Sequence Variations Of Rice OsAGP Genes And Their Associations With 1000-grain Weight

The grain weight is one of important component traits that determine rice yield. ADP-glucose pyrophosphorylase (AGPase) is a rate limiting enzyme participating in starch biosynthesis, which may be responsible for the filling rate and starch accumulation in developing rice kernel. Whether the naturally occurring variations in the sequences of ADP-glucose pyrophosphorylase of rice (OsAGP) are related the grain weight is not known, and thus was the objective of this study. The main results are summarized as follows:1. Partial sequences of the seven OsAGP isoform genes were sequenced among 30 rice accessions with diverse variations in agronomic traits. A total of 38 single nucleotide polymorphisms (SNPs) or insertion/deletion (InDels) were resolved. Association test indicated some of them might be associated with 1000-grain weight (TGW).2. To further test the association of the SNPs of OsAGPs with TGW, six cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers were developed. Together with other four markers, they were used to genotype an association mapping population of 416 rice accessions. It was found that the marker of OsAGPL2 had the lowest polymorphic information content (PIC) of 0.06-0.08, whereas the marker for OsAGPLl had the highest PIC of 0.5.3. Candidate gene association indicated that one InDel of OsAGPL4 was associated with TGW in two environments, while an SNP of OsAGPL2 was associated with TGW in one environment. Genome-wide association mapping revealed another ten markers that were associated with TGW in at least one environment. Most of them were located in regions where QTLs had previously been identified. Of them, both of the RM246 and RM237 on chromosome 1 was located nearby the OsAGPL2, so their associations with TGW might be derived from the linkage disequilibrium (LD) with OsAGPL2. The Rc gene on chromosome 7 was close to the OsAGPL4. This study indicated that TGW is a complex trait that is controlled by multiple genes/QTLs distributing on the whole genome, the markers identified would help us to understand the genetic control of TGW, and would be used in molecular breeding to improve the grain yield.