Single‐marker and haplotype‐based association analysis of anthracnose (Colletotrichum dematium)resistance in spinach (Spinacia oleracea)

Abstract

Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype‐based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose‐associated molecular markers were identified using single‐SNP (sSNP), pairwise haplotype (htP) and multi‐marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype‐based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

“…GWAS, based on the genotyping and phenotyping of a natural germplasm population and high-density markers, has been employed to map simple to complex traits and identify candidate genes in many crops [ 20 – 22 ]. GWAS has been used in spinach for many traits, including surface texture, edge shape, and petiole color [ 23 ]; bolting, tallness, and erectness [ 24 ]; leafminer resistance [ 25 ]; oxalate concentration [ 26 ]; Verticillium wilt resistance [ 27 ], Stemphylium leaf spot resistance [ 28 ]; mineral nutrient contents [ 29 ]; white rust resistance [ 30 ]; growth habit [ 31 ]; anthracnose resistance [ 32 ]; and downy mildew resistance [ 33 – 36 ]. The identification of single nucleotide polymorphism (SNP) markers for the traits has provided valuable molecular tools for breeders to develop spinach cultivars more efficiently.…”

Genomics and Marker-Assisted Improvement of Vegetable Crops

“…(Shi et al, 2016a), Verticillium wilt caused by race 2 (isolate So 923) of V. dahliae Kleb. (Shi et al, 2016d), leaf spot disease caused by Stemphylium botryosum (Shi et al, 2016c) and S. vesicarium (Bhattarai et al, 2020b), anthracnose disease caused by Colletotrichum dematium (Awika et al, 2020), white rust caused by Albugo occidentalis (Awika et al, 2019), Fusarium wilt caused by Fusarium oxysporum f. sp. spinaciae (Fos) (Gyawali et al, 2019), and the diseases caused by Pythium species (ongoing project).…”

A Genome-Wide Association Study Reveals the Genetic Mechanisms of Nutrient Accumulation in Spinach

“…GWAS has been widely utilized to identify genes associated with quantitative traits in various crops, such as rice [18], maize [19], snap bean [20], tomato [21], cucumber [22], pepper [23], melon [24], and carrot [25]. For spinach, GWAS has been used to identify markers and genes associated with features such as disease resistance [26][27][28][29][30], sex determination [31], oxalate concentration [15], and mineral element content [14]. However, few GWASs have been reported on the comprehensive nutritional quality of spinach.…”