Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice
Abstract Background Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling complex traits, the attention has not been given to grain size until recently...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2018-08-01
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| Series: | Rice |
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| Online Access: | http://link.springer.com/article/10.1186/s12284-018-0236-z |
| _version_ | 1818025620545732608 |
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| author | Qing Dong Zhen-Hua Zhang Lin-Lin Wang Yu-Jun Zhu Ye-Yang Fan Tong-Min Mou Liang-Yong Ma Jie-Yun Zhuang |
| author_facet | Qing Dong Zhen-Hua Zhang Lin-Lin Wang Yu-Jun Zhu Ye-Yang Fan Tong-Min Mou Liang-Yong Ma Jie-Yun Zhuang |
| author_sort | Qing Dong |
| collection | DOAJ |
| description | Abstract Background Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling complex traits, the attention has not been given to grain size until recently. In previous studies, five QTL having small effects for grain size were resolved on the long arm of chromosome 1 using populations derived from indica rice cross Zhenshan 97///Zhenshan 97//Zhenshan 97/Milyang 46. One of them, qTGW1.2c that was located in a 2.1-Mb region, was targeted for fine-mapping in the present study. Results Firstly, the qTGW1.2c region was narrowed down into 1.1 Mb by determining genotypes of the cross-over regions using polymorphic markers newly developed. Then, one BC2F9 plant that was only heterozygous in the updated QTL region was identified. A total of 12 populations in generations from BC2F11:12 to BC2F15:16 were derived and used for QTL mapping. Two QTL linked in a 460-kb region were separated. The qGS1-35.2 was delimited into a 57.7-kb region, containing six annotated genes of which five showed nucleotide polymorphisms between the two parental lines. Quantitative real-time PCR detected expression differences between near isogenic lines for qGS1-35.2 at three of the six annotated genes. This QTL affected grain length and width with opposite allelic directions, exhibiting significant effect on ratio of grain length to width but showing little influence on yield traits. The other QTL, qGW1-35.5, was located within a 125.5-kb region and found to primarily control grain width and consequently affect grain weight. Conclusions Our work lays a foundation for cloning of two minor QTL for grain size that have potential application in rice breeding. The qGS1-35.2 could be used to modify grain appearance quality without yield penalty because it affects grain shape but hardly influences grain yield, while qGW1-35.5 offers a new gene recourse for enhancing grain yield since it contributes to grain size and grain weight simultaneously. |
| first_indexed | 2024-12-10T04:19:00Z |
| format | Article |
| id | doaj.art-12bf8b6a56da427d97aec6aaaa4928c6 |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-12-10T04:19:00Z |
| publishDate | 2018-08-01 |
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| series | Rice |
| spelling | doaj.art-12bf8b6a56da427d97aec6aaaa4928c62022-12-22T02:02:28ZengSpringerOpenRice1939-84251939-84332018-08-0111111110.1186/s12284-018-0236-zDissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of riceQing Dong0Zhen-Hua Zhang1Lin-Lin Wang2Yu-Jun Zhu3Ye-Yang Fan4Tong-Min Mou5Liang-Yong Ma6Jie-Yun Zhuang7State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural UniversityState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteState Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research InstituteAbstract Background Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling complex traits, the attention has not been given to grain size until recently. In previous studies, five QTL having small effects for grain size were resolved on the long arm of chromosome 1 using populations derived from indica rice cross Zhenshan 97///Zhenshan 97//Zhenshan 97/Milyang 46. One of them, qTGW1.2c that was located in a 2.1-Mb region, was targeted for fine-mapping in the present study. Results Firstly, the qTGW1.2c region was narrowed down into 1.1 Mb by determining genotypes of the cross-over regions using polymorphic markers newly developed. Then, one BC2F9 plant that was only heterozygous in the updated QTL region was identified. A total of 12 populations in generations from BC2F11:12 to BC2F15:16 were derived and used for QTL mapping. Two QTL linked in a 460-kb region were separated. The qGS1-35.2 was delimited into a 57.7-kb region, containing six annotated genes of which five showed nucleotide polymorphisms between the two parental lines. Quantitative real-time PCR detected expression differences between near isogenic lines for qGS1-35.2 at three of the six annotated genes. This QTL affected grain length and width with opposite allelic directions, exhibiting significant effect on ratio of grain length to width but showing little influence on yield traits. The other QTL, qGW1-35.5, was located within a 125.5-kb region and found to primarily control grain width and consequently affect grain weight. Conclusions Our work lays a foundation for cloning of two minor QTL for grain size that have potential application in rice breeding. The qGS1-35.2 could be used to modify grain appearance quality without yield penalty because it affects grain shape but hardly influences grain yield, while qGW1-35.5 offers a new gene recourse for enhancing grain yield since it contributes to grain size and grain weight simultaneously.http://link.springer.com/article/10.1186/s12284-018-0236-zClose linkageGrain sizeMinor effectQuantitative trait locusRice |
| spellingShingle | Qing Dong Zhen-Hua Zhang Lin-Lin Wang Yu-Jun Zhu Ye-Yang Fan Tong-Min Mou Liang-Yong Ma Jie-Yun Zhuang Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice Rice Close linkage Grain size Minor effect Quantitative trait locus Rice |
| title | Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice |
| title_full | Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice |
| title_fullStr | Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice |
| title_full_unstemmed | Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice |
| title_short | Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice |
| title_sort | dissection and fine mapping of two qtl for grain size linked in a 460 kb region on chromosome 1 of rice |
| topic | Close linkage Grain size Minor effect Quantitative trait locus Rice |
| url | http://link.springer.com/article/10.1186/s12284-018-0236-z |
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