Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions
Rice (<i>Oryza sativa</i> L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits...
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MDPI AG
2023-01-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/3/419 |
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| author | Nansheng Wang Huguang Chen Yingzhi Qian Zhaojie Liang Guiqiang Zheng Jun Xiang Ting Feng Min Li Wei Zeng Yaling Bao Erbao Liu Chaopu Zhang Jianlong Xu Yingyao Shi |
| author_facet | Nansheng Wang Huguang Chen Yingzhi Qian Zhaojie Liang Guiqiang Zheng Jun Xiang Ting Feng Min Li Wei Zeng Yaling Bao Erbao Liu Chaopu Zhang Jianlong Xu Yingyao Shi |
| author_sort | Nansheng Wang |
| collection | DOAJ |
| description | Rice (<i>Oryza sativa</i> L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (<i>qTGW4.1</i>, <i>qTGW4.2</i>, <i>qGL4.1</i>, <i>qGL12.1</i>, <i>qGL12.2</i>, <i>qGW2.1</i>, <i>qGW4.1</i>, <i>qGW6.1</i>, <i>qGW8.1</i>, <i>qGW8.2</i>, <i>qGW9.1</i>, <i>qGW11.1</i>, <i>qGLWR2.1</i>, <i>qGLWR2.2</i>, <i>qGLWR4.2</i>, <i>qPGWC5.1</i> and <i>qDEC6.1</i>) were identified for haplotype analysis. Among these QTLs, two (<i>qTGW4.2</i> and <i>qGW6.1</i>), were overlapped with <i>FLO19</i> and <i>OsbZIP47</i>, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction. |
| first_indexed | 2024-03-11T09:30:22Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T09:30:22Z |
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| spelling | doaj.art-5d5336db8b9a4de8bf380e56a242b77a2023-11-16T17:42:05ZengMDPI AGPlants2223-77472023-01-0112341910.3390/plants12030419Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian AccessionsNansheng Wang0Huguang Chen1Yingzhi Qian2Zhaojie Liang3Guiqiang Zheng4Jun Xiang5Ting Feng6Min Li7Wei Zeng8Yaling Bao9Erbao Liu10Chaopu Zhang11Jianlong Xu12Yingyao Shi13College of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaRice (<i>Oryza sativa</i> L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (<i>qTGW4.1</i>, <i>qTGW4.2</i>, <i>qGL4.1</i>, <i>qGL12.1</i>, <i>qGL12.2</i>, <i>qGW2.1</i>, <i>qGW4.1</i>, <i>qGW6.1</i>, <i>qGW8.1</i>, <i>qGW8.2</i>, <i>qGW9.1</i>, <i>qGW11.1</i>, <i>qGLWR2.1</i>, <i>qGLWR2.2</i>, <i>qGLWR4.2</i>, <i>qPGWC5.1</i> and <i>qDEC6.1</i>) were identified for haplotype analysis. Among these QTLs, two (<i>qTGW4.2</i> and <i>qGW6.1</i>), were overlapped with <i>FLO19</i> and <i>OsbZIP47</i>, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction.https://www.mdpi.com/2223-7747/12/3/419riceGWASQTLsgrain shapechalkiness |
| spellingShingle | Nansheng Wang Huguang Chen Yingzhi Qian Zhaojie Liang Guiqiang Zheng Jun Xiang Ting Feng Min Li Wei Zeng Yaling Bao Erbao Liu Chaopu Zhang Jianlong Xu Yingyao Shi Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions Plants rice GWAS QTLs grain shape chalkiness |
| title | Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions |
| title_full | Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions |
| title_fullStr | Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions |
| title_full_unstemmed | Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions |
| title_short | Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions |
| title_sort | genome wide association study of rice grain shape and chalkiness in a worldwide collection of xian accessions |
| topic | rice GWAS QTLs grain shape chalkiness |
| url | https://www.mdpi.com/2223-7747/12/3/419 |
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