Correlation Analysis Of Molecular Markers And Genetic Diversity And Heterosis In Rice

Rice is one of the staple food crops in the world. Detection and utilization of the genetic diversity in crop genomes has been the most important tasks for plant geneticists and breeders for understanding the genome architecture and also devising strategies for crop modification and improvement. The development and widespread adoption of molecular markers for genetic studies and heterosis prediction on rice haave attracted great interest, providing the most promising results with reduced cost and time required to perform the hybrid combinations. In this research, two sets of tropical rice germplasm were selected:one was from the mini-core subset of USDA rice germplasm collection based on mini-core clusters, representing the germplasm from Asia, America and Africa with higher genetic and geographic distances; another one was from IRRI consisting of inbred lines with relative lower genetic distances and closer pedigree relationship. SSR and ILP markers were used for the genetic diversity and structure analysis of the materials mentioned above. Two sets of testing crosses, as well as two sets of incomplete diallel crosses, were developed for the correlation analysis of genetic molecular with phenotype, combining ability and heterosis of all traits of the hybrids. The main results and conclusion were:1. The genetic diversity and structure were analyzed of the 59 IRRI inbred indica or NPT (progenies of indica/japonica) varieties and USDA rice varieties using molecular markers and pedigree.1) for the IRRI inbred rice The genetic distance (GD) based on ILP and SSR markers varied a lot, GDs based on SSR was higher than GDs based on ILPs; the genetic information like PIC, Shannon index, He revealed by SSRs were also higher than that by ILPs; nevertheless, the ILPs presented subspecies subspecific discriminating ability. The results of the clustering and genetic structure analysis based on molecular markers or pedigree showed that the whole level of genetic diversity of the IRRI inbred lines was high, but the genetic background was still narrow which need to be developed further because most of the lines carried more or less the shared ancestries as indicated by the pedigree information.2) for the USDA rice Genetic diversity of 36 rice varieties from USDA rice collection was assessed using 103 ILPs and 54 SSRs. A total of 236 and 332 alleles were detected by ILP and SSR, respectively. On the average, SSRs produced higher PIC value and number of alleles than ILPs. The Nei's genetic distance matrices were considerably different, while Mantel's test indicated that there was a statistically significant correlation between the two marker systems. UPGMA clustering based on ILPs and SSRs resulted in consensus dendrograms. The 36 varieties were divided into four groups. Four African Oryza glaberrima varieties were clustered within a distinct group (â…¡); the remaining varieties were separated into three groups (I, III and IV). Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III which had 7 admixtures sharing from 19.5% to 30% of ancestry with group IV (based on SSRs). It was suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.2,The results of the two sets of the testcrosses, one of which had been analyzed in two successive seasons, showed that among the combinations between the inbred and sterile lines, the Fl's performances not always increased as its male parent increased. The phenomenon of "The ship rises as the tide" could not be adapted to the hybrid rice breeding as proved in present research.3,The combining ability effect for the yield and heading date was studied using the tow sets of testcrosses. The variances of GCA and SCA for the two traits were significantly different, indicating that GCA and SCA were controlled by addictive gene and non-addictive gene, respectively. Comparison analysis of the variances of GCA and SCA using Griffing model-â… was conducted. It showed that in set2WS, the GCA for yield per plant of the female parents was higher than that of the male parents; the effect of SCA was relatively higher than that of GCA; while it showed the opposite results in setl for two seasons. For the heading date, the effect of SCA was higher than that of GCA, meaning that the heading date of the hybrid was affected by its SCA. During the wet season, the female's GCA was significantly higher than that of male while the difference was not so obvious during the dry season.The results also illuminated that the yield trait of the hybrid was lightly affected by GCA or SCA of the parents, but considerably affected by environment (seasons); for heading date, although not so obviously affected by environment, it differed. So we considered that the necessity of eco-breeding was high, especially for the countries and regions where there are obvious different seasons in a year. The eco-breeding is to develop varieties which can adapt to the particular season with high yield output, to increase the yield of rice production and to insure the food safety.4,Relationship between molecular marker based GD and heterosis1) Testcrosses The relationship between GD and heterosis for yield and yield components traits was not strong. GD revealed by QTLs associated with yield components traits had significant correlation coefficients with the over-male-parent heterosis for the traits of yield per plant, filled grains percentage and total grain number per panicle; but the correlation was too low to predict heterosis.2) Incomplete diallel crosses The results showed ILPs were significantly correlated to heterosis for yield while SSRs had the lower relationship. It was suggested that ILPs can be used to predict yield performance for the hybrid breeding using inbred lines. Interestingly, ILPs had the positive correlation coefficient with the heterosis in the diallel crosses using inbred parents with lower GDs, while negative correlation was found in another set of diallel crosses developed by the USDA parents with higher GDs. The same marker system had opposite significantly correlation with yield heterosis in two sets of diallel crosses mainly because of the different GD level of the parents. This result suggested that the prediction of heterosis using ILPs has the restriction or confidence interval of GDs of the parents.3) QTLs and heterosis The correlation between GDs based on QTLs associated with yield and components traits and heterosis for yield and yield related traits was not significant or was very low although significant. The main explain was that QTLs were not enough for the precise prediction; or QTLs were not linked to the traits tightly enough; or QTLs had small contribution. Many reports showed that the extent of the QTLs linked to the trait decided the correlation between GDs based on QTLs and heterosis; the low relationship may due to the heterozygosity revealed by markers had nothing to do with that revealed by QTLs; or there was epistatic effect among QTLs while its heterozygosity was not correlated to heterosis.4) Single locus and heterosis Positive locus (PL), effect-increasing locus (DL) and effect-decreasing locus (IL) were screened from all the loci revealed by ILPs and SSRs, respectively. Results showed that the ILs based GDs could predict heterosis in the two diallel crosses with obviously different GDs. Some common DLs and ILs were screened in both sets of crosses. It convincingly suggested that we can predict heterosis for specific target using ILs or DLs. For the trait that need to be increased, we can use ILs to predict heterosis such as yield per plant, filled grains percentage and so on; for the traits that need to be decreased such plant height, tiller number, heading date, etc., we can use DLs for the prediction. Thus, combing the usage of ILs and DLs, it is easy to develop new materials with high yield and proper plant height and tillers and heading date to satisfy the farmers'need.