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 (

The aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis across the recombinant inbred lines (RILs) derived from a cross between a susceptible line, TAG 24, and a resistant line, GPBD 4. A total of 171 SNPs from the ddRAD-Seq together with 282 markers published in the previous studies were mapped on a genetic map covering 1510.1 cM. Subsequent quantitative trait locus (QTL) analysis revealed major genetic loci for LLS and rust resistance on chromosomes A02 and A03, respectively. Heterogeneous inbred family-derived near isogenic lines and the pedigree of the resistant gene donor, A. cardenasii Krapov. & W.C. Greg., including the resistant derivatives of ICGV 86855 and VG 9514 as well as GPBD 4, were employed for whole-genome resequencing analysis. The results indicated the QTL candidates for LLS and rust resistance were located in 1.4- and 2.7-Mb genome regions on A02 and A03, respectively. In these regions, four and six resistance-related genes with deleterious mutations were selected as candidates for LLS and rust resistance, respectively. These delimited genomic regions may be beneficial in breeding programs aimed at improving disease resistance and enhancing peanut productivity.

TMV 2 is a very popular peanut variety among the Indian farmers, but it is highly susceptible to fungal foliar diseases like late leaf spot (LLS) and rust. Marker‐assisted backcrossing (MABC) in TMV 2 using foliar disease‐resistant donor, GPBD 4 and the disease resistance‐linked markers (GM2009, GM2079, GM2301, GM1839 and IPAHM103) resulted in a large number of backcross populations and also straight cross populations. Foreground selection followed by field evaluation under disease epiphytotic conditions could identify a few superior genotypes. Two homozygous backcross lines TMG‐29 and TMG‐46 showed enhanced resistance to LLS and rust diseases (score of 3.00 for both) along with 71.0% and 62.7% increase in the pod yield per plot, respectively, over the check, TMV 2. These foliar disease‐resistant and productive lines can be released as commercial varieties or can be used as genetic resources in the peanut improvement.

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