Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Abstract

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

“…The shattering and seed dormancy phenotypes acquired in weedy rice are presumably adaptive in wild conditions, potentially further facilitating feralization. A crop-weed-wild complex is found throughout regions where wild and cultivated rice overlap, and gene flow among components within the species complex is frequently observed (Ellstrand et al 2013;Pusadee et al 2013Pusadee et al , 2016Song et al 2014). In Asia, rice cultivation has been performed for thousands of years, and rice feralization has likely happened throughout this period as well (Vaughan et al 2005).…”

“…These observations indicate that rice could frequently revert to the wild state in domestication traits. Weedy rice is a conspecific form of cultivated rice, while displaying distinguishing features including shattering grains and strong seed dormancy typical of wild rice (Ferrero 2003;Song et al 2014). The shattering and seed dormancy phenotypes acquired in weedy rice are presumably adaptive in wild conditions, potentially further facilitating feralization.…”

Cross-Resistance to Imazapic and Imazapyr in a Weedy Rice (Oryza sativa) Biotype Found in Malaysia

“…Moreover, Malaysian weedy rice is highly diverse in morphology and phenology. Molecular (Song et al, 2014) and morphological (Sudianto et al, 2016) studies collectively have claimed that the local conventional indica rice cultivars and wild rice (Oryza rufipogon) populations genetically contributed to the complexity of weedy rice in Malaysia. Therefore, synchronization in flowering period between the weedy and cultivated rice and genetic compatibility are expected to support intermittent gene flow across these Oryza groups.…”

Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

“…The genetic diversity and origins of weedy rice have been studied extensively, and research to date suggests that weed strains in different world regions have evolved independently from different cultivated rice varieties, including indica , aus , and japonica rice (Reagon et al 2010; Song et al 2014). In Southeast Asia, where rice is grown in close proximity to populations of its wild ancestor, O. rufipogon , hybridization with wild populations also appears to have also contributed to the genetic composition of weed populations (Pusadee et al 2013; Song et al 2014).…”

“…In Southeast Asia, where rice is grown in close proximity to populations of its wild ancestor, O. rufipogon , hybridization with wild populations also appears to have also contributed to the genetic composition of weed populations (Pusadee et al 2013; Song et al 2014). Although weedy rice is specifically adapted to agricultural fields, there are some traits in wild Oryzas that would likely be adaptive for the weedy life history strategy if introgressed into nearby weed populations.…”