Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato

Dawei Li, Zedong Geng, Shixuan Xia, Hui Feng, Xiuhan Jiang, Hui Du, Pei Wang, Qun Lian, Yanhui Zhu, Yuxin Jia, Yao Zhou, Yaoyao Wu, Chenglong Huang, Guangtao Zhu, Yi Shang, Huihui Li, Thomas Städler, Wanneng Yang (), Sanwen Huang () and Chunzhi Zhang ()
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Dawei Li: Chinese Academy of Agricultural Sciences
Zedong Geng: Huazhong Agricultural University
Shixuan Xia: Chinese Academy of Agricultural Sciences
Hui Feng: Huazhong Agricultural University
Xiuhan Jiang: Chinese Academy of Agricultural Sciences
Hui Du: Chinese Academy of Agricultural Sciences
Pei Wang: Chinese Academy of Agricultural Sciences
Qun Lian: Chinese Academy of Agricultural Sciences
Yanhui Zhu: Chinese Academy of Agricultural Sciences
Yuxin Jia: Yunnan Normal University
Yao Zhou: Chinese Academy of Agricultural Sciences
Yaoyao Wu: Nanjing Agricultural University
Chenglong Huang: Huazhong Agricultural University
Guangtao Zhu: Yunnan Normal University
Yi Shang: Yunnan Normal University
Huihui Li: Chinese Academy of Agricultural Sciences
Thomas Städler: ETH Zurich
Wanneng Yang: Huazhong Agricultural University
Sanwen Huang: Chinese Academy of Agricultural Sciences
Chunzhi Zhang: Chinese Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding.

Date: 2024
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DOI: 10.1038/s41467-024-53044-4

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