Genomic provenance and genetic providence in domesticated barley

Abstract

In the context of plant improvement, it is important to identify the sources of genetic diversity that are available for use, and to understand how current genetic diversity is being utilized. Comparative population genetic analyses provide a means of identifying new sources of genetic variation as well as changes in allele frequencies governed by selection or demographic processes. Considering the broad geographic distribution of both wild and cultivated barley, it is likely that many traits have multiple origins. Thus, the identification of the source population that contributed to a specific chromosomal region in landraces can help identify genetic variants that contribute to agronomic traits. In Chapter 1, I use genotyping data for a set of 803 barley landrace and 277 wild barley accessions to address two primary questions (i) Do specific wild populations contribute disproportionately to barley landraces?, (ii) does the genetic contribution of wild populations to landraces vary across the genome or across the broad geographical range of landrace cultivation? I find that multiple wild populations contributed to the genetic composition of the landraces. Their contribution differs across the genome and across the geographic range. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to landraces. Barley was introduced to North America (NA) by early European colonist as early as 1602. Adaptation to diverse environments has involved many generations of selection towards ideal phenotypes. In Chapter 2, I analyze a data set comprised of 3,613 barley accessions representative of NA barley breeding programs. I aim to determine: (i) the patterns of recents and long-term selection, (ii) assess the effects of drift and linked selection, and (iii) identify the extent of gene flow among barley breeding programs. I identify loci known to be controlling major traits and a series of loci putatively involved in recent and older bouts of selection. There is clear evidence of genetic drift and linked selection acting in these populations. There is evidence of possible gene flow among populations with similar growth habit and inflorescence type.