Genetic Diversity and Association Analysis in Spinach

Spinach (Spinacia oleracea L., 2n=2x=12) is an economically important vegetable crop worldwide. The objective of this project is to build a molecular breeding platform to augment ongoing classic breeding efforts in spinach in order to expedite genetic gain and release improved spinach cultivars. Analysis of genetic diversity was conducted on 462 spinach genotypes, including 365 USDA-GRIN germplasm accessions, originally collected from 33 countries, using SNPs postulated from GBS. STRUCTURE 2.3.4 and MEGA 7 were used for population structure and genetic diversity analysis. The genetic diversity analysis indicated that there was a geographic (country) factor during spinach cultivar development and spinach production. Association analysis 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. The general linear mode and mixed linear mode from TASSEL, and compressed mixed linear model from GAPIT were used for association analysis. SNP markers were identified to be associated with resistance to downy mildew, white rust, Verticillium wilt, or Stemphylium leaf spot, and also to be associated with mineral elements and oxalate content in spinach. The SNP markers identified from this study provide breeders with a tool to select associated traits in spinach breeding programs through marker-assisted selection.