Genomic insight into genetic changes and shaping of major inbred rice cultivars in China

Abstract

The annual planting area of major inbred rice (Oryza sativa) cultivars reach more than half of the total annual planting area of inbred rice cultivars in China. However, how the major inbred rice cultivars changed during decades of genetic improvement and why they can be prevalently cultivated in China remains unclear.Here, we investigated the underlying genetic changes of major inbred cultivars and the contributions of landraces and introduced cultivars during the improvement by resequencing a collection of 439 rice accessions including major inbred cultivars, landraces, and introduced cultivars.The results showed that landraces were the main genetic contribution sources of major inbred Xian (Indica) cultivars, while introduced cultivars were that of major inbred Geng (Japonica) cultivars. Selection scans and haplotype frequency analysis shed light on the reflections of some well-known genes in rice improvement, and breeders had different preferences for the Xian's and Geng's breeding. Six candidate regions associated with agronomic traits were identified by genome-wide association mapping, five of which were under positive selection in rice improvement.Our study provides a comprehensive insight into the development of major inbred rice cultivars and lays the foundation for genomics-based breeding in rice.

Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China

“…The major breakthrough of “green revolution” leads quantum leaps of rice productivity (Cheng et al 2020 ), intensive breeding efforts and artificial selection have facilitated the significant improvement of indica rice yield in Guangdong, where the “green revolution” started in China. Unlike previously reported selection analysis of rice accession from multiple geographic positions (Li et al 2020a , b ; Lv et al 2020 ; Xie et al 2015 ; Xu et al 2016 ; Ye et al 2022 ), we focusing on the locally adaptative selection of rice in Guangdong by comparing the genomic variations and agronomic traits of locally cultivated landraces by farmers before “green revolution” and modern improved cultivars. For example, modern breeding of rice quality started from the end of last century in Guangdong favors slender grain type for regional appetite in southern Aisa, which makes the increase of grain length and width ratio, and decrease of grain weight in subpopulation of modern cultivars.…”