Genetic basis of early heading genes for weedy rice in Northeast China

Abstract

Weedy rice (Oryza spp.) is a semi-domesticated genetic resource. In high-latitude paddy ecosystems, weedy rice tends to head earlier than accompanied japonica rice. However, the heading allele genes underlying this weedy rice de-domestication, which is crucial for understanding the genetic basis and repeatability of the heading, remain largely unexplored. Therefore, this study aims to investigate the allelic variation of nine heading genes using 46 weedy rice from three areas in northeast China (weedy rice from northeast China [WRNC]) and 32 of their accompanying japonica rice (Oryza sativa L.) varieties. The heading time of WRNC was 3–20 days earlier than that of the accompanying japonica rice. The heading-promotion genotype heading date 1 (Hd1) was the main factor aiding WRNC heading earlier than its accompanying japonica rice. Functional haplotypes of heading date 2 (Hd2), grains height date 7 (Ghd7), and days to heading 2 (Dth2) may affect the early heading of weedy rice from Liaoning, Jilin, and Heilongjiang in northeast China. Phylogenetic tree analysis showed that WRNC is closely related to the cultivated rice in Northeast China and has no direct relationship with southern indica weedy rice. The results showed that some heading genes in the study differentiated during the divergence of indica and japonica rice; these genes in WRNC are not only affected by the differentiation of indica and japonica rice but also by the domestication of cultivated rice, forming an independent heading genotype distinct from northern japonica rice. This serves as a basis for research aimed at improving the heading period of cultivated rice by utilizing traits from weedy rice.