Contribution Of Indica-Japonica Hybridization To Rice Breeding In Northeast China

Indica and japonica are subspecies of Asian cultivated rice (Oryza sativa L.) and possess different biological characteristics.The strategy of breeding high-yielding rice is developing superiority gene of subspecies. In recent years, most cultivated varieties were bred by indica-japonica hybridization in northeast China through seeking pedigree, which realize further increases in rice yieldhave contributed to an improved understanding of the genetic and food security. However, how subspecific hybrid vigor contributes to the high yields of northern japonica rice cultivars is not thoroughly understood. Recent studies of genome-wide sequencing of ’Nipponbare’ and ’93-11’ were developed permit quantitative analysis of indica and japonica components of the rice genome. In this study, we used sinple nucleotide polymorphism (SNP) to analyze genetic diversity and structure of rice cultivars that were cultivated in northern China,47large-effect SNP loci,33subspecies-differentiating InDel and55subspecies-specific intron length polymorphism (SSILP) molecular markers to study genotype frequencies based on subspecies-differentiating loci and detect genomic subspecies lineages compared with Japanese varieties and indica. By combining the relationship between indica or japonica pedigree and yield components, grain quality with correlation analysis to obtain molecular evidence for the contribution of indica-japonica hybridizationto rice breeding in northern China. The major results were as follows:1The present research showed that genetic diversity of novel rice cultivars bred in northern China were significantly lower than early breeding phase varieties and exotic varieties. Vigor genes of indica-japonica hybridization were fixed through ’selection’, at the same time many functional alleles and their genetic linkage blocks to be purified at the population level along with the elimination of negative heterosis traits, which lead the decreased diversity at the functional genome level. Genetic structure and phylogenetic analyse ssuggest that the independent and unique phylogenetic status of modern breeding phase japonica has gradually arisen through the introduction of the indica lineage and natural selection in northern China.2Subspecies-specific functional molecular markers were developed that permit quantitative analysis of indica and japonica components of the rice genome. The genotype frequencies of subspecies-differentiating InDel, SSILP markers and large-effect SNP loci were significantly positively correlated. Indica and japonica import another subspecies allele respectively through hybridization and natural selection. Indica-type allele frequency of rice cultivars in northeast China, ranked from highest to lowest, was Liaoning (0.0588)> Jilin (0.0514)> Heilongjiang (0.0368), and significantly higher than Japan, which reflect the contribution of indica-japonica hybridization to rice breeding in northeast China.3The method of researching subspecies differentiation was very important. The consistent degree of classification based on Cheng’s index, the vascular bundles characters and subspecies-specific markers was above90%. The correlation analysis of subspecies characters, japonica-type allele frequency and yield components indicated:secondary branches, grains on secondary branches, secondary branches grains rate, spikelets density and spikelets per panicles of novel rice cultivars bred in northeast China has increased and paniclesreduced through indica-japonica hybridization; Primary branches, seed setting rate of primary branches and103-grain weight kept on a higher level, all of these characters lead the yield significantly increased.4The correlation analysis of subspecies characters, japonica-type allele frequency and grain quality indicated:rice milling quality of novel rice cultivars bred in northeast China had reduced but maintain in the range of high quality standard; Exterior quality had improved since the chalky grain rate and chalkiness dropt, while ratio of grain length to width added; Taste score was not as great as Japanese varieties, breeding of northeast China had perfectly coordinated the relationship of high-yielding and high-quality generally though the process of achieving the objective was very difficult.5The135subspecies-specific functional markers used in our study were distributed among the12rice chromosomes. Indica-type loci on No.5, No.6and No.10was more than other chromosomes on neutrally-evolving loci; On large phenotypic effects functional loci level, the percentage of indica-type loci on No.2and No.10chromosomes achieved18.14%and13.38%, respectively. The correlation analysis of important cloning genes of agronomic characteristics and sample percentage of indica-type loci indicated:indica-type loci of large phenotypic effects functional loci was0on chromosomes9which hold the erect panicle gene DEP1; Two sides loci of shattering gene qSHl were all japonica-type on chromosomes1. Among these genes controlling agronomic traits, although did not know which gene was utilized, advantageous gene have already reserved in japonica rice and unfavourable gene was eliminated by selection during the process of breeding japonica rice in northeast China.