Weedy rice refers to the unwanted plants of the genus Oryza that have some undesirable agronomic traits and pose a major threat to sustainable rice production worldwide. Widespread adoption of direct seeded rice and hybridization or gene flow between cultivated rice and their wild relatives has resulted in the creation and dissemination of weedy rice. Currently, weedy rice (Oryza sativa f. spontanea) has become one of the most common weeds infesting rice fields worldwide. In this paper, we review the biology, physiology, evolution, and genetic features of weedy rice. We also discuss the major obstacles in weedy rice management, including high diversity of weedy rice, ecological impacts of gene flow on weedy rice, changing climate, and weedy rice management. We then present a framework for the sustainable management and utilization of weedy rice. Our main emphasis is to explore the reservoir of natural variations in weedy germplasm and to utilize them for crop improvement. This review outlines some of the latest biotechnological tools to dissect the genetic backgrounds of several favorable traits of weedy rice that may prove beneficial for breeding and evolutionary studies on cultivated rice. We suggest that by merging the disciplines of genomics, breeding, and weed management, we can achieve the goal of sustainable rice production.

The embryo sac plays a vital role in sexual reproduction of angiosperms. LysM domain containing proteins with multiple lysin motifs are widespread proteins and are involved in plant defense responses against fungal chitins and bacterial peptidoglycans. Various studies have reported the role of LysM domain-containing proteins in plant defense mechanisms but their involvement in sexual reproduction remains largely unknown. Here, we report the involvement of a LysM domain-containing gene, EMBRYO SAC 1 (OsEMSA1), in the sexual reproduction of rice. The gene encoded a LysM domain-containing protein that was necessary for embryo sac development and function. The gene was expressed in root, stem, leaf tissues, panicle and ovaries and had some putative role in hormone regulation. Suppression of OsEMSA1 expression resulted in a defective embryo sac with poor differentiation of gametophytic cells, which consequently failed to attract pollen tubes and so reduced the panicle seed-setting rate. Our data offers new insight into the functions of LysM domain-containing proteins in rice.

To 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.