Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato
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 F<sub>2</sub> 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.
Authors
- Hui Feng (ORCID: https://orcid.org/0000-0003-1318-821X)
- Zedong Geng
- Thomas Städler (ORCID: https://orcid.org/0000-0003-4513-8583)
- Guangtao Zhu (ORCID: https://orcid.org/0000-0003-4226-4410)
- Yuxin Jia (ORCID: https://orcid.org/0000-0001-8808-2466)
- Wanneng Yang (ORCID: https://orcid.org/0000-0003-1095-1355)
- Sanwen Huang (ORCID: https://orcid.org/0000-0002-8547-5309)
- Yi Shang (ORCID: https://orcid.org/0000-0001-5795-1198)
- Shixuan Xia
- Xiuhan Jiang
- Yao Zhou (ORCID: https://orcid.org/0000-0001-9791-7664)
- Yaoyao Wu (ORCID: https://orcid.org/0000-0003-0766-1541)
- Dawei Li (ORCID: https://orcid.org/0000-0002-3243-2911)
- Huihui Li (ORCID: https://orcid.org/0000-0002-9117-5011)
- Chunzhi Zhang
- Pei Wang (ORCID: https://orcid.org/0000-0002-8149-756X)
- Qun Lian (ORCID: https://orcid.org/0000-0001-8734-8357)
- Hui Du (ORCID: https://orcid.org/0000-0002-2196-0014)
- Yanhui Zhu (ORCID: https://orcid.org/0000-0003-4908-886X)
- Chenglong Huang
Institutions
- Chinese Academy of Tropical Agricultural Sciences (CN)
- Nanjing Agricultural University (CN)
- Yunnan Normal University (CN)
- Huazhong Agricultural University (CN)
- ETH Zurich (CH)
- Agricultural Genomics Institute at Shenzhen (CN)
- Institute of Plant Biology (HU)
- Sanya University (CN)
- Institute of Crop Sciences (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-10-05
- DOI
- https://doi.org/10.1038/s41467-024-53044-4
- Citations
- 19
- Primary Topic
- Plant Pathogens and Resistance
- Type
- article
- Field-Weighted Citation Impact
- 11.39
Funders
- National Natural Science Foundation of China
- China Postdoctoral Science Foundation
- Natural Science Foundation of Hubei Province
- Shanghai Normal University
- Chinese Academy of Agricultural Sciences
- Agricultural Science and Technology Innovation Program