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

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

SampleDescription

List of rice genotypes used in genetic study, genotype source, grain attributes, and presence or absence of 14-basepair deletion in Rc gene

GeneticData

Genotype data from 99 genetic markers described in the file GeneticMarkers.csv for 96 rice samples described in the file SampleDescription.csv. Data contains codominant marker data with two columns for each locus and one line per sample. Alleles are numbered 1 through n for each marker. Missing data is coded as 0

Data from: Genetic variation and possible origins of weedy rice found in California

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

GeneticMarkers

Distribution and allele variation of 98 microsatellite markers and 1 Rc gene-specific marker among 96 weedy, cultivated and wild rices. Microsatellite marker primer sequences are most accessible from the Gramene database (http://archive.gramene.org/markers/microsat/) but were published in: International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800. The Rc marker is published in Subudhi et al. 2012: Subudhi, P.K, Parco, A., Singh, P.K., De Leon, T., Karan, R., Biradar, H., Cohn, M.A., Brar, D.S., & Sasaki, T. (2012) Genetic architecture of seed dormancy in US weedy rice in different genetic backgrounds. Crop Science 52: 2564-2575

Setting research and extension priorities for agronomic crops in California

Agronomic crops, including grains, forages, and fiber, are central to California agriculture, yet face many challenges. To ensure resilience, a statewide survey was conducted by the University of California Cooperative Extension service (UCCE) to identify high-priority needs and inform extension programming based on grower, consultant, and allied industry input. The goal was to compare the importance of different topics with the level of satisfaction regarding UCCE’s delivery of information on these topics. Survey respondents identified integrated pest management, nutrient and irrigation management, and variety testing as high-priority needs, with overall high satisfaction regarding UCCE’s program delivery on these topics. Topics needing more focus (high priority but below-average level of satisfaction) included testing new products, soil health management, and water conservation and storage. Areas of low priority and low satisfaction included niche marketing, emerging crops, organic production, harvest/post-harvest technology, salinity management, compost and manure management, and greenhouse gas emission reductions. To address stakeholder challenges, results from this study suggest that research and extension efforts should prioritize issues directly impacting on-farm crop production. At the same time, areas of low interest reflect a need for more support to engage farmers on these topics, particularly those concerning state environmental regulations and challenges to local and global food production and security