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BMC Genet. 2018 Jan 15;19(1):5. doi: 10.1186/s12863-017-0591-6.

Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice.

Author information

1
Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
2
Graduate School of Integrated Bioindustry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul, 05006, South Korea. jhchin@sejong.ac.kr.
3
Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. heejkoh@snu.ac.kr.

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.

KEYWORDS:

Candidate gene association analysis; Haplotype; Panicle-related traits; Rice; Single nucleotide polymorphisms; The number of spikelets per panicle

PMID:
29334899
PMCID:
PMC5769279
DOI:
10.1186/s12863-017-0591-6
[Indexed for MEDLINE]
Free PMC Article

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