A model of the relationship between weedy rice seed-bank dynamics and rice-crop infestation and damage in Jiangsu Province, China

Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice

Seed dormancy (SD) and longevity (SL) may share developmental and genetic mechanisms, as both traits are developed in the same maternal environment and evolved to coordinate the timing of germination and the life span of seedbanks. To test the hypothesis, allelic variants at the SD1-2, 7-1, 7-2, and 12 loci from weedy and cultivated rice (Oryza sativa) were assembled into the same genetic background, and 16 homozygous lines selected as a tetragenic system. These lines were evaluated for SD measured by germination at 7, 21, 35, and 150 days of after-ripening (DAR), and for SL measured by the seed decay rate and survivability in the soil of a rice field for 7 months. Pyramiding the alleles from weedy rice lengthened the dormancy duration, and seeds survived in the soil remained dormant at the excavation. Germination levels at 7 to 150 DAR were correlated positively with the seed decay rate (r = 0.41-0.53) and negatively with the survivability (r = -0.45 to -0.28) in the tetragenic system. All four loci contributed to genotypic variation for each of the SD and SL measurements through main and/or epistatic (two- to four-order interactions) effects. SD7-1 (identical to the pericarp color gene Rc) played a major role in regulating seedbank longevity when interacted with the other SD gene(s). This research provided evidence that natural genes controlling SD are involved in regulation of soil seedbank longevity. Thus, accumulation of SD genes in a population could result in persistence of wild plants and weeds in conventional tillage systems.

Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes

Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced seed shattering in crop-weed hybrid descendants by partially silenced expression of the seed-shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence seed-shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.

Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticated indica and japonica rice. Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide. While its formation is poorly understood, massive amounts of rice genomic data may provide new insights into this issue. In this study, we determined genomes of three weedy rice samples from the lower Yangtze region, China, and investigated their phylogenetics, population structure and chromosomal admixture patterns. The phylogenetic tree and principle component analysis based on 46,005 SNPs with 126 other Oryza accessions suggested that the three weedy rice accessions were intermediate between japonica and indica rice. An ancestry inference study further demonstrated that weedy rice had two dominant genomic components (temperate japonica and indica). This strongly suggests that weedy rice originated from indica-japonica hybridization. Furthermore, 22,443 novel fixed single nucleotide polymorphisms were detected in the weedy genomes and could have been generated after indica-japonica hybridization for environmental adaptation.