Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs
Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was cons...
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| Published in | Molecular breeding Vol. 44; no. 6; p. 39 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Dordrecht
Springer Netherlands
01.06.2024
Springer Nature B.V |
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| Abstract | Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including
qGL12
,
qGW12
, and
qRLW12
, were identified through the F
2
population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of
qGL12
for grain length and
qGW12
for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. |
|---|---|
| AbstractList | Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F₂ population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including , , and , were identified through the F population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of for grain length and for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. The online version contains supplementary material available at 10.1007/s11032-024-01480-x. Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12 , qGW12 , and qRLW12 , were identified through the F 2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design.Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design.The online version contains supplementary material available at 10.1007/s11032-024-01480-x.Supplementary informationThe online version contains supplementary material available at 10.1007/s11032-024-01480-x. |
| ArticleNumber | 39 |
| Author | Xiao, Wenwen Zhang, Ting Wu, Ruhui Zhao, Fangming He, Guanghua Wei, Mi You, Jing Zhang, Yi Wang, Dachuan Liu, Jinyan Ye, Li |
| Author_xml | – sequence: 1 givenname: Jing surname: You fullname: You, Jing organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 2 givenname: Li surname: Ye fullname: Ye, Li organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 3 givenname: Dachuan surname: Wang fullname: Wang, Dachuan organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 4 givenname: Yi surname: Zhang fullname: Zhang, Yi organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 5 givenname: Wenwen surname: Xiao fullname: Xiao, Wenwen organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 6 givenname: Mi surname: Wei fullname: Wei, Mi organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 7 givenname: Ruhui surname: Wu fullname: Wu, Ruhui organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 8 givenname: Jinyan surname: Liu fullname: Liu, Jinyan organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 9 givenname: Guanghua surname: He fullname: He, Guanghua organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 10 givenname: Fangming surname: Zhao fullname: Zhao, Fangming email: zhaofangming2004@163.com organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University – sequence: 11 givenname: Ting surname: Zhang fullname: Zhang, Ting email: tingzhang@swu.edu.cn organization: Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/38766512$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1111/jipb.12727 10.1126/science.1223702 10.1038/nplants.2015.203 10.1111/tpj.14793 10.1104/pp.111.187567 10.1186/s12284-021-00477-w 10.1093/aobpla/ply060 10.1093/genetics/127.1.181 10.1016/j.tplants.2012.11.001 10.1038/ng2014 10.3390/ijms19071904 10.1093/jxb/erac088 10.1186/s12284-021-00496-7 10.1371/journal.pgen.1003391 10.1105/tpc.20.00351 10.1016/j.xplc.2022.100450 10.1105/tpc.17.00959 10.1038/ng.3518 10.1111/pbi.13075 10.1038/ng.3352 10.1146/annurev-arplant-042809-112209 10.1016/j.pbi.2016.05.008 10.1016/j.scib.2023.01.026 10.1556/0806.44.2016.022 10.1016/s0065-3233(08)60520-3 10.1093/plcell/koab041 10.1111/pbi.13005 |
| ContentType | Journal Article |
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| Keywords | Chromosome Segment Substitution Lines (CSSL) grain shape candidate gene QTLs |
| Language | English |
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| SubjectTerms | Biomedical and Life Sciences Biotechnology Breeding Chromosomes Cloning Crop yield DNA DNA sequencing family Gene mapping Gene sequencing Genes genetic background Germplasm Life Sciences Plant Genetics and Genomics Plant Pathology Plant Physiology Plant Sciences prediction Protein structure Proteins Quantitative trait loci Rice Segments Substitutes substitution lines Ubiquitin zinc finger motif Zinc finger proteins |
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| Title | Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs |
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