| The genetic distance of indica and japonica subspecies of rice is larger, and the progenies of inter-subspecies hybrid have great genetic variation and transgressive heterosis. So to make full use of the different ecotype heterosis in inter-and intra-subspecies has been to become one of the main ways in hybrid rice breeding today. Study on analysis of diversity and heterosis is of important theoretical and practical significance for rational utilization of the heterosis between rice subspecies.Therefore, with 39 derivative lines of indica-japonica hybrid rice and 17 indica and japonica parents as materials, the heterotic grouping, the comparative study and the genetic diversity analysis were researched, and the genetic diversity and indica-japonica categorical attributes of indica and japonica subspecies of rice were also discussed in this paper, by the cluster analysis of phenotypic traits and SSR molecular markers.Meanwhile, using 12 representative rice of indica-japonica cross and 8 widely applied two-and three-line male sterile in production as parents, hybrid rice combinations were established and the genetic distance was calculated by the molecular genetic diversity analyzed by SSR molecular markers, then the correlation between the genetic distance and their heterosis performance was analyzed. The aim was to provide reference meaning for parent selection in breeding, reducing blindness of combining, improving validity of the heterosis of indica-japonica cross, enhancing the work efficiency in hybrid rice breeding and so on several aspects. The main results were as follows:1,The results showed that, though the cluster analysis of phenotypic traits failed to accurately reflect the relationship among the materials, it could more accurately reveal the phenotypic differences and cluster dominant groups. It was of important reference value for the combination of heterosis in different materials. In this test, we found that the third group was the dominant group in the cluster of phenotypic traits, and should be emphatically studied and extensively combined in breeding. The first subgroup in the third group was indica and indica-clinous rice and had good combining ability. The heterosis combinations could be established using the sterile lines and the first subgroup as parents. The second subgroup in the third group was intermediate type of indica-japonica rice and had the characteristics of indica and japonica rice, good combining ability. The strong heterotic combinations could be easily established using the sterile lines of good tillering ability, dwarf plant type, good compatibility and the second subgroup as parents.2,And the results showed that, the result of the cluster analysis of SSR molecular markers was similar with the one of the cluster analysis of phenotypic traits. The differences could be reflected among the strain at the molecular level, and the relationship could be more accurately revealed among the materials, by comparing of the result of the molecular cluster with the pedigree of the test materials. It showed that the cluster analysis of SSR molecular markers could be used to group for the relationship and the heterotic for unknown materials.3,The results showed that, the maximum values of Nei gene diversity index, Shannon diversity index and polymorphism information content (PIC) of strain of indica-japonica cross were all more than the parents'values. The maximum value of Nei gene diversity index of strain of indica-japonica cross was 0.819 and the one of their parents'was 0.796. The maximum value of Shannon diversity index of strain of indica-japonica cross was 1.856 and the one of their parents' was 1.677. The maximum value of polymorphism information content (PIC) of strain of indica-japonica cross was 0.796 and the one of their parents'was 0.766. It indicated that, there was more abundant allelic variations in strain of indica-japonica cross than that of their parents by generation selection of many years.4,Two division standards were proposed to classify indica and japonica rice in DNA level in this paper. The classification method of standard of 85% DNA japonica components, mainly divided strain of indica-japonica cross into four groups:japonica rice (85%-100%), japonica-clinous rice (50%-85%), indica-clinous rice (15%-50%) and indica rice (0%-15%). And the classification method of standard of 70% DNA japonica components, mainly divided strain of indica-japonica cross into four groups:japonica rice (70%-100%), japonica-clinous rice (30%-70%), indica-clinous rice (15%-30%) and indica rice (0%-15%).From the experimental analysis we could see that the correlations of the two classification methods'and Cheng's classification method's displayed remarkably. The highly significant correlation between the classification method of standard of 85% DNA japonica components and Cheng's morphological classification method (r=0.96**) was observed. And the significant correlation were found between the