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

Khan, S A and Chen, H and Deng, Y and Chen, Y and Zhang, C and Cai, T and Ali, N and Mamadou, G and Xie, D and Guo, B and Varshney, R K and Zhuang, W (2020) High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea). Theoretical and Applied Genetics (TSI), 133 (7). pp. 2239-2257. ISSN 0040-5752

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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.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Groundnut, Aflatoxin, Genetics, Genomics
Subjects:	Mandate crops > Groundnut Others > Genetics and Genomics Others > Plant Disease Others > Aflatoxins
Depositing User:	Mr Arun S
Date Deposited:	08 Sep 2020 06:05
Last Modified:	08 Sep 2020 06:05
URI:	http://oar.icrisat.org/id/eprint/11617
Official URL:	https://doi.org/10.1007/s00122-020-03594-0
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	Current work was supported by The National Science Foundation of People’s Republic of China (U1705233; 31601337; 31701463). The authors are thankful to Fujian Key Laboratory of Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China, for providing research facilities and technical guidance. Special acknowledgment to Meng Yang from Nextomics Biosciences Institute, Wuhan, China for his help in bioinformatics analysis.
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