The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China

Abstract

Hybridization between indica and japonica rice combined with utilization of ideal plant type has led to the development of high-yielding japonica rice in northern China. However, the contribution at the genomic level of intersubspecific hybridization to the increased yield of northern Chinese japonica rice is uncertain. In this study, we analyzed the genomic pedigree of descendants of hybridization between indica and japonica rice grown in northeastern China between 1963 and 2008. Simple sequence repeat markers indicated that since 1990 the genetic diversity among northern japonica cultivars was enriched. Genome-wide analysis with subspecies-specific indel and intron length polymorphism markers showed indica-allele frequencies were significantly increased in cultivars bred after 1990, and were significantly positively correlated with spikelet number per panicle and significantly negatively correlated with panicle number per plant. Among eight genes controlling agronomic traits, GN1a and GS3 were partially fixed in the genome of northern japonica cultivars. In contrast, Waxy and qSH1 were eliminated, whereas DEP1 and qSW5 were retained. Indica germplasm is an important contributor to the increased yield of northern japonica rice. Breeding for high yield and grain quality in combination is a complicated process and difficult to achieve when relying on only one or several functional genes, thus the selection expertise of the breeder remains critical.

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars

“…Combining diverse alleles from indica and japonica is one way to produce desirable genotypes for high-yielding rice. To achieve this, cross-breeding has been conducted for over 30 years and, in fact, significant increases in yield potential have been achieved [13, 29]. It is expected that such high-yielding cultivars resulted from unique combinations of the indica and japonica genomes, but until now, no report has presented the genome-wide genotypes of such high-yielding cultivars.…”

Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China

“…Deliberate introduction of germplasm of indica subspecies into temperate japonica cultivars has been largely responsible for the increased rice yield in northern China (Sun et al, 2012). Therefore, it is possible that the donation of genetic material from indica through hybridization may have led to the formation of WRNC.…”

Different effects of DEP1 on vascular bundle- and panicle-related traits under indica and japonica genetic backgrounds

“…In total, 90 sets of subspecies-specific insertion-deletion (INDEL) and subspecies-specific intron length polymorphism (SSILP) markers in indica and japonica rice cultivars were used to analyze the proportion of indica alleles in the genome of each RIL. The clone names and physical distances of 34 INDEL and 56 SSILP markers were obtained from the marker-based physical maps produced by the International Rice Genome Sequencing Project, based on previous studies (Sun et al 2012;Lu et al 2009;Zhao et al 2009a). The two marker types were integrated into one genetic map based on physical distances using MapChart software (Fig.…”

“…All of the INDEL and SSILP markers were used to genotype the 200 RILs. The PCRs were performed as described elsewhere (Shen et al 2004;Wang et al 2006;Zhao et al 2009b;Sun et al 2012) using the primers listed in Table S1. The indica allele frequency was calculated as the ratio of the number of indicatype markers to the total number of markers.…”