classification method of standard of 70% DNA japonica components and Cheng's morphological classification method (r=0.89*). It indicated that, the two classification methods effectively classified strain of indica-japonica cross, and compared with the latter, the former was more suitable for classifying. Starting from the angle of the parents and the strain of indica-japonica cross, the inconsistency values of the classification method of standard of 85% DNA japonica components were all less than the one of the classification method of standard of 70% DNA japonica components as compared with the morphological classification method. The inconsistency values of the parents were 5.88% and 11.76% respectively, and the one of the strain of indica-japonica cross were 20.51% and 25.64% respectively.The inconsistency values of the two methods, the morphological classification method and the classification method of DNA molecular markers, for classifying strain of indica-japonica cross was obviously higher than that of the parents. At the same time, the total score of the morphological index of the strain of indica-japonica cross was lower than that of the parents, and the correlation degree of gene frequency for japonica (r=0.65**) was lower than that of the parents (r=0.89**). It verified complexity of classification of strain of indica-japonica cross again. For strain of indica-japonica cross, it was comparatively difficult in determining the position of indica and japonica because most of strain of indica-japonica cross were intermediate type, lay between indica and japonica, and possessed characteristics of indica and japonica.So it is considered that, for strain of indica-japonica cross, it should be advocated the dominant role of the classification method of the morphological index and the subsidiary role of the classification method of the molecular markers, and in the meantime for indica and japonica, it should be advocated the dominant role of the classification method of the molecular markers and the subsidiary role of the classification method of the morphological index.5,The analysis of heterosis for combinations of strain of indica-japonica cross showed that, the characteristics of MingHui series strain of indica-japonica cross were as follows:The plant height showed obvious positive heterosis with less variation range, only 1 combination expressed negative heterosis in the 96 combinations. The panicle length showed positive transgressive heterosis with less variation range. The 1000-grain weight showed positive mid-parent heterosis with little variation range. The grain number per panicle and the seed setting rate showed positive heterosis with relatively larger variation range, and the problem of the low seed setting rate for the progenies of inter-subspecies cross basically overcome. Certain-difference existed in the progenies of inter-subspecies cross in the MingHui series stains. The effective panicle number showed negative mid-parent heterosis, and this showed that the tillering ability was relatively weaker in the Fl progenies of inter-subspecies cross and should be improved.lt could be seen that, the unbalance existed in the effective panicle number, the grain number per panicle and the 1000-grain weight in the F1 progenies of inter-subspecies cross in the MingHui series stains, and individual main yield characters showed no obvious positive heterosis, but there were strong yield heterosis in the the choised combinations because complementarity of characters existed in their parents.6,The results of analysis on correlation between heterosis and the genetic distance based on simple sequence repeat markers indicated, the parental of 96 F1 hybrid at the genetic distance for 0.2547-0.5660, the correlation between heterosis of F1 seed setting rate,1000-grain weight and GD has negligible effect, the correlation between heterosis of effective panicles and GD has no significant correlation (r=011. r=0.14), However the correlation between heterosis of plant height and GD appeared to be significant at P<0.01 (r=0.44**,r=0.45**), the correlation between heterosis of panicle length and GD appeared to be significant at P<0.01 (r=0.39**,r=0.29**), the correlation between heterosis of total spikelets per panicle and GD appeared to be significant at P<0.01 (r=0.30**,r=0.32**), the correlation between mid-parent heterosis of spikelets per panicle and GD appeared to be significant at P<0.05(r=0.23*), and the heterobeltiosis appeared to be significant at P<0.01 (r=37**), the correlation between Yield per plant of spikelets per panicle and GD appeared to be significant at P<0.05 (r=0.23*), and the heterobeltiosis appeared to be significant at P<0.01 (r=34**). Therefore, at the parental genetic distance of 96 F1 hybrid for 0.2547-0.5660,the yield per plant can be predicted on simple sequence repeat markers, In ensuring the panicles per mu and setting rate to be stable。...
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