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Front. Plant Sci. | doi: 10.3389/fpls.2018.01727

Sequencing analysis of genetic loci for resistance for late leaf spot and rust in peanut (Arachis hypogaea L.)

 Kenta Shirasawa1*,  Ramesh S. Bhat2,  Yogendra P. Khedikar2, Venkataswamy Sujay2, Rohini M. Kolekar2, Sharanabasappa B. Yeri2, Mallenahally Sukruth2, Sarvamangala Cholin2, Byregowda Asha2,  Manish K. Pandey3,  Rajeev K. Varshney3 and  Makanahally V. Gowda2
  • 1Kazusa DNA Research Institute, Japan
  • 2University of Agricultural Sciences, Dharwad, India
  • 3International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India

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.

Keywords: Late leaf spot and rust resistance, Peanut (Arachis hypogaea L), Quantitative trait locus (QTL) analysis, Restriction-site associated DNA sequencing (RAD-Seq), Whole genome sequencing analysis

Received: 03 Aug 2018; Accepted: 07 Nov 2018.

Edited by:

Petr Smýkal, Palacký University, Olomouc, Czechia

Reviewed by:

Harsh Raman, New South Wales Department of Primary Industries, Australia
Amit A. Deokar, University of Saskatchewan, Canada  

Copyright: © 2018 Shirasawa, Bhat, Khedikar, Sujay, Kolekar, Yeri, Sukruth, Cholin, Asha, Pandey, Varshney and Gowda. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Kenta Shirasawa, Kazusa DNA Research Institute, Kisarazu, Japan, shirasaw@kazusa.or.jp