Genetic variation and possible origins of weedy rice found in California.

Teresa B De Leon,Elizabeth Karn,Whitney Brim‐Deforest,Virgilio C Andaya,Timothy Blank,Luis Espino,Cynthia B Andaya,Kassim Al‐Khatib

doi:10.1002/ece3.5167

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.

Highlights

Plant domestication is the process of conversion of wild plants into domesticated crop plants through artificial selection
The increasing spread of weedy rice in California and the recent report of weedy rice originating from cultivated California rice va‐ rieties (Kanapeckas et al, 2016) raised questions about the origin of California weedy rice and its management
Weedy rice individu‐ als clustered together by biotype, indicating that for California weedy rice biotypes, samples can be classified by pheno‐ type into groups that are biologically and genetically meaningful (Figure 2, Table 2)

Summary

| METHODS

Wild, and cultivated rice samples selected for genotyping analysis totaled 96 samples. The California weedy rice samples were grouped into four clusters, which correspond to five distinct biotypes categorized by hull color, grain type, and presence of awn (Figure 2, Table 2). Analysis of molecular variance (AMOVA) indicated that California weedy rice collections are very diverse, with the majority of the vari‐ ation (55%) due to differences among groups (biotypes) while 40% is due to variation among individuals, and differences within group or biotype account for only 5% of genetic variation (Table 3). Type 1 rice clustered closely with aus rice, Basmati, the single temperate japonica individual that clustered separately from the others in phylogenetic analysis (Cal4810A1‐3), and BH southern weedy rice.

| DISCUSSION

Findings

CONFLICT OF INTEREST