Genetic variation and possible origins of weedy rice found in California

Abstract

Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.

Italian weedy rice—A case of de‐domestication?

“…Today, it is generally accepted that weedy rice has originated independently in different geographical areas of the world. Both exoferality and endoferality have been shown to contribute to the establishment of weedy rice populations (De Leon et al, 2019;Huang et al, 2017;Li, Li, Jia, Caicedo, & Olsen, 2017;Reagon et al, 2010;Song, Chuah, Tam, & Olsen, 2014;Vigueira et al, 2019).…”

Effects of competition from California weedy rice (Oryza sativa f. spontanea) biotypes on a cultivated rice variety

“…These biotypes are distinguishable from each other by phenotypic differences, including presence and length of awns, hull color, and grain size (Table 1). They are also genetically distinct and have separate origins from diverse rice ancestors (De Leon et al 2019). Although the effects of weedy rice competition on cultivated rice yield has been studied for other locations and weedy rice biotypes, the effects of competition on growth and yield of California rice cultivars due to local weedy rice biotypes have not been previously investigated, to our knowledge.…”

Phenotypic diversity of weedy rice (Oryza sativaf.spontanea) biotypes found in California and implications for management

“…Accessions were obtained from growers' rice fields in Glenn, Colusa, Butte, Yuba, and Sutter counties in the northern Sacramento Valley region of California. The five biotypes of California weedy rice used in this study are characterized by genetic differences (De Leon et al 2019), which correspond with observed differences in hull color, presence of awns, plant stature, and grain size (Table 2). To enable comparison with other weedy and wild rice, we included 5 weedy rice accessions from the southern United States (Arkansas, Mississippi, and Texas) and 3 wild rice species.…”

“…Some studies of southern U.S. weedy rice have indicated that weedy rice biotypes similar in height to cultivated rice may be hybrids with local cultivars (Burgos et al 2014;Gealy et al 2003;Singh et al 2017b), although there are exceptions (Gealy et al 2012). Type 4 weedy rice is likely not a hybrid with cultivated rice, as it is otherwise not phenotypically similar to California rice varieties ( Figure 1A) and is genetically distant from them (De Leon et al 2019). Weedy rice biotypes from the southern United States have large variation in heading or flowering date, similar to California biotypes (Kanapeckas et al 2017;Shivrain et al 2010;Thurber et al 2013).…”

“…Studies of California weedy rice collected in 2008 described all samples as strawhull awned (Kanapeckas et al 2016(Kanapeckas et al , 2017. Weedy rice consisting of several phenotypically and genetically distinct biotypes (De Leon et al 2019) has since been identified infesting more than 130 fields and 5,600 ha in California as of 2018 (L Espino, personal communication, August 4, 2019). The recent rapid increase in reports of diverse weedy rice in California calls for new studies examining the biology of California weedy rice and identification of traits that could be exploited for managing weedy rice infestations.…”