title: 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.
authors.affiliation: School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia; Genomics Facility, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia.
authors.forename: Beng-Kah
authors.initials: BK
authors.lastname: Song
authors.forename: Tse-Seng
authors.initials: TS
authors.lastname: Chuah
authors.forename: Sheh May
authors.initials: SM
authors.lastname: Tam
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Olsen
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D014644:Genetic Variation; D005828:Genetics, Population; D008296:Malaysia; D018895:Microsatellite Repeats; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D057685:Plant Weeds / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: agricultural weeds; genetic introgression; hull colour; red rice; shattering; wild crop relatives