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Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice
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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769279/ https://www.ncbi.nlm.nih.gov/pubmed/29334899 http://dx.doi.org/10.1186/s12863-017-0591-6 |
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author | Jang, Su Lee, Yunjoo Lee, Gileung Seo, Jeonghwan Lee, Dongryung Yu, Yoye Chin, Joong Hyoun Koh, Hee-Jong |
author_facet | Jang, Su Lee, Yunjoo Lee, Gileung Seo, Jeonghwan Lee, Dongryung Yu, Yoye Chin, Joong Hyoun Koh, Hee-Jong |
author_sort | Jang, Su |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-017-0591-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5769279 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57692792018-01-25 Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice Jang, Su Lee, Yunjoo Lee, Gileung Seo, Jeonghwan Lee, Dongryung Yu, Yoye Chin, Joong Hyoun Koh, Hee-Jong BMC Genet Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-017-0591-6) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-15 /pmc/articles/PMC5769279/ /pubmed/29334899 http://dx.doi.org/10.1186/s12863-017-0591-6 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Jang, Su Lee, Yunjoo Lee, Gileung Seo, Jeonghwan Lee, Dongryung Yu, Yoye Chin, Joong Hyoun Koh, Hee-Jong Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice |
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 | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769279/ https://www.ncbi.nlm.nih.gov/pubmed/29334899 http://dx.doi.org/10.1186/s12863-017-0591-6 |
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