High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea)

Abstract

Key message Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq. Abstract Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts.Communicated by David A. Lightfoot. Shahid Ali Khan and Hua Chen have equally contributed.

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

“…The deployment of the "Axiom_Arachis" array with 58,233 SNPs [25] in groundnut facilitated generation of high-throughput genotyping data for high-resolution trait mapping [45]. The studies also showed that SLAF-seq can help developing denser genetic map than GBS or SNP array [46][47][48].…”

Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

“…and core-collections [29]. In peanut, Agarwal et al [30] and Khan et al [31] reported the fine mapping of QTLs involved in disease (ELS, LLS and rust) and Aspergillus resistances respectively, using RIL populations and high density SNP genetic maps. Luo et al [20] succeeded in mapping major and stable QTLs related to weight and size of pods in 280 kb and 1.48 Mb intervals on chromosome A05 and A07, respectively, thanks to a genetic map constructed with 817 SSRs and a RIL population of 187 lines.…”

High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut

“…avus infection were identi ed on chromosomes A05, A08, B01, B03 and B10. These QTLs were novel because the previously reported QTLs by Yu et al (2019) and Khan et al (2020) were on A03, A10 and B04. Notably, the favorable alleles of ve of the six novel QTLs were from J11, but these QTLs were not stable across environments.…”

“…In recent years, QTL mapping was successfully used to identify QTLs with resistance to A. avus infection from two newly identi ed resistant germplasm named ICG12625 (Yu et al 2019) and Xinhuixiaoli (Khan et al 2020). ICG12625 is a landrace from Ecuador, and Yu et al (2019) constructed a recombination inbred line (RIL) population from the cross between ICG12625 and a susceptible variety Zhonghua 10.…”

“…A genetic map with 1,219 SSR loci were constructed and two QTLs were identi ed on chromosomes A03 and A10 with 7.96% and 12.16% phenotypic variation explained (PVE), respectively. On the other hand, Xinhuixiaoli is a Chinese landrace with resistance to A. avus infection and it was crossed with a susceptible variety Yueyou 92 to generated a RIL population (Khan et al 2020). A SNPbased genetic map was constructed by speci c length-ampli ed fragment sequencing (SLAF-seq), and a major QTL on A03 with 18.11% PVE and a minor QTL with 4.40% PVE on B04 were identi ed.…”