QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)

Abstract

The linkage map for the recombinant inbred line (RIL) mapping population derived from late leaf spot (LLS) and rust disease susceptible (TAG 24) and resistant (GPBD 4) varieties of peanut was improved by adding 139 new SSR and transposable element (TE) markers. The improved map now has 289 mapped loci with a total map distance of 1730.8 cM and average inter-marker distance of 6.0 cM across 20 linkage groups. Quantitative trait loci (QTL) analysis using improved genetic map with 289 markers and comprehensive phenotypic data for LLS and rust from 11 seasons could identify a region on linkage group AhXV (B03 linkage group of B genome) which contributed significantly towards LLS and rust resistance. Of the five QTL mapped in this region, three showed high phenotypic variance explained (PVE) for both LLS and rust, and two QTL showed high PVE for only rust. The QTL flanked by GM2009-IPAHM103 had very high PVE of 44.5 % and 53.7 %, respectively for LLS and rust response. Another genomic region on AhXII (B10 linkage group of B genome) contained a QTL flanked by GM1839-GM1009 which had a PVE of 14.1-35.2 % for LLS resistance. A new QTL with marker interval GM1989-AhTE0839 on AhV (A05 linkage group of A genome) showed a PVE of 10.2 % for rust resistance. The new markers, AhTE0498 and AhTE0928 linked to rust resistance were validated using another RIL population of TG 26 9 GPBD 4. The marker AhTE0498 showed 49.3-52.3 % PVE, indicating a strong marker validation in the new population. The improved map, QTL and markers for LLS and rust resistance reported in this study will be of immense utility in peanut molecular breeding. Keywords Peanut Á Recombinant inbred lines Á SSR and AhTE markers Á Late leaf spot and rust resistance Á Improved molecular map Á QTL analysis and validation Electronic supplementary material The online version of this article (

Quantitative Trait Locus Analysis of Late Leaf Spot Resistance and Plant-Type-Related Traits in Cultivated Peanut (Arachis hypogaea L.) under Multi-Environments

“…These results indicated that the resistance to LLS in cultivated peanut was controlled by several major QTLs and many minor QTLs, consistent with previous research results [15,46]. When comparing the QTLs for LLS in this study with previous studies (S3 Table) [14,15,46,52,53,54], six major and 10 minor QTLs for LLS in our study were shown to be novel QTLs. This could be due to different genetic backgrounds of the used materials.…”

“…Due to that genome fragments from wild peanut were transferred into cultivated peanuts, this population therefore had high genetic variation and the map had so many polymorphic markers [29]. In the previous studies of QTL mapping for resistance to LLS, GPBD 4 was usually used as a resistant parent [14,15,53]. The source of resistance of GPBD 4 can be traced back to wild species of A .…”

Utility of AhTE Markers for Genetic and Genomic Studies in Groundnut (Arachis hypogaea L.)

“…Therefore, AhTE markers might provide an efficient marker system, like SSR markers (Li et al, 2011;Ren et al, 2014), for genetic and genomic studies in groundnut. Recently, AhTE markers have been successfully employed for trait mapping in groundnut (Shirasawa et al, 2012b;Kolekar et al, 2016). They were also used to identify and clone the gene governing various traits (Lee et al, 2006;Monden et al, 2009;Sato et al, 2013) since the transposable element served as a DNA tag.…”

“…Due to the large number and variation for transpositional activity of AhMITE1, AhTE markers show considerably high (27.4%) polymorphism (Shirasawa et al, 2012a;Kolekar et al, 2016). In this study, an effort was made to analyze the population genetic parametersusing AhTE markers among a mutant population and a recombinant inbred line (RIL) population of groundnut to assess the utility of AhTE markers in genetic and genomic studies.…”

Marker‐assisted backcrossing to develop foliar disease‐resistant genotypes in TMV 2 variety of peanut (Arachis hypogaea L.)

“…The QTL region on A03 was further resolved to 3.06 Mb (131.60–134.66 Mb) genomic region on the A03 pseudomolecule of A genome (Pandey et al., ), which carried ~25 putative candidate genes associated with LLS and rust resistance. SSR (Sujay et al., ), SNP (Pandey et al., ) and AhTE (Kolekar et al., ) markers linked to the QTL/genes were identified. Some of these markers were validated (Sukruth et al., ; Yeri et al., ) and also used for developing foliar disease‐resistant backcross lines (Pasupuleti, Pandey, Manohar, et al., ; Varshney et al., ; Yeri & Bhat, ).…”