Abstract
BackgroundBalancing 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.ResultsIn 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.ConclusionsFavorable 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.
Highlights
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
The objectives of this study were to (1) identify novel sequence variants in the coding regions of panicle development genes which were previously reported to control panicle development and investigate genetic information, (2) identify sequence variants associated with paniclerelated traits, including panicle length (PL), The number of primary branches per panicle (PB), and secondary branches per panicle (SB), and (3) find combinations of favorable alleles for each trait that could contribute to increasing spikelets per panicle (SPP) in rice
The MONOCULM 1 (MOC1)-C allele was detected in 35 varieties and mainly distributed in japonica varieties (62.8%), and the MOC1G allele was observed in ten varieties, including eight varieties of indica and two tong-il
Summary
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. 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. SPP is determined by several panicle-related traits, such as the number of primary branches per panicle (PB), the number of secondary branches per panicle (SB), and panicle length (PL). It is important to identify DNA sequence variation of genes controlling agronomic traits and discover beneficial sequence variants for some traits in that they allow opportunity for molecular application in rice breeding to improve target traits [12]
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