QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and ‘Nipponbare’

Abstract

Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar ‘Nipponbare’ as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.

Short Communication: Correlation and regression among rice panicle branches traits

“…Even, the relationship between the PBN vs SBL and PBN vs GN per SB showed a negative correlation. This result was in line with that reported by Sun et al (2017), where all populations being studied showed the striking positive correlations among the panicle length, grains number per panicle, primary panicle branch, and secondary panicle branch, but there was still no report about the other panicle branching traits. Bagheri et al (2011) and Norain et al (2014) reinforced the statement that there was a high significant and positive correlation between the number of grains per panicle and panicle length.…”

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

“…The location of qpl6‐2 identified by Kobayashi et al () and Cho et al () shared the similar region. The location of qpl6 identified by Mei et al (), Liu et al (), Guo and Hong (), Sun et al () and our group shared the nearby region at the tip of the long arm of chromosome 6, and qPL6‐2 , which we identified, exhibited a large effect on PH and GW. Moreover, the location of qPL7 ‐1 identified by Cho et al () and our group shared the nearby region at the short arm of chromosome 7.…”

“…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.…”

Back to the future: revisiting MAS as a tool for modern plant breeding

“…However, a ‘domestication’ construct could be created and introduced via gene editing which would permit pre-breeders to more effectively explore wild genetics. Such a construct containing key domestication loci (Zhu et al 2013 ; Li et al 2013 ; Sun et al 2017 ) could reduce the phenotypic noise in mapping populations, enhance the ability to introgress discovered genes/QTL, and reduce the generation time for creating and evaluating populations.…”