Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum)

Abstract

Patterns of nucleotide sequence diversity in the predominantly self-fertilizing species Hordeum vulgare subspecies spontaneum (wild barley) are compared between the putative alcohol dehydrogenase 3 locus (denoted "adh3") and alcohol dehydrogenase 1 (adh1), two related but unlinked loci. The data consist of a sequence sample of 1,873 bp of "adh3" drawn from 25 accessions that span the species range. There were 104 polymorphic sites in the sequenced region of "adh3." The data reveal a strong geographic pattern of diversity at "adh3" despite geographic uniformity at adh1. Moreover, levels of nucleotide sequence diversity differ by nearly an order of magnitude between the two loci. Genealogical analysis resolved two distinct clusters of "adh3" alleles (dimorphic sequence types) that coalesce roughly 3 million years ago. One type consists of accessions from the Middle East, and the other consists of accessions predominantly from the Near East. The two "adh3" sequence types are characterized by a high level of differentiation between clusters ( approximately 2.2%), which induces an overall excess of intermediate frequency variants in the pooled sample. Finally, there is evidence of intralocus recombination in the "adh3" data, despite the high level of self-fertilization characteristic of wild barley.

Figure 1

Gene structure of “adh3” in barley. PCR primers are indicated by arrows.

Figure 2

Expected number of polymorphic sites under a neutral model calculated by using equation 51 of Tajima (26) and observed number of polymorphic sites at various frequencies in the whole sample and in all regions of “adh3” (A) and adh1 (B) in wild barley.

Figure 3

Neighbor-joining tree depicting the genealogical relationships of alleles of “adh3” in wild barley. Country of origin is shown in parentheses. Scale indicates percentage of variation.

Figure 4

Polymorphic sites in the “adh3” region among 25 accessions of wild barley. Sequences are divided into four types with four blocks of sequences of different origins. Boundary point between two blocks was determined as the mid-point between two adjacent polymorphisms belonging to the two blocks. Sites in exons are highlighted. Type of polymorphism: N, noncoding; S, synonymous; R, replacement. Dash denotes deletion, and dot denotes consensus sequence.

Figure 5

Southern blot of genomic DNA from nine wild barley accessions digested with BclI and probed with a ³²P-labeled fa-ra PCR product. Approximate sizes of the fragments are shown.

Figure 6

Hypothetical evolutionary history of wild barley based on patterns of sequence variation at adh1 and “adh3.” Estimates of coalescent time are indicated. yra, years ago.