Nucleotide polymorphisms in OsAGP genes and their possible association with grain weight of rice

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 the developing rice kernel. However, it is still unknown whether the naturally occurring variation in the sequence of ADP-Glucose pyrophosphorylase of rice (OsAGP) is related to the grain weight (GW). In this study, we discovered a total of 38 single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the partial sequences of six OsAGP isoform genes from 30 rice accessions with diverse agronomic traits. We then developed ten cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers for genotyping the SNPs and InDels for an association mapping population consisting of 416 rice accessions. Candidate gene association study indicated that an InDel of OsAGPL4 was associated with GW in two environments and an SNP of OsAGPL2 was associated with GW in one environment. Each gene marker only explained 1% of the variation of GW, thus it could be concluded that both genes contributed little to GW of rice. However, the markers identified in this study could be used for tagging other traits of interests and in molecular breeding.

► We sequenced partial sequences of six ADP-Glucose pyrophosphorylase of rice (OsAGP) among 30 rice accessions.
► We found a total of 38 single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) six OsAGP genes.
► We developed 10 SNP markers, and genotyped other 416 rice.
► Sequence variation in OsAGPL4 and OsAGPL2 are associated with grain weight of rice.
► But their effects are minor, each explaining 1% of the variation of GW.