Nucleotide Diversity in Waxy Gene and Validation of Single Nucleotide Polymorphism in Relation to Amylose Content in Chinese Microcore Rice Germplasm

The waxy protein primarily controls the synthesis of amylose, which is a key determinant of rice (Oryza sativa L.) cooking and processing qualities. Knowledge of the diversity of waxy gene in Chinese rice is essential to validate molecular markers for marker-assisted selection and to trace the origin of Chinese glutinous rice. The waxy (W(x)) gene in the wild rice has rarely been studied, and the origin of Chinese glutinous rice is not well understood. The objectives of our investigation were (i) to identify the diversity of W(x) and molecular markers for marker-assisted breeding and (ii) trace the origin of Chinese glutinous rice. We examined the sequence variations for the waxy gene of 98 accessions of cultivated rice and 134 accessions of wild rice from a previously established microcore collection of Chinese rice germplasm. A total of 51 and 226 single nucleotide polymorphisms (SNPs) or insertions or deletions were found in the cultivated rice and the wild rice, respectively. Wild rice accessions had much higher diversity than cultivated rice and nonglutinous rice had much higher diversity than glutinous rice whereas the genetic diversity of indica rice was similar to that of japonica rice. Polymorphisms of CTn microsatellite, G/T SNP, and 23-bp insertion in the waxy gene and their relationship to amylose content were explored using cultivated rice. The G/T allele and 23-bp insertion were better associated with amylose content than with the CTn alleles, and they were validated as molecular markers for marker-assisted selection. All the wild rice accessions with 23-bp insertion or T allele came from South China and the glutinous rice originated from wild rice of South China parallel with indica and japonica differentiation.