Allelic Variations of the Waxy Gene and Their Associations with Indica–Japonica Differentiation and Amylose Content in Yunnan Local Rice Germplasm

Objectives: To provide insights for breeding high-quality rice varieties, we analyzed local rice (Oryza sativa L.) germplasm from Yunnan Province, China, focusing on the relationships among Waxy gene alleles, indica–japonica differentiation, and amylose content (AC). Methods: We examined 201 local rice accessions. Two functional molecular markers for the Waxy gene were used to detect four alleles (Wxa, Wxb, Wxin, Wxmw). Additionally, 33 InDel markers were employed to classify indica–japonica attributes, and AC was measured according to GB/T 15683-2008. Results: We detected 175 accessions with Wxa, 20 with Wxb, 4 with Wxin, and 2 with Wxmw, indicating Wxa dominance and a diverse genetic basis at the Waxy locus. Indica–japonica classification identified 180 indica-type, 19 japonica-type, and 2 intermediate-type accessions, confirming predominant indica differentiation in Yunnan rice. Integrating Waxy allele detection, indica–japonica attributes, and AC showed that Wxa occurred primarily in indica rice with higher AC (mean 22.55%), comparable to Wxin (mean 24.33%); Wxb was mainly found in japonica rice with lower AC (mean 13.46%), similar to Wxmw (mean 15.65%). Conclusions: Local Yunnan rice exhibits Wxa predominance at the Waxy locus and clear indica differentiation. The observed associations between Waxy alleles, subspecies attributes, and AC provide useful references for marker-assisted breeding of premium rice and for exploiting indica–japonica heterosis.