DNA markers are widely accepted as potentially valuable tools for crop improvement in rice. There are two main marker resources that can be used in breeding practice. The first is QTLs from a specific mapping population with two parents. This kind of marker is population-dependent. Thus, in a cross with two other parents, further verification is needed as to whether the QTLs are still related to the traits using the same mapping approaches. The second resource is that of markers derived from specific genes. These markers are functional and may be invariably associated with specific traits.
The starch synthase IIa (SSIIa) gene was sequenced among 30 rice accessions, and we found that two continuous SNPs (GC/TT) showed a very strong association with peak gelatinization temperature (Tp, P < 0.0001). This GC/TT polymorphism alone can differentiate rice with high or intermediate gelatinization temperature (GT, possessing the GC allele) from those with low GT (possessing the TT allele). A further 509 rice varieties were genotyped for the SSIIa GC/TT alleles. Association test was conducted using all starch gene markers, and results indicated that Wx SSR and SNPs were strongly associated with amylose content, pasting viscosities, gel hardness, and retrogradation properties, whereas the SSIIa GC/TT SNPs were strongly associated with the pasting temperature and retrogradation properties, which confirmed the findings from QTL mapping.
In this poster, we describe how to discover functional molecular markers from starch biosynthetic genes, and conduct association mapping for starch quality properties in a set of rice varieties and germplasms, the results of which will be useful in marker-assisted breeding for the improvement of rice quality.