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.

Figure 1. Seed shattering phenotype in weedy, wild and cultivated Oryza

Distributions are of average accession BTS values for each Oryza group. The black line represents the median of each distribution, and the grey dot the mean; white dots represent outliers. Numbers in parenthesis correspond to sample sizes. Weedy rice groups are as follows: SH (straw-hulled), BHA1 and BHA2 (black hulled and awned), BRH (brown hulled) and MIX (mixed origin). Both O. rufipogon and O. nivara accessions have been grouped together under the heading O. rufipogon.

Figure 2. Phylogenies of flanking regions surround sh4

Neighbor Joining trees for each of eight ~500 bp regions at varying distances from the sh4 locus. Diagram is to scale. Only branches with bootstrap values over 50% are shown. The star on the sh4 locus tree denotes the T substitution associated with loss of shattering. For clarity, all tropical japonica, temperate japonica and aromatic rice have been grouped under the japonica heading and colored green. Additionally, all weed groups have been colored red, but the main groups are distinguishable via icons placed to the right of each tree.

Figure 3. Graphical view of concatenated sh4 haplotypes

Haplotypes across the genomic region surrounding sh4 are shown for the 90 individuals (wild, weedy, and cultivated) that share the common sh4 haplotype containing the T SNP. The numbers across the top represent flanking regions (1- 6 = sh4f_001- _006). Yellow squares represent SNPs found in at least one haplotype. A tally of individuals from each cultivated, weedy, or wild group is shown to the right. Colors of accession counts indicate haplotypes that are identical across a 6.2 Mb region (up to sts_040) containing sh4.

Figure 4. Extended Haplotype Homozygosity surrounding sh4

EHH was performed on concatenated alignments containing the sh4 gene and all eight flanking regions in order as they appear on the chromosome. Sts_040 and sts_021 were not included for O. rufipogon as haplotype homozygosity had already reached zero. The grey triangle atop each panel represents the location of the T mutation associated with loss of shattering in sh4. Numbers under black bars represent flanking regions (1- 6 = sh4f_001- _006). A. EHH for O. rufipogon groups possessing a T or a G at the SNP associated with shattering variation. B. EHH results for three cultivated rice groups. C. EHH results for the main U.S. weedy rice groups.