Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa)

Abstract

*Red rice, a major agricultural weed, is phenotypically diverse and possesses traits that are similar to both wild and cultivated rice. The genetic resources available for rice make it possible to examine the molecular basis and evolution of traits characterizing this weed. Here, we assess the phenol reaction - a classical trait for distinguishing among cultivated rice varieties - in red rice at the phenotypic and molecular levels. *We phenotyped more than 100 US weed samples for the phenol reaction and sequenced the underlying Phr1 locus in a subset of samples. Data were analyzed in combination with previously published Phr1 data for cultivated rice. *Most weed accessions (96.3%) are positive for the phenol reaction, and samples with a negative response carry loss-of-function alleles that are rare or heretofore undocumented. One such allele may have evolved through mutational convergence of a 1-bp frameshift insertion. Haplotype sharing between red rice and US cultivars suggests occasional crop-weed hybridization. *Our discovery of previously undocumented nonfunctional phr1 alleles suggests that there are likely to be other loss-of-function mutations segregating in Oryza sativa around the world. Red rice may provide a useful study system for understanding the adaptive significance of Phr1 variation in agricultural settings.

Fig. 1

Schematic diagram of sequenced regions of the Phr1 locus. Exons are shown as rectangles and introns are shown as connecting lines. Locations of insertions and deletions resulting in loss-of-function mutations are shown above the exons. The 1-bp deletion in exon 3 was newly documented in this study. Shading corresponds to the branches in Fig. 2. Distances are approximately to scale.

Fig. 2

Neighbor-joining tree for Phr1 haplotypes using the majority-rule, extended method of consensus tree construction. Bootstrap values indicate nodes with at least 50% support based on 1000 bootstrap replicates of the data. Alleles with loss-of-function mutations are shown in color according to the key; all other alleles are shown in black.