Genome-wide dissection of Quan9311A breeding and application

Abstract

Germplasm resource innovation is the key to variety development. Quan9311A is a three-line cytoplasmic male sterile (CMS) line of rice used for hybrid rice breeding based on the three-line system. It is the first CMS line that has been successfully cultivated with rice restoration materials and widely applied as a female parent line for hybrid breeding in China. The variety improvement of Quan9311A is based on an ingenious design. It was screened from the cross progeny of the three-line sterile line Zhong9A and the two-line restorer line 93 − 11, which are the core germplasms used to breed Quan9311A. According to phenotype, China breeders removed the restorability of 93 − 11, and cultivated Quan9311A: it combines the desirable agronomic traits of both 93 − 11 and Zhong9A, such as a moderate plant height, suitable heading date, and more tillers. In this study, genome-wide analysis was performed to investigate how Quan9311A was bred. RiceNavi analysis technology was used to dissect its functional genes associated with desirable agronomic traits based on whole-genome sequencing. The results show that rice breeders removed the fertility restorer gene Rf3 in 93 − 11 but retained the sterility gene WA352c of Zhong9A during the breeding process of Quan9311A. Not only are there many 93 − 11 chromosomal segments in the Quan9311A genome background but also multiple superior alleles of the parental 93 − 11 and Zhong9A lines are pyramided, conferring to Quan9311A excellent agronomic traits that were unavailable in earlier three-line sterile lines. We also found that Quanyou Simiao, a hybrid rice combination bred with Quan9311A as the female parent, harbors more superior alleles which could explain its high grain yield and wide adaptability. This study’s findings will promote the utilization of hybrid rice pairing groups and guide future breeding efforts. Meanwhile, it also provides fresh ideas for further promoting the closer integration of genomics with traditional breeding methods.

Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses

“…Gene chips play an increasingly important role in modern rice breeding, as they enable high-throughput detection of a large number of target genes ( Li et al., 2023 ; Zhang et al., 2023 ). However, the current high cost of gene chip testing, ranging from USD 70 to 80 per rice sample in China, makes it impractical for large-scale screening of target genes in individual plants from segregating populations.…”