Molecular evolution of shattering loci in U.S. weedy rice

Abstract

Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re-acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms.

Weedy rice in sustainable rice production. A review

“…According to De-Wet and Harlan (1975), weedy rice originated from the selection and adaptation of wild rice to agricultural habitats. In regions where no wild rice has been grown, weedy rice may instead originate from cultivated rice through de-domestication with adaptive mutations and the accumulation of beneficial mutants (Ishikawa et al 2005;Cao et al 2006;Reagon et al 2011;Thurber et al 2010;He et al 2014;Qiu et al 2014;Lu et al 2016;Li et al 2017;Qiu et al 2017). In the case of Brazil and Italy, where no wild Oryza types are indigenous, contamination of seed stocks with wild Oryza species has been proposed as a source of weedy rice (Carney 2004;Grimm 2014).…”

“…Sequence comparisons of the mutation site of the gene revealed its presence in all the domesticated rice cultivars. Thurber et al (2010) evaluated allelic identity and the diversity of shattering locus sh4 in US weedy rice. The haplotypes contained a single derived mutation at the sh4 locus.…”

Genetic analysis of seed-shattering genes in rice using an F3:4 population derived from an Oryza sativa x Oryza rufipogon cross

“…Additionally, QTL analysis identified sh4 between SSR markers RC4-123 and RM280, which had a physical distance of ~1360 kb in the O. sativa genome. Thurber et al (2010) assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice. They demonstrated that all cultivated and weedy rice, regardless of the population, shared similar haplotypes at sh4 and all contained a single mutation associated with decreased seed shattering.…”

Use of Multicopy Transposons Bearing Unfitness Genes in Weed Control: Four Example Scenarios

“…). An even more striking mitigation gene to use would be the various antiseed shatter genes (Thurber et al, 2010;Akasaka et al, 2011;Zhu et al, 2012), which would prevent the weed from reseeding itself. A crop-related weed with an antiseed shatter gene growing in the crop will be harvested with the crop, and will not reseed itself, if the farmer uses weed-free certified seed in the next season.…”