Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies

Zhou, X and Guo, J and Pandey, M K and Varshney, R K and Huang, L and Luo, H and Liu, N and Chen, W and Lei, Y and Liao, B and Jiang, H (2021) Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies. Frontiers in Plant Science (TSI), 12 (637284). pp. 1-14. ISSN 1664-462X

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Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. We sequenced the Chinese peanut mini-core collection using genotyping-by-sequencing approach and identified 105,814 high-quality single nucleotide polymorphisms (SNPs). The population structure analysis showed essentially subspecies patterns in groups and obvious geographical distribution patterns in subgroups. A total of 79 significantly associated loci (P < 4.73 x 10-7 were detected for the six yield-related traits through GWAS. Of these, 31 associations were consistently detected in multiple environments, and 15 loci were commonly detected to be associated with multiple traits. Two major loci located on chromosomal pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits, explaining 20% phenotypic variations across environments. The two genomic regions were found 46 putative candidate genes based on gene annotation and expression profile. The diagnostic marker for the yield-related traits from non-synonymous SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation between nucleotide polymorphism and phenotypic variation. This study provided insights into the genetic basis of yield-related traits in peanut and verified one diagnostic marker to facilitate marker-assisted selection for developing high-yield peanut varieties.

Item Type: Article
Divisions: Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: Yield-related traits, Mini-core collection, GWAS, Diagnostic marker, Peanut
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Arun S
Date Deposited: 09 Aug 2021 05:53
Last Modified: 09 Aug 2021 05:59
URI: http://oar.icrisat.org/id/eprint/11865
Official URL: https://doi.org/10.3389/fpls.2021.637284
Funders: National Natural Science Foundation of China, Special Fund for Basic Scientific Research of Central Public Welfare Research Institutes, National Crop Germplasm Resources Center
Acknowledgement: The authors would like to thank Pengfei Jin for his help in SNP calling. The authors are also grateful to Jiaojiao Zhao and Huaiwen Chen for their help in the experiments. Thanks to Kede Liu and Liyun Wan for their suggestions on the article. Thanks also to Bolun Yu, Zhihui Wang, and Xiaomeng Xue for their valuable discussion.
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