Footprints of Selection Derived From Temporal Heterozygosity Patterns in a Barley Nested Association Mapping Population

Abstract

Nowadays, genetic diversity more than ever represents a key driver of adaptation to climate challenges like drought, heat, and salinity. Therefore, there is a need to replenish the limited elite gene pools with favorable exotic alleles from the wild progenitors of our crops. Nested association mapping (NAM) populations represent one step toward exotic allele evaluation and enrichment of the elite gene pool. We investigated an adaptive selection strategy in the wild barley NAM population HEB-25 based on temporal genomic data by studying the fate of 214,979 SNP loci initially heterozygous in individual BC₁S₃ lines after five cycles of selfing and field propagation. We identified several loci exposed to adaptive selection in HEB-25. In total, 48.7% (104,725 SNPs) of initially heterozygous SNP calls in HEB-25 were fixed in BC₁S_3:8 generation, either toward the wild allele (19.9%) or the cultivated allele (28.8%). Most fixed SNP loci turned out to represent gene loci involved in domestication and flowering time as well as plant height, for example, btr1/btr2, thresh-1, Ppd-H1, and sdw1. Interestingly, also unknown loci were found where the exotic allele was fixed, hinting at potentially useful exotic alleles for plant breeding.

Keywords: adaptive evolution; artificial selection; barley; heterozygosity; natural selection; selection; temporal genomic data; unconscious selection.

Figure 1

Population conservation and sampling strategy from generation BC₁S₃ to BC₁S_3:8. Exemplified for one heterozygous SNP in BC₁S₃, which is traced through four seasons of field propagation (2011–2014) followed by pooled DNA sampling of 12 seedlings in BC₁S_3:8. Heterogeneity within these 12 seedlings leads to heterozygous allele calls in Illumina 50k genotyping and is termed “reconstructed heterozygosity”. The expected segregation of a single SNP in HEB-25 generation BC₁S₃ is equal to 71.875% homozygous Barke, 6.25% heterozygous, and 21.875% homozygous wild barley. Without selection, the expected SNP segregation of the offspring of a heterozygous HEB-25 plant in generation BC₁S_3:8 is equal to 48.4375% homozygous Barke, 3.125% heterozygous, and 48.4375% homozygous wild barley, giving rise to a reconstructed heterozygous genotype B, resulting in a score of 0 in the reconstructed genotype matrix; Supplementary Table S1). A and C indicate different possible scenarios of allele distribution in case of selection for Hsp allele A, resulting in a score of 1 in the reconstructed genotype matrix) or Hv allele (C, resulting in a score of −1 in the reconstructed genotype matrix) in previous generations (here exemplified for BC₁S_3:7). Note that a homozygously fixed allele call in Illumina genotyping can be obtained despite the presence of small amounts of opposite alleles in the pooled sample C.

Figure 2

Allele fixation from BC₁S₃ to BC₁S_3:8 generations in HEB-25. Barley chromosomes are indicated as inner circle of colored bars; centromeres are highlighted as transparent boxes. Grey connector lines represent the genetic position (in cM) of SNPs on chromosomes based on Maurer et al. (2015). The black line indicates the allele fixation rate (AFR) of SNPs in BC₁S_3:8 calculated from originally heterozygous HEB-25 lines, summarized over 10 consecutive SNPs. The central reference line indicates the average AFR of 0.486, while the limits of the heat map represent AFRs of 0 (inner) and 1 (outer). AFRs higher than 0.5 represent locus-specific above-average fixation throughout the whole HEB-25 population in BC₁S_3:8. The heat map represents the relative fixation direction (RFD), indicating the tendency which allele was fixed in originally heterozygous HEB-25 lines, summarized over 10 consecutive SNPs. Red regions in the outer line indicate significant deviations of RFD from an equal segregation at P(Bonferroni)<0.01. Candidate genes of barley domestication and flowering time as well as further striking genomic regions are indicated outside.

Figure 3

Relative fixation direction (RFD) compared to Hsp allele effects of different agronomic traits. Barley chromosomes are indicated as inner circle of colored bars; centromeres are highlighted as transparent boxes. Grey connector lines represent the genetic position (in cM) of SNPs on chromosomes based on Maurer et al. (2015). The inner heat map (I) represents the RFD, indicating the tendency which allele was fixed in originally heterozygous HEB-25 lines, summarized over 10 consecutive SNPs. The other heat maps (A-H) indicate Hsp allele effect size and direction as compared to the Hv allele, based on linear regression. The extreme values of the heat maps were standardized to the most extreme observed absolute Hsp allele effect for each trait. Candidate genes of barley domestication and flowering time as well as further striking genomic regions are indicated outside.

Figure 4

Regression of estimated Hsp allele SNP effect for plant height on RFD. The Pearson correlation coefficient (r) is 0.48. The blue dashed line indicates the linear regression line.