SSR Analysis Of Genetic Diversity Injaponica Rice (Oryzasativa L.) From Different Regionsand Its Relation To Heterosis Prediction

The limitation of genetic resources and narrow gene pool is a major bottleneck in Japonica hybrid rice breeding.One effective way of addressing this challenge would require analyses or screening rice materials with typical japonica genetic background.The other strategy is to determine the genetic differentiation of inter-subspecies using molecular approaches to enhance rational utilization of heterosis between the materials.These strategies will enable efficient utilization of genetic resources,predict heterosis,match new hybrid combinations and improve breeding efficiency.In order to explore the genetic differentiation of rice varieties with complex sources,create new germplasm of Japonica rice,widen the range of parental mating and select excellent combination for breeding and utilization,SSR molecular markers were employed.By means of the SSR marker selection,heterosis,geographical distribution of populations,genetic structure,genetic evolution and differentiation between indica and japonica rice lines were predicted.SSR marker assisted selection was also employed for integrating technical system.In this study,three genetic parameters : different genetic diversity index,differentiation and molecular genetic distance were analyzed among 196 rice varieties of Indica and Japonica.Hybrid progeny traits of 67 national and international materials(included 5 American materials)were also investigated by means of incomplete diallel crossing.The combining abilities of parents were analyzed in F1 by comparison of 9 traits.Furthermore,we employed F1,F2 and BC1 traits test data to verify the correlation between the parental SSR fingerprint data and the traits of the hybrid progeny by using three the same parameters above.The main results obtained as expressed as follows:1)An average of 11.31 alleles were identified on each chromosome by 33 SSR pairs of primers(RM204 et al.).The efficiency of the average alleles detected were higher compared with genetic diversity parameters.However,the average number of alleles detected on chromosomes 1,5,8 and 11 showed uniform gene distribution frequency whereas those on chromosomes 3,6,10 and 12 were unevenly distributed.In comparison to the above,gene distribution frequency of alleles on chromosomes 2,4,7 and 9 were worse.A large number of rare alleles were detected in the tested materials.The highest proportion of rare alleles was detected on chromosome 12,which accounted for 71.01%.The least was recorded on chromosome 2 which accounted for 61.33%.A total of 93 tested-varieties which accounts for 47.45% were identified to possess unique alleles.Among the varieties with unique alleles,Moon rice(a local variety in Yunnan)contained the largest number(17 alleles)of unique alleles.Generally,the distribution of unique alleles were unevenly uniform on the chromosomes of the various tested varieties.2)The 196 assembled materials were clustered into 13 sub-groups with varieties from Yunnan distributed among them.Out of the assembled rice population from Taiwan,only 83.3% of total portion were clustered together in one subgroup(cluster 10).Similarly,only 64.1% and 80% of each rice populations from Central China and northeast China respectively were clustered together in sub-groups(cluster 11 and 3).Genetic differentiation of the study materials into Indica and Japonica varieties were also determined.Genetic differentiation analysis revealed 3 typical indica,2 partial indica and 1 intermediate indica varieties among the assembled materials.Furthermore,nine(4.6%),100(51%)and 81(41.3%)of the remaining 190 varieties were detected as partial japonica rice,japonica rice and typical japonica rice varieties correspondingly.There was significant and highly significant positive correlation between the length of SSR makers and the relevant indica gene frequency of F1 in 14 specific locus.Significant or extremely significant negative correlation between the length of SSR makers and the corresponding F1 varieties in 8 specific locus.These indicated that the genetic differentiation between indica and Japonica rice may be closely correlated with changes in SSR sequence specific sites.3)The recorded general combining abilities variance of plant height,effective spike number,total grain number and the grain fertility were higher(52.68%-87.97%).The narrow-sense heritability was greater than 40% and was associated with high heritability traits.Combining ability variance of spike length,seed setting rate and other traits was higher(64.47%-93.98%)and greater than the general combining ability variance.Effect of paternal combining ability of most traits in general combining ability effect value was higher than the maternal parent.Analysis of combining ability and multiple comparison of yield characters,showed two heterotic groups with prominent main yield traits.Two maternal parents of the heterotic groups were American and Japonica ecotype.Thirty-two,paternal parents were from China,which were typical Japonica,Japonica ecotypes,and intermediate types.The total grain number,fertile grain number and seed setting rate of the hybrid populations were significantly higher than those of other groups.Two heterotic groups of 64(2*32)hybrid combinations will be the focus of the follow-up study.4)There were 20 varieties(lines)as the recurrent parent.The average yield were higher in back-cross offspring which includes 8 varieties(lines)of parents with good combining ability.There were 6 pairs of Indica-Japonica Hybrid combinations.The F1 of these showed strong heterosis and the seed setting rate of BC1(Back-cross 1)was more than 50%.This provides important information required for development of breeding materials and indica-japonica hybrid breeding.5)Based on the SSR fingerprinting data,the genetic parameters indicated above were again utilized to predict heterosis in rice.which were based on the genetic distance,the genetic differentiation index and the length of the amplified fragments of the parents.There was significant and highly significant correlation between the SSR fingerprinting data of the rice parents and traits of hybrid progeny.These three methods could provide some reference for the prediction of heterosis.In this study,the genetic diversity and genetic differentiation of the complex breeding materials were demonstrated.Large number of new Japonica rice varieties were bred to widen the gene pool for rice breeding.The utilization of SSR markers for prediction of rice heterosis coupled with research results provides a new idea which would serve as a benchmark in rice breeding.