Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Abstract

Background Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM’s parents across three environments and gene-based analyses. Results Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF1 hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. Conclusions The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.

Simulated Nitrogen Deposition Decreases the Ratios of Soil C to P and N to P, Changes Soil Enzyme Activity, and Reduces Soil Microbial Biomass in Paddy Soil in Southern China

“…In this study, the N application rate of 180 kg•ha −1 was set for the ZN treatment combined with two N deposition levels of 40 kg•ha −1 and 120 kg•ha −1 . The results showed that the N deposition treatment significantly increased some components of the rice biomass (i.e., the grain number per panicle and the 1000-grain weight) but had no significant effect on the yield, which is consistent with the previous studies [22,23]. This may be because the rice leaves absorbed a small amount of the N sprayed on the rice leaves, which promoted the photosynthesis of the rice leaves and the accumulation of the grain dry matter and finally increased the number of grains per panicle and the 1000-grain weight of the rice [24].…”

“…Therefore there were no significant changes in the TC or TN content or in the C/N ratio in the rice plants. Inconsistent with the previous study [22], the TP content of the rice roots significantly increased under N deposition in this study due to the effect of N deposition in stimulating an increase in the soil S-ACP activity (Figure 2A). That caused soil decomposition to release phosphorus for the rice roots absorbing to maintain the TC/TP and TN/TP ratios of the rice.…”

“…Nitrogen is one of the important nutrient elements affecting rice growth; it can promote rice tillering, speed up rice growth, enhance rice stress resistance and dry matter accumulation, and ultimately increase the rice yield [22].…”