Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice
Abstract Background Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and...
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| Format: | Article |
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BMC
2018-01-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-017-0591-6 |
| _version_ | 1828528160684113920 |
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| author | Su Jang Yunjoo Lee Gileung Lee Jeonghwan Seo Dongryung Lee Yoye Yu Joong Hyoun Chin Hee-Jong Koh |
| author_facet | Su Jang Yunjoo Lee Gileung Lee Jeonghwan Seo Dongryung Lee Yoye Yu Joong Hyoun Chin Hee-Jong Koh |
| author_sort | Su Jang |
| collection | DOAJ |
| description | Abstract Background Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. Results In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle. Conclusions Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice. |
| first_indexed | 2024-12-11T21:48:28Z |
| format | Article |
| id | doaj.art-03829cab9dd2476cb2e97b497cb923b7 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-11T21:48:28Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-03829cab9dd2476cb2e97b497cb923b72022-12-22T00:49:32ZengBMCBMC Genetics1471-21562018-01-0119111110.1186/s12863-017-0591-6Association between sequence variants in panicle development genes and the number of spikelets per panicle in riceSu Jang0Yunjoo Lee1Gileung Lee2Jeonghwan Seo3Dongryung Lee4Yoye Yu5Joong Hyoun Chin6Hee-Jong Koh7Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityGraduate School of Integrated Bioindustry, Sejong UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National UniversityAbstract Background Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. Results In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle. Conclusions Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.http://link.springer.com/article/10.1186/s12863-017-0591-6RiceSingle nucleotide polymorphismsHaplotypeThe number of spikelets per paniclePanicle-related traitsCandidate gene association analysis |
| spellingShingle | Su Jang Yunjoo Lee Gileung Lee Jeonghwan Seo Dongryung Lee Yoye Yu Joong Hyoun Chin Hee-Jong Koh Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice BMC Genetics Rice Single nucleotide polymorphisms Haplotype The number of spikelets per panicle Panicle-related traits Candidate gene association analysis |
| title | Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| title_full | Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| title_fullStr | Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| title_full_unstemmed | Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| title_short | Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| title_sort | association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
| topic | Rice Single nucleotide polymorphisms Haplotype The number of spikelets per panicle Panicle-related traits Candidate gene association analysis |
| url | http://link.springer.com/article/10.1186/s12863-017-0591-6 |
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