QTL Analysis of Yield-Related Traits in Both Huangnuo2^# and Changbai7^# of Perennial Chinese Rice

The analysis of quantitative trait loci (QTL) underlying yield-related traits of perennial Chinese rice laid a good foundation for fine mapping, cloning, and functional research of yield-related traits genes. Meanwhile, it also provided technical support for revealing the genetic mechanism of yield-related traits in perennial Chinese rice and breeding perennial rice variety.

Two perennial Chinese japonica rice, namely, Huangnuo2^# (HN2^#) and Changbai7^# (CB7^#), and two half-sib (Huangnuo2^#/XieqingzaoB and Changbai7^#/XieqingzaoB) F₂ populations and their bi-parents were selected as experimental materials. Sixteen yield-related traits, including heading date, plant height, and thousand-grain weight of HN2^# and CB7^# in major crop (MC) and ratooning crop (RC) of 2024, were investigated for phenotypic analysis. Fifteen yield-related traits, including plant height, panicle plant^-1, and thousand-grain weight, in HN2^# and CB7^#-populations and their bi-parents were investigated for phenotypic analysis and QTL mapping.

Between MC and RC of 2024, seven yield-related traits of HN2^#, including heading date, plant height, and thousand-grain weight, exhibited significant phenotypic differences (P<0.05). Three yield-related traits of CB7^#, including plant height, grain setting density, and grain weight panicle^-1, displayed significant phenotypic differences. Among 15 yield-related traits, 34 pairs of significantly positive correlations were calculated in the HN2^#-population. A total of 39 pairs of significantly positive correlations were calculated in the CB7^#-population. Exactly 29 QTLs were detected in the HN2^#-population, accounting for 2.61% to 29.41% of the phenotypic variation. Thirteen novel QTLs were detected in the HN2^#-population. Of these, seven QTLs with additive effects were derived from HN2^#, and the other six with additive effects were derived from XQZB. Five pleiotropic QTL were detected in the HN2^# HN2^#-population. A total of 22 QTLs were detected in the CB7^#-population, accounting for 2.77% to 27.94% of the phenotypic variation. Ten novel QTLs were detected in the CB7^#-population. Of those, six QTLs with additive effects were derived from CB7^#, and the other four with additive effects as well were derived from XQZB. Five pleiotropic QTL were detected in the CB7^#-population.

These novel and pleiotropic QTL are unique to HN2^# and CB7^#, which should be the primary focus of future research.