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.

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

“…Further gene annotation for the candidate genes of some of the marker like AhTE0442, AhTE0205, and AhTE0474 on chromosome number A03 showed functions related to oxidoreductase activity. Several reports in peanut showed markers associated with disease resistance were also localized on A03 that was evident from QTL mapping and sequencing (59,60,85). The occurrence of genes encoding for antioxidant activity at A03 might provide disease resistance in peanut.…”

Translational genomics for achieving higher genetic gains in groundnut

“…The low coverage sequencing approaches include GBS (Elshire et al 2011;Poland et al 2012), RADseq (Miller et al 2007), ddRADseq (Peterson et al 2012) and SLAF-seq (Sun et al 2013), and high coverage sequencing approach, namely WGRS, was used in groundnut for getting large-scale genome-wide SNPs in mapping populations and developing high-density genetic maps for conducting high-resolution trait mapping. The RADseq technology was initially checked for level of polymorphism among a set of parental genotypes of genetic populations (Gupta et al 2015); however, it yielded a low-density genetic map (171 SNP loci) when deployed in a RIL population segregating for rust and late leaf spot (LLS) resistance in TAG 24 × GPBD 4 (Shirasawa et al 2018). Nevertheless, the improved technology named ddRADseq provided much better results when deployed for construction of dense genetic maps (1,621 SNP loci) in RIL population derived from Zhonghua 5 and ICGV86699 (Zhou et al 2014).…”

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

“…It was interesting to note the methylation pattern within Arahy.1XYC2X differed between the resistant and susceptible groups, indicating the epialleles at this locus. The candidate genes identified for late leaf spot (four genes) and rust (six genes) resistance in the previous study [33] did not show any DNA methylation, indicating that breeding for foliar disease resistance can depend only on the genetic variation. FPKM values for the transcripts at these loci were on par between the resistant and the susceptible genotypes.…”

“…In total, 731 methylation sites were in the inter-genic regions and 35 were in the genic regions (19 in exons and 16 in introns). Interestingly, four differentially DNA methylated sites (1,001,785, 1,001,813, 1,021,671 and 1,305,680) mapped to the QTL region (for LLS) on A02 and one (134,350,159) mapped to the QTL region (for rust) on A03 [33]. Of these sites, only one (1,305,680) was in a genic (Arahy.42YDET) region.…”

“…Of these sites, only one (1,305,680) was in a genic (Arahy.42YDET) region. However, this gene has not been regarded as a candidate gene for foliar disease resistance [33]. Based on the genomic position of the DNA methylation sites, 25 genes were found to be differentially methylated (q ≤ 0.01) between resistant and susceptible genotypes.…”