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

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.

Keywords: late leaf spot and rust diseases; peanut; quantitative trait locus; restriction-site associated DNA sequencing; whole-genome resequencing analysis.

FIGURE 1

SNP signals detected by bulked segregant analysis by sequencing. Frequencies of GPBD 4 alleles of genome-wide SNPs in bulk samples of rust-disease susceptible lines, bulk S (A), and those of resistant lines, bulk R (B), are plotted. Differences between the bulks R and S (bulk R – bulk S) are shown in (C) with an arrow indicating a prominent peak at the end of the chromosome A03. Twenty chromosomes were painted by different colors.

FIGURE 2

Density of SNPs in resistant lines with respect to TAG 24. Numbers of SNPs every 100-kb length over the genome between TAG 24 and either ICGV 86855 (A), GPBD 4 (B), or VG 9514 (C) are plotted.

FIGURE 3

Graphical genotypes of A03 for resistant lines. Black bars show chromosome segments derived from the resistant donor, GPBD 4. Numbers on the top are chromosome positions in a mega-base scale. An arrow indicates an overlapping region of the GPDB 4 genome corresponding to the candidate region for rust resistance.