QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study
Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k sin...
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PeerJ Inc.
2022-05-01
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| Online Access: | https://peerj.com/articles/13407.pdf |
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| author | Feng Mao Depeng Wu Fangfang Lu Xin Yi Yujuan Gu Bin Liu Fuxia Liu Tang Tang Jianxin Shi Xiangxiang Zhao Lei Liu Lilian Ji |
| author_facet | Feng Mao Depeng Wu Fangfang Lu Xin Yi Yujuan Gu Bin Liu Fuxia Liu Tang Tang Jianxin Shi Xiangxiang Zhao Lei Liu Lilian Ji |
| author_sort | Feng Mao |
| collection | DOAJ |
| description | Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding. |
| first_indexed | 2024-03-09T06:54:44Z |
| format | Article |
| id | doaj.art-02670610437a43298952dbaf379f51f3 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:54:44Z |
| publishDate | 2022-05-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-02670610437a43298952dbaf379f51f32023-12-03T10:06:11ZengPeerJ Inc.PeerJ2167-83592022-05-0110e1340710.7717/peerj.13407QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association studyFeng Mao0Depeng Wu1Fangfang Lu2Xin Yi3Yujuan Gu4Bin Liu5Fuxia Liu6Tang Tang7Jianxin Shi8Xiangxiang Zhao9Lei Liu10Lilian Ji11School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaJiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, ChinaSchool of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, ChinaLow temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.https://peerj.com/articles/13407.pdfGenome wide association studyLow temperature germinationHaplotype analysisRice |
| spellingShingle | Feng Mao Depeng Wu Fangfang Lu Xin Yi Yujuan Gu Bin Liu Fuxia Liu Tang Tang Jianxin Shi Xiangxiang Zhao Lei Liu Lilian Ji QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study PeerJ Genome wide association study Low temperature germination Haplotype analysis Rice |
| title | QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study |
| title_full | QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study |
| title_fullStr | QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study |
| title_full_unstemmed | QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study |
| title_short | QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study |
| title_sort | qtl mapping and candidate gene analysis of low temperature germination in rice oryza sativa l using a genome wide association study |
| topic | Genome wide association study Low temperature germination Haplotype analysis Rice |
| url | https://peerj.com/articles/13407.pdf |
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