Construction Of An Association Population And Association Analysis For Some Quality Traits In Rice (Oryza Sativa L.)

Most agronomic traits such as yield, quality and stress-tolerance of rice are quantitativetraits. Dissection of the genetic basis for these traits is difficult, because they are controlledby multi-genes that are affected by environmental factors, Rice improvement and dissectionof complex traits require germplasm diversity and understanding the genetic basis of thesetraits. With the development of genomics and biostatistics software and applications ofmolecular markers in crop breeding, association analysis based on the linkage disequilibrium(LD) offers a new method for identifying of loci controlling those traits. Combination ofquantitative trait loci (QTL) mapping and association analysis facilitates dissection ofcomplex traits, which results in important information and markers for molecular breeding bydesign in crops. In the present study, association analysis (mapping) and QTL mapping wereused to study genetic basis for starch quality and nutritional quality of rice grain, facilitatingmolecular improvement of rice quality. The main results are summarized as follows:1. One hundred genome-wide simple sequence repeat (SSR) markers were used toassess the genetic diversity, population structure, and LD of a set of 416 rice accessionsincluding landraces, cultivars and breeding lines. Results showed that the population includeda diverse genetic variation. A model-based population structure analysis subdivided thepopulation into 7 clusters. LD was significant at a 0.05 level among 62.8% of the SSR pairsin the entire sample and with a range of 5.9～22.9% in each cluster. On average, theestimates of population structure account for 27.7% of phenotypic variation, ranging from6.2% to 46.6%. The results suggested that the population could be used for detection ofgenome-wide SSR marker-phenotype association mapping.2. Association analysis was carried out between the starch gene markers and starchquality traits based on population structure. Results confirmed that Wx SSR and singlenucleotide polymorphism (SNP) were strongly associated with apparent amylose content(AAC), pasting viscosities (HPV, CPV, BD and SB), gel hardness (HD), whereas the SSâ…¡aGC/TT SNPs were strongly associated with the pasting temperature (PT). These markers areuseful in molecular breeding for improvement of rice eating and cooking qualities.3. In addition, a genome-wide scan was performed using 100 SSR markers to identifyQTL associated with starch quality in rice. A total of 21 SSR loci were found to besignificant associated (P＜0.001 ) with 5 starch quality traits. Five SSR loci were found to besignificant associated with AAC, but all the five SSR loci explained less than 5% of the totalphenotypic variations. The RM346 on chromosome 7 was associated simultaneously with the 5 traits. RM276 on chromosome 6 explained more than 5% of the total phenotypic of PT.Two associated markers (RM253, RM484) were located in regions where QTL hadpreviously been identified. These results suggested that the association analysis approachcould be a useful alternative to linkage mapping for the identification of unreported regionsof the rice genome containing putative QTL of starch quality.4. A recombinant inbred line (RIL) population derived from the reciprocal cross ofLemont (a premium high-quality tropical japonica rice)and Jiayu 293 (a high-yield butlow-quality indica rice) was used to test the association of microsatellite markers ofstarch-synthesizing genes with starch quality parameters. The results confirmed theassociation of Wx and starch synthase 1 (SSl) alleles with various starch properties measuredin rice flour. However, the starch properties were not associated with the starch branchingenzyme 1 (SBE l) gene alleles.5.â…¡-32B is a key Chinese maintainer line used for hybrid rice breeding. However, it isof poor quality because of a high AAC, a high gelatinization temperature (GT), andnon-fragrant. It is known that the AAC, GT and fragrance traits are controlled by the Wx,starch synthaseâ…¡a (SSâ…¡a) and fragrance (fgr) genes. The quality ofâ…¡-32B was improved byintrogressing the Wx, SSâ…¡a and fgr genes from YixiangB, another maintainer line, that has alow AAC, a low GT and fragrant sensory, with the assistance of the functional markers. TheWx microsatellite [(CT)₁₇ allele] SSâ…¡a single nucleotide polymorphism (TT allele) and fgrinsertion/deletion allele (8 bp), were transferred toâ…¡-32B by two backcrosses and twoselfings. Molecular marker-assisted selection was applied in the series to select forindividuals carrying Wx-(CT)₁₇, SSâ…¡a-TT and fgr alleles. According to the marker genotypes,17 homozygous lines for Wx, SSâ…¡a and fgr gene were finally selected. The improvedâ…¡-32Blines were fragrant with reduced AAC and GT.6. Association analyses were performed between the Rc, Ra, fgr and starch gene markersto grain color and nutritional quality traits in the 416 rice accessions. The result showed thatRc and Ra gene markers were strongly associated with grain color traits, whereas the RM316might be a putative QTL of grain color. A total of 15 SSR loci were found to be significantassociated (P＜0.001) with 3 nutritional traits i.e. total phenolics content, flavonoids contentand antioxidant capacity. Ra explained more than 44% of the total phenotypic variations forthe three nutritional traits. For total phenolics contents and antioxidant capacity, Rc explained27.39% and 23.09% of the total phenotypic variations, respectively. RM316 explained morethan 10% of the total phenotypic variations for the three nutritional traits. The resultconfirmed that Ra and Rc were main-effect loci for rice grain color and nutritional quality traits, whereas RM316 might be an important putative QTL.7. Association analysis between the fgr, starch gene markers and SSRs and grain colorand nutritional quality traits in the 361 white rice accessions were also performed. A total of34 markers were found to be significant associated (P＜0.001 ) with the five grain color traits,which showed these traits were controlled by polygenes with minor effects. Five SSR lociwere found to be significant associated (P＜0.001 ) with total phenolics contents, whichexplained more than 30% of the total phenotypic variations. Among them, RM336 explained7.16% of the total phenotypic variations of total phenolics content. RM251 was the onlylocus associated with antioxidant capacity, which explained 7.16% of the total phenotypicvariations. No SSR locus was found to be significant associated with flavonoids content.8. Mapping of quantitative trait loci (QTL) for grain color, Total phenolics, flavonoids,antioxidant capacity was carried out using a doubled haploid (DH) population derived from across between indica variety Zaiyeqing 8 (ZYQ8) and japonica variety Jingxi 17 (JX17). Theresults indicated that all three parameters were continuously distributed among the DH lines,but many DH lines showed transgressive segregation for all traits. A total of 12 QTLs wereidentified for five color parameters, three of which, qL-2, qB-2 and qC-2 shared the sameregion on chromosome 2. A total of three QTLs on chromosome 2, 4, 12 were identified fortotal phenolic content, which explained more than 43% of the total phenotypic variations.Three QTLs on chromosome 2, 11 were identified for total flavonoid content, whichexplained more than 26% of the total phenotypic variations. Three QTLs on chromosome 1, 7,11 were identified for antioxidant capacity, which explained more than 32% of the totalphenotypic variations.