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

Authors: KHAN, SHAHID - Fujian Agriculture And Forest University; CHEN, HUA - Fujian Agriculture And Forest University; DENG, YE - Fujian Agriculture And Forest University; CHEN, YUHUA - Fujian Agricultural & Forestry University; ZHANG, CHONG - Fujian Agriculture And Forest University; CAI, TIECHENG - Fujian Agriculture And Forest University; ALI, NIAZ - Fujian Agriculture And Forest University; MAMADOU, GANDEKA - Fujian Agriculture And Forest University; XIE, DONGYANG - Fujian Agricultural & Forestry University; Guo, Baozhu; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; WEIJIAN, ZHUANG - Fujian Agriculture And Forest University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2020
Publication Date: 4/13/2020
Citation: Khan, S.A., Chen, H., Deng, Y., Chen, Y., Zhang, C., Cai, T., Ali, N., Mamadou, G., Xie, D., Guo, B., Varshney, R.K., Weijian, Z. 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. 133:2239-2257. https://doi.org/10.1007/s00122-020-03594-0.
DOI: https://doi.org/10.1007/s00122-020-03594-0

Interpretive Summary: Aflatoxin contamination in peanut caused is a serious food safety issue for human health around the world. Our goal was to identify host plant resistance genes to the fungal infection and aflatoxin contamination in order to mitigate this problem. In this study, one high-density genetic linkage map was constructed to fine map the potential location in the genome associated with the resistance the fungal infection and the resulting aflatoxin contamination. Two high density genetic linkage maps were developed, and two peanut genome regions, named qRAF-3-1 and qRAF-14-1, were identified in linkage groups A03 and B04, respectively. In comparison with the reference genome, these two regions, qRAF-3-1 and qRAF-14-1, were located within physical distance of 1.45 Mbp and 2.22 Mbp, harbouring 67 and 137 genes, respectively. Then using microarray gene expression study, the genes responded to A. flavus infection were WRKY mRNA ion factor 51, cytochrome P450 71B34, pentatricopeptide repeat-containing protein At4g02750, and putative disease resistance RPP13-like protein 1. Using the markers, we selected several recombinant inbred lines as germplasm with significant lower in aflatoxin levels. These results indicated that the resistance regions in the genome could be used for potential marker development and as candidate genes for further study.

Technical Abstract: Aflatoxin contamination in peanut caused by Aspergillus flavus is a serious food safety issue for human health around the world. Our goal was to identify host plant resistance to the fungal infection and aflatoxin contamination in order to mitigate this food safety problem. In this study, one high-density genetic linkage map was constructed using specific length amplified fragment (SLAF) sequencing approach to fine map the QTLs associated with resistance to A. flavus infection and resulting aflatoxin contamination. Two high density genetic linkage maps were developed, one with 1,975 SNP markers and a 979.91 cM map distance and the other with 5,022 SNP markers and a 2,231.25 cM map distance. Two consistent QTLs, qRAF-3-1 and qRAF-14-1, were identified in linkage groups (LGs) A03 and B04, respectively. QTL qRAF-3-1 was mapped within 0.38 cM and had more than 19 % phenotypic variance explained (PVE). In comparison with the reference genome, these two QTLs, qRAF-3-1 and qRAF-14-1, were located within physical distance of 1.45 Mbp and 2.22 Mbp, harbouring 67 and 137 genes, respectively. Genes identified in the qRAF-3-1 region included those coding for WRKY mRNA ion factor 51, putative disease resistance RPP13-like protein 1, and cytochrome P450 71B34. using microarray gene expression study, these genes responded to A. flavus infection: WRKY mRNA ion factor 51, cytochrome P450 71B34, pentatricopeptide repeat-containing protein At4g02750, and putative disease resistance RPP13-like protein 1. Several recombinant inbred lines were evaluated and selected as germplasm with significant lower in aflatoxin levels. These results revealed resistant QTLs with potential marker development for marker-assistant selection in breeding and candidate genes for further study.