Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.).

Kenta Shirasawa,Ramesh S Bhat,Venkataswamy Sujay,Rajeev K Varshney,Manish K Pandey,Sarvamangala Cholin,Yogendra P Khedikar,Mallenahally Sukruth,Makanahally V C Gowda,Rohini M Kolekar,Byregowda Asha,Sharanabasappa B Yeri

doi:10.3389/fpls.2018.01727

Abstract

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.

Highlights

Peanut (Arachis hypogaea L.), so-called groundnut, is an important legume crop widely cultivated for food, oil, and fodder productions
An average of 1.7 million (M) high-quality ddRAD-Seq reads per sample were obtained from a TAG 24 × GPBD 4 recombinant inbred lines (RILs) population (Supplementary Table S2)
These single-nucleotide polymorphism (SNP) together with the 326 single sequence repeat (SSR) (Sujay et al, 2012) and A. hypogaea L. transposable element (AhTE) (Kolekar et al, 2016) markers were used for a linkage analysis

Summary

Introduction

Peanut (Arachis hypogaea L.), so-called groundnut, is an important legume crop widely cultivated for food, oil, and fodder productions. Peanut productivity in most areas is hampered by foliar diseases, late leaf spots (LLS) caused by Mycosphaerella berkeleyi W.A. Jenkins, known as Phaeoisariopsis personata & M.A. Curtis) van Arx, and rust by Puccinia arachidis Speg. Curtis) van Arx, and rust by Puccinia arachidis Speg These diseases can reduce yield by up to 70% (Subrahmanyam et al, 1984) and can adversely affect kernel and fodder quality (Dwivedi et al, 2002).

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