Abstract
SummaryWhole‐genome resequencing (WGRS) of mapping populations has facilitated development of high‐density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP‐based high‐density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence‐based high‐density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the ‘T’ population (Tifrunner × GT‐C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high‐density genetic map and multiple season phenotyping data identified 35 main‐effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major‐effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R‐genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics‐assisted breeding in peanut.
Highlights
IntroductionThe genetic yield potential of peanut cultivars has been continuously challenged by several diseases including early leaf spot (ELS) caused by Cercospora arachidicola, late leaf spot (LLS) caused by Cercosporidium personatum and Tomato spotted wilt virus (TSWV)
Peanut, Arachis hypogaea (2n = 4x = 40), is an allotetraploid with an AABB genomic constitution which originated from a single recent hybridization and spontaneous tetraploidization of two ancestral diploid species, A. duranensis (A-genome) and A. ipaensis (B-genome) approximately 4000–6000 years ago (Bertioli et al, 2016; Halward et al, 1992; Moretzsohn et al, 2013)
The current study identified seven major quantitative trait locus (QTL) for early leaf spot (ELS) with four of them having negative additive effects suggesting contribution by parent 1, Tifrunner (R), of which two were located on linkage groups (LGs) B03 and B05 contributing over 47% phenotypic variation explained (PVE) each (Table 2, Figure 2)
Summary
The genetic yield potential of peanut cultivars has been continuously challenged by several diseases including early leaf spot (ELS) caused by Cercospora arachidicola, late leaf spot (LLS) caused by Cercosporidium personatum and Tomato spotted wilt virus (TSWV). These foliar diseases cause yield losses of up to 70%, resulting in approximately $600 million in losses (Food and Agriculture Organization (FAO), 2004; Ogwulumba et al, 2008). While insecticides and fungicides have been used as part of an integrated pest management approach, breeding disease-resistant cultivars with high yield and good agronomic performance is the most economical and sustainable solution (Guo et al, 2013; Pandey et al, 2012; Varshney et al, 2013)
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