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Guo D, Jiang H, Yan W, Yang L, Ye J, Wang Y, Yan Q, Chen J, Gao Y, Duan L, Liu H, Xie L. Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection. FRONTIERS IN PLANT SCIENCE 2020; 10:1682. [PMID: 32010166 PMCID: PMC6976528 DOI: 10.3389/fpls.2019.01682] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/29/2019] [Indexed: 05/13/2023]
Abstract
Seed size and weight are key traits determining crop yield, which often undergo strongly artificial selection during crop domestication. Although seed sizes differ significantly between oil flax and fiber flax, the genetic basis of morphological differences and artificial selection characteristics in seed size remains largely unclear. Here we re-sequenced 200 flax cultivated accessions to generate a genome variation map based on chromosome assembly reference genomes. We provide evidence that oil flax group is the ancestor of cultivated flax, and the oil-fiber dual purpose group (OF) is the evolutionary intermediate transition state between oil and fiber flax. Genome-wide association studies (GWAS) were combined with LD Heatmap to identify candidate regions related to seed size and weight, then candidate genes were screened based on detailed functional annotations and estimation of nucleotide polymorphism effects. Using this strategy, we obtained 13 candidate genes related to seed size and weight. Selective sweeps analysis indicates human-involved selection of small seeds during the oil to fiber flax transition. Our study shows the existence of elite alleles for seed size and weight in flax germplasm and provides molecular insights into approaches for further improvement.
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Affiliation(s)
- Dongliang Guo
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Haixia Jiang
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Wenliang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Liangjie Yang
- Herbal Medicine Innovation Research Center, Agricultural Bureau of Zhaosu County, Yili, China
| | - Jiali Ye
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yue Wang
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Qingcheng Yan
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Jiaxun Chen
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yanfang Gao
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Lepeng Duan
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Huiqing Liu
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Liqiong Xie
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
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