that the optimum number of S. pimpinellifolium ancestral subpopulations was 13 three, and accessions were classified into seven groups. In contrast to the 14 SolCAP SNP genotypic data of previous studies, our SNP genotypic data 15 consistently confirmed the population differentiation, achieving a relatively 16 uniform correction of population stratification. Moreover, as expected, rapid 17 linkage disequilibrium decay was observed in S. pimpinellifolium, especially in 18 euchromatic regions. Approximately two-thirds of the flanking SNP markers 19 did not display linkage disequilibrium. Our result suggests that higher density 20 of molecular markers and more accessions are required to conduct the 21 genome-wide association study utilizing the Solanum pimpinellifolium 22 collection. 23 4 6 MATERIALS AND METHODS 72 Plant materials 73All plant materials and their information were obtained from TGRC (Table 74 S1; http://tgrc.ucdavis.edu/). In this study, 12 accessions from Ecuador and 87 75 accessions from Peru were utilized. According to their mating types, 43 76 accessions were facultative self-compatible (FSC) and 56 accessions were 77 autogamous self-compatible (ASC). Seeds were propagated by self-pollination 78 for two generations using the method of single-seed descent in a greenhouse. 79Young leaves collected from plants of these single-seed descendent seeds 80 were used for DNA extraction.