Genetic Dissection of Yield-Related Traits Using an Inter-Subspecific Chromosome Segment Substitution Line Population in Rice

Rice yield is a complex quantitative trait. Although a lot of genes for yield have been cloned, their genetic basis remains unknown. In the present study, a set of chromosome segment substitution line population (CSSL) was developed, derived from the indica variety Huanghuazhan as the recipient parent and the Aus variety N22 as the donor parent, and a high-density bin map containing 609 bins was constructed by resequencing. The CSSL population comprised 155 families with an average background recovery rate of 93.02%. Nine yield-related traits, including plant height, panicle number, panicle length, primary branch number, spikelet number per panicle, grain number per panicle, seed setting rate, 1000-grain weight, and grain yield per plant, were evaluated across four environments. The results showed significant differences in yield-related traits between the two parents across four environments. All nine traits showed continuous distribution with transgressive segregation. Spikelet number per panicle, grain number per panicle and 1000-grain weight showed strong correlations with each other, whereas panicle number had weak correlations with them. A total of 80 main-effect quantitative trait loci (QTLs) affecting yield-related traits were identified, among which 13 QTLs were repeatedly detected in multiple environments, 45 QTLs were located in 8 pleiotropic QTL regions, and 47 QTLs showed significant interactions with environments. In addition, 260 pairs of epistatic QTLs underlying yield-related traits were identified, of which 2 pairs stably expressed across different environments, and 11 pairs controlled more than two traits. These findings provide a theoretical basis for clarifying the genetic differentiation between indica and Aus and cloning yield-related genes, and offer valuable gene resources for molecular breeding of high-yield rice varieties.