BSA-seq-based identification of a major additive plant height QTL with an effect equivalent to that of Semi-dwarf 1 in a large rice F_(2) population

Bulked-segregant analysis is a time-and cost-saving strategy for identifying major quantitative trait loci(QTL) in a mapping population. Bulked-segregant analysis combined with whole-genome sequencing(BSA-seq) was performed to rapidly identify QTL for heading date, plant height, and panicle length in a large F_(2) population derived from two landraces: Chuan 7(C7) and Haoboka(HBK). Twenty plants with extremely low or high phenotypic values for the target traits were selected from an F_(2) population of 940 plants to construct low-and high-value bulks. Three pairs of bulks for the three traits were constructed, resulting in six DNA pools. BSA-seq revealed nine QTL: four for heading date, three for plant height, and two for panicle length. These QTL were validated in a random F_(2) population or BC_(4)F_(2) populations. The major novel plant height QTL, qPH8, acting additively with an effect equivalent to that of semi-dwarf 1(sd1), is potentially valuable for hybrid rice breeding. qPH8 controls mainly the elongation of basal internodes. The C7 allele of qPH8 reduces plant height and increases lodging resistance without yield penalty, suggesting a potential role for qPH8 in improving rice plant architecture.

Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice

In rice,the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance,as shown by their extremely high yield.However,the mechanisms underlying the success of these rice hybrids are unclear.In this study,three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids.Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies,respectively,although introgression of 20%of the Xian ancestry and 14%of the Geng ancestry are observed.Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments,which harbors hybrid sterility genes such as Sd,Sc,f5,and q S12 and favorable alleles of key yield-related genes,including NAL1,Ghd7,and Ghd8.None of the parents carries the S5+killer of the S5 killer-protector system.Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids.Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values.Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis.These factors result in an extremely high yield of the hybrids.These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.