Genetic Contribution Of Founder Parent Balilla To Progeny Derivatives And Association Analysis Of Important Agronomic Traits In Japonica Rice

Rice (Oryza sativa L.) is one the most important grain crops in the world. It has provided the principal food supply and the calorie intake for the nearly half of global population. Also, rice is the model monocotyledonous plant for genome research. The research related genetics and genomics in rice has been at the forefront of the other crops. Optimization the platform of the rice functional genome research will provide leading in the genomic research in other crops such as wheat, corn, cotton, rape, soybean and peanut. This strategy will comprehensively promote the innovation in genomic research and genetic improvement, which provides provide the technological strength and the genetic resources for our country.In rice breeding in China, the plant breeders had developed a series of founder genotype varieties, which were widely used as cross parents during past decades. The japonica rice variety Balilla, introduced from Italy, is considered as one of the most important founder genotypes. Balilla and its derivative Guihuanghuang, with wide compatibility and typical erect panicle character, were widely used in the japonica rice breeding program. By tracing the genealogical record of the japonica varieties with erect panicle, the gene which controlled the dense and erect panicle of most of the varieties with erect panicle in China, is from the transmittance of parent Balilla. The erect panicle has advantages in improvement ecological environment and contribution for yield improvement in the japonica rice. In order to study the genetic contribution and genetic effect of the rice founder genotype Balilla to its derivative variety, the rules of major genes or key chromosome fragments transmittance, and understand the genetic basis transmission mechanism and the favourable alleles discovery, we carried out entire genome scanning using microsatellites in a total of 137 varieties in Balilla pedigree tree. By combining with genealogical information, the genotyping and the phenotype information, we mapped QTL associated 11 agronomic traits through empirical Bayesian estimation approach and analyzed the allele effect. These results were as follows:1. For 12 traits assyssed, there exhibited extremely remarkable variations among them (P<0.001). Moreover, all traits in two year experiments, also exhibited the extremely remarkable variation. The PH had the highest heritability, whereas the PPP had smallest one.2. The results of principal components analysis demonstrated that the first principal component of the transmittance from the parent to the progeny is mainly integrated eigenvector of SPP, FGPP, KGW, GD, PPP and PL. And the second principal component is mainly integrated eigenvector of PA and GYPP. These results indicated PM is the major phenotypic contribution from Balilla to its progeny.3. In this pedigree-based natural population, we detected a total of 88 QTL for 11 agronomic traits, including three type effects:the main effect, epistasis and gene interaction with environment. About 36% of QTLs explained less than 5% phenotypic variation individually, and about 10% of QTLs explained more than 20% phenotypic variation individually.4. In rice Balilla and its derivative varieties, we detected 34 conservative fragments in all across on 11 chromosomes. We found 35 QTLs located in these 16 fragment regions, which influenced 9 important agronomic traits. These results indicated that conservative fragments we detected were under strong selection in rice breeding program. For example, the region RM105-RM6771 on chromosome 9, was detected in many progeny, which could transmitted steadily from parent to many generations. Actually, the progenies containing this fragment exhibited semi-erect or erect panicles characteristic. Moreover, we also identified the transmitted chromosome fragments from parent Balilla to the progeny. In addition, we perform the association analysis in japonica germplasm. A unified mixed linear model was used to identify marker-trait associations, taking into account population structure and kinship. A total of 51 and 69 significant marker-trait associations were identified in the two years, respectively, with 18 common to the two years. It is noteworthy that the loci exhibiting significant marker-trait associations were in genomic regions also identified as such in previous reports.These results strongly indicate convergence of important gene/QTLs controlling important agronomic traits in genomic regions under selection by plant breeders in the plant breeding programs. And these key chromosomal segements could transmite by human selection. Our results demonstrate that using pedigree analysis and association analysis to examine different varieties is an efficient approach and provides indicators that can be used in practical rice breeding.