2017 ASHS Annual Conference

Spinach (Spinacia oleracea L., 2n=2x=12) is an economically important vegetable crop worldwide. The purpose of this research is to build a molecular breeding platform integrated into a classical breeding approach in spinach through next generation sequencing technology including whole-genome sequencing (WGS), whole-genome resequencing (WGR), and genotyping by sequencing (GBS). So far, three levels of genome sequencing have been conducting in spinach: (1) WGS using 10X Genomics Chromium System powered by 10X GemCode Technology combined with the Illumina HiSeq X Ten sequencing platform with 100X sequencing depth and 200X sequencing data in one spinach genotype NIL1; (2) WGR using the Illumina HiSeq X Ten sequencing platform with 33X sequencing depth and 33 Gb sequencing data in 30 cowpea genotypes; and (3) GBS and ddRADseq using Illumina HiSeq series sequencing platform with 0.1-0.3X depth and 100 – 200 Mb data in 1000 spinach genotypes. The de novo genome assembly of spinach NIL1 was created; whole genome variations were analyzed; genetic diversity was determined on 462 spinach genotypes originally collected from 33 countries, and genome-wide association study (GWAS) was conducted for disease resistance to downy mildew (Peronospora effusa), white rust (Albugo occidentalis), Verticillium wilt (Verticillium dahliae), and Stemphylium leaf spot (Stemphylium botryosum f. sp. spinacia); for pest tolerance to leafminer (Liriomyza spp.); for morphological traits: leaf texture, leaf base color, bolting, and height; and for mineral elements: B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, S, and Zn. SNP markers were identified to be associated with these traits in spinach. The SNP markers identified from this study will provide breeders with a tool to select associated traits in spinach breeding programs through marker-assisted selection (MAS) and genomic selection (GS).