Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage
Drought is an important factor limiting the growth and development of rice and thereby seriously affects rice yield. The problem may be effectively solved by dissecting the drought-resistance mechanism of rice, creating excellent drought-resistant germplasm, and mining new drought-resistant genes. I...
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MDPI AG
2023-08-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/13/8/2096 |
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| author | Nansheng Wang Zhiyuan Gao Wanyang Zhang Yingzhi Qian Di Bai Xueyu Zhao Yaling Bao Zhenzhen Zheng Xingmeng Wang Jianfeng Li Wensheng Wang Yingyao Shi |
| author_facet | Nansheng Wang Zhiyuan Gao Wanyang Zhang Yingzhi Qian Di Bai Xueyu Zhao Yaling Bao Zhenzhen Zheng Xingmeng Wang Jianfeng Li Wensheng Wang Yingyao Shi |
| author_sort | Nansheng Wang |
| collection | DOAJ |
| description | Drought is an important factor limiting the growth and development of rice and thereby seriously affects rice yield. The problem may be effectively solved by dissecting the drought-resistance mechanism of rice, creating excellent drought-resistant germplasm, and mining new drought-resistant genes. In this study, 305 accessions (189 <i>Xian</i>, 104 <i>Geng</i>, 5 <i>Aus</i>, and 7 <i>Basmati</i>) were used to identify drought-related phenotypes such as grain yield per plant (GYP), grain number per panicle (GNP), panicle number per plant (PNP), and plant height (PH) under two-year drought stress. The 2017 GYP and 2018 GNP were <i>Xian</i> max, 2018 GYP, 2017 GNP, 2017 and 2018 PNP, and 2018 PH were <i>Basmati</i> max, and only the 2017 PH was <i>Geng</i> max. The population genetic diversity and population structure were analyzed by combining 404,388 single nucleotide polymorphism (SNP) markers distributed on 12 chromosomes. A total of 42 QTLs with significant correlations was identified, among which 10 were adjacent to the loci reported to be associated with drought resistance. Four candidate genes, <i>LOC_Os03g48890</i>, <i>LOC_Os04g35114</i>, <i>LOC_Os11g45924</i>, and <i>LOC_Os06g38950</i>, were identified by functional annotation and haplotype analysis. The R<sup>2</sup> of <i>qGYP3.1</i> was 11.53%, the R<sup>2</sup> of <i>qGNP4.2</i> was 12.09%, the R<sup>2</sup> of <i>qPNP11.1</i> was 10.01%, and the R<sup>2</sup> of <i>qPH6.1</i> was 13.06%. The results have an important theoretical significance and practical application value for the improvement of drought resistance in rice. |
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| spelling | doaj.art-0f9acc7ac7284d999fec0d913ceea5272023-11-18T23:54:57ZengMDPI AGAgronomy2073-43952023-08-01138209610.3390/agronomy13082096Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive StageNansheng Wang0Zhiyuan Gao1Wanyang Zhang2Yingzhi Qian3Di Bai4Xueyu Zhao5Yaling Bao6Zhenzhen Zheng7Xingmeng Wang8Jianfeng Li9Wensheng Wang10Yingyao Shi11College of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230000, ChinaDrought is an important factor limiting the growth and development of rice and thereby seriously affects rice yield. The problem may be effectively solved by dissecting the drought-resistance mechanism of rice, creating excellent drought-resistant germplasm, and mining new drought-resistant genes. In this study, 305 accessions (189 <i>Xian</i>, 104 <i>Geng</i>, 5 <i>Aus</i>, and 7 <i>Basmati</i>) were used to identify drought-related phenotypes such as grain yield per plant (GYP), grain number per panicle (GNP), panicle number per plant (PNP), and plant height (PH) under two-year drought stress. The 2017 GYP and 2018 GNP were <i>Xian</i> max, 2018 GYP, 2017 GNP, 2017 and 2018 PNP, and 2018 PH were <i>Basmati</i> max, and only the 2017 PH was <i>Geng</i> max. The population genetic diversity and population structure were analyzed by combining 404,388 single nucleotide polymorphism (SNP) markers distributed on 12 chromosomes. A total of 42 QTLs with significant correlations was identified, among which 10 were adjacent to the loci reported to be associated with drought resistance. Four candidate genes, <i>LOC_Os03g48890</i>, <i>LOC_Os04g35114</i>, <i>LOC_Os11g45924</i>, and <i>LOC_Os06g38950</i>, were identified by functional annotation and haplotype analysis. The R<sup>2</sup> of <i>qGYP3.1</i> was 11.53%, the R<sup>2</sup> of <i>qGNP4.2</i> was 12.09%, the R<sup>2</sup> of <i>qPNP11.1</i> was 10.01%, and the R<sup>2</sup> of <i>qPH6.1</i> was 13.06%. The results have an important theoretical significance and practical application value for the improvement of drought resistance in rice.https://www.mdpi.com/2073-4395/13/8/2096ricedroughtyield traitsGWASQTLs |
| spellingShingle | Nansheng Wang Zhiyuan Gao Wanyang Zhang Yingzhi Qian Di Bai Xueyu Zhao Yaling Bao Zhenzhen Zheng Xingmeng Wang Jianfeng Li Wensheng Wang Yingyao Shi Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage Agronomy rice drought yield traits GWAS QTLs |
| title | Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage |
| title_full | Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage |
| title_fullStr | Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage |
| title_full_unstemmed | Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage |
| title_short | Genome-Wide Association Analysis Reveals the Gene Loci of Yield Traits under Drought Stress at the Rice Reproductive Stage |
| title_sort | genome wide association analysis reveals the gene loci of yield traits under drought stress at the rice reproductive stage |
| topic | rice drought yield traits GWAS QTLs |
| url | https://www.mdpi.com/2073-4395/13/8/2096 |
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