Genetic Differentiation of Asian Weedy Rice Revealed with InDel Markers

Abstract

ABSTRACTTo elucidate occurrence patterns and genetic differentiation of weedy rice (Oryza sativa f. spontanea) from diverse geographical regions, we analyzed 142 weedy rice accessions, 25 cultivated rice varieties (Oryza sativa L.), and 9 common wild rice accessions (Oryza rufipogon Griff.) from various regions in Asia using InDel molecular markers. Principal component analysis revealed significant genetic differentiation of weedy rice into 2 distinct groups. Results indicated a significant indica–japonica differentiation of weedy rice. Analysis of the geographic distribution indicated that the indica types were found across latitudes from 5 to 40° N without a significant correlation with latitude (R2 = 0.1041, P > 0.05). Japonica types were mostly limited to latitudes >35°N and correlated with latitude gradients (R2 = 0.426, P < 0.05). Most intermediate types were distributed in regions at latitudes <35° N. The relationship among weedy, cultivated, and wild rice as analyzed by a neighbor‐joining phylogenetic tree revealed a two‐group classification. The first group included japonica‐type weedy rice accessions and japonica cultivars from higher latitude gradients (>35° N), suggesting that in these regions, the Asian weedy rice varieties are genetically closer to japonica cultivars—particularly to local cultivars—and have probably originated from local cultivars. The second group included indica cultivars and wild rice entries, indicating that weedy rice entries from latitude gradients (≤35° N.) are genetically closer to wild rice. Thus, weedy rice may have genetically evolved from wild rice or resulted from natural crossing of wild rice and cultivars. These findings provide a strong scientific basis for the occurrence patterns and control strategy of weedy rice.