Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6

Luo, H and Pandey, M K and Zhi, Y and Zhang, H and Xu, S and Guo, J and Wu, B and Chen, H and Ren, X and Zhou, X and Chen, Y and Chen, W and Huang, L and Liu, N and Sudini, H and Varshney, R K and Lei, Y and Liao, B and Jiang, H (2020) Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. Theoretical and Applied Genetics (TSI). ISSN 0040-5752

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Key message Two novel and adjacent genomics and candidate genes for bacterial wilt resistance were identified on chromosome B02 in peanut variety Zhonghua 6 using both traditional QTL mapping and QTL-seq methods. Abstract Peanut (Arachis hypogaea) is an important oilseed crop worldwide. Utilization of genetic resistance is the most economic and effective approach to control bacterial wilt, one of the most devastating plant diseases, in peanut production. To accelerate the genetic improvement of bacterial wilt resistance (BWR) in peanut breeding programs, quantitative trait locus (QTL) mapping has been conducted for two resistant varieties. In this context, we deployed linkage mapping as well as sequencing-based mapping approach, QTL-seq, to identify genomic regions and candidate genes for BWR in another highly resistant variety Zhonghua 6. The recombination inbred line population (268 progenies) from the cross Xuhua 13 × Zhonghua 6 was used in BWR evaluation across five environments. QTL mapping using both SSR- and SNP-based genetic maps identified a stable QTL (qBWRB02-1) on chromosome B02 with 37.79–78.86% phenotypic variation explained (PVE) across five environments. The QTL-seq facilitated further dissection of qBWRB02-1 into two adjacent genomic regions, qBWRB02-1-1 (2.81–4.24 Mb) and qBWRB02-1-2 (6.54–8.75 Mb). Mapping of newly developed Kompetitive allele-specific PCR (KASP) markers on the genetic map confirmed their stable expressions across five environments. The effects of qBWRB02-1-1 (49.43–68.86% PVE) were much higher than qBWRB02-1-2 (3.96–6.48% PVE) and other previously reported QTLs. Nineteen putative candidate genes affected by 49 non-synonymous SNPs were identified for qBWRB02-1-1, and ten of them were predicted to code for disease resistance proteins. The major and stable QTL qBWRB02-1-1 and validated KASP markers could be deployed in genomics-assisted breeding (GAB) to develop improved peanut varieties with enhanced BWR.

Item Type: Article
Divisions: Research Program : Asia
Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Groundnut, Plant Disease, Wilt, Disease Resistance
Subjects: Others > Plant Breeding
Mandate crops > Groundnut
Others > Genetics and Genomics
Others > Plant Disease
Depositing User: Mr Arun S
Date Deposited: 05 Feb 2020 05:54
Last Modified: 05 Feb 2020 06:11
Official URL:
Acknowledgement: This study was supported by the National Natural Science Foundations of China (Grant Nos. 31601340, 31571713, 31761143005, 31461143022), the Youth Chenguang Project of Science and Technology of Wuhan City (Grant No. 2017050304010285), the Natural Science Foundation of Hubei Province (Grant No. 2017CFB540) and the Central Public-interest Scientific Institution Basal Research Fund (Grant No. 1610172019008). This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of CGIAR Consortium. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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