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

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.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0591-6) contains supplementary material, which is available to authorized users.

A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits

“…Alternatively sequence variations might occur at very low frequency and thus not be observed or filtered out in our analysis. Nevertheless a recent analysis revealed that a combination of favourable alleles for these genes might collectively produce a higher spikelet number in a specific panel, supporting the notion that there is a complex genetic network regulating this phenotypic feature [ 58 ].…”

Designing of a mini-core that effectively represents 3004 diverse accessions of rice

“…Contrastingly, H4 haplotype showed inclination towards dense branching trait. One recent study has shown the association of gene SHORT PANICLE 1 (SP1) and elevated haplotype diversity among japonica than indica group (Jang et al, 2018).…”

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

“…Rice panicle length (PL), as a yield‐related trait determined by the rachis length plus primary branch length above the rachis tip, is a key agronomic characteristic that varies widely amongst cultivars (Ikeda, Sunohara, & Nagato, ). This trait strongly impacts grain yield by affecting several panicle‐related traits, such as the number of primary branches per panicle, the number of secondary branches per panicle and the grain density per panicle (Jang et al, ; Peng et al, ). Elite indica rice cultivars with high yield have more spikelets than japonica cultivars because of the longer panicle and they are under different genetic control as revealed by genome‐wide association analysis (Bai et al, ).…”

“…Additionally, the interaction of genotype by genotype (G × G) and genotype by environment (G × E) contributed to the trait variation (Cho et al, ; Hittalmani et al, ; Zhang et al, ). Correlation analysis also revealed the strong relationship between PL and other agronomic traits, including panicle culm length, plant height, heading stage, secondary branch number and spikelet number per panicle, and these correlated traits are usually mapped synchronously (Dang et al, ; Guo & Hong, ; Huang et al, ; Jang et al, ; Liang, Shang, Lin, Lou, & Zhang, ; Lu et al, ; Miura et al, ; Sun et al, ; Wu et al, ; Yan et al, ; Zhang, Luo, Xu, Zhang, & Xing, ), Genetic dissection for rice plant architecture showed that the PL QTL is co‐localised with either culm length, tiller number or both (Kobayashi et al, ) and finely mapped with the same locus for spikelet number per panicle (Guo & Hong, ; Xie et al, ). However, whether the loci are in tight linkage or genes are in pleiotropy is unclear.…”

“…Currently, the genetic factors of PL and their effect on the rice yield component are not well‐understood (Zhang et al, ). A favourable allele combination shows that the relevant sequence variant of panicle‐related traits is beneficial in increasing the number of spikelets per panicle (Jang et al, ), indicating that the PL trait can be used as a selection parameter and PL QTLs are effective for high‐yield breeding (Ikeda et al, ; Zhang et al, ).…”