Analysis of dog breed diversity using a composite selection index

Abstract

During breed development, domestic dogs have undergone genetic bottlenecks and sustained selective pressures, as a result distinctive genomic diversity occurs to varying degrees within and between breed groups. This diversity can be identified using standard methods or combinations of these methods. This study explored the application of a combined selection index, composite selection signals (CSS), derived from multiple methods to an existing genotype dataset from three breed groups developed in distinct regions of Asia: Qinghai-Tibet plateau dogs (adapted to living at altitude), Xi dogs (with superior running ability) and Mountain hounds (used for hunting ability). The CSS analysis confirmed top ranked genomic regions on CFA10 and CFA21 in Qinghai-Tibet plateau dogs, CFA1 in Xi dogs and CFA5 in Mountain hounds. CSS analysis identified additional significant genomic regions in each group, defined by a total of 1,397, 1,475 and 1,675 significant SNPs in the Qinghai-Tibetan Plateau dogs, Xi dogs and Mountain hounds, respectively. Chitinase 3 Like 1 (CHI3L1) and Leucine Rich Repeat Containing G Protein-Coupled Receptor 6 (LGR6) genes were located in the top ranked region on CFA7 (0.02-1 Mb) in the Qinghai-Tibetan Plateau dogs. Both genes have been associated with hypoxia responses or altitude adaptation in humans. For the Xi dogs, the top ranked region on CFA25 contained the Transient Receptor Potential Cation Channel Subfamily C Member 4 (TRPC4) gene. This calcium channel is important for optimal muscle performance during exercise. The outstanding signals in the Mountain dogs were on CFA5 with 213 significant SNPs that spanned genes involved in cardiac development, sight and generation of biochemical energy. These findings support the use of the combined index approach for identifying novel regions of genome diversity in dogs. As with other methods, the results do not prove causal links between these regions and phenotypes, but they may assist in focusing future studies that seek to identify functional pathways that contribute to breed diversity.

Figure 1

Composite selection signals associated with adaptation to high altitude. CSS statistics were determined with Qinghai-Tibetan Plateau dogs as the target group. The canine chromosomal positions of SNP markers are plotted on the x-axis. The observed values for selection scan statistics based on the combination of Fst, ∆DAF and XP-EHH are highlighted in blue and orange. Each point represents the smooth CSS value in a 1 Mb overlapping sliding window across the autosomes. The two-dashed horizontal lines indicate threshold values for the top 0.1% (top) or 0.5% (bottom) of CSS values.

Figure 2

Functional annotation groups for genes associated with adaptation to high altitude. See Table S4 for details.

Figure 3

Composite selection signals associated with running speed. CSS statistics were determined with Xi dogs as the target group. The canine chromosomal positions of SNP markers are plotted on the x-axis. The observed values for selection scan statistics based on the combination of Fst, ∆DAF and XP-EHH are highlighted in blue and orange. Each point represents the smooth CSS value in a 1 Mb overlapping sliding window across the autosomes. The two-dashed horizontal lines indicate threshold values for the top 0.1% (top) or 0.5% (bottom) of CSS values.

Figure 4

Functional annotation groups for genes associated with running speed. See Table S8 for details.

Figure 5

Composite selection signals associated with hunting ability. CSS statistics were determined with Mountain hounds as the target group. The canine chromosomal positions of SNP markers are plotted on the x-axis. The observed values for selection scan statistics based on the combination of Fst, ∆DAF and XP-EHH are highlighted in blue and orange. Each point represents the smooth CSS value in a 1 Mb overlapping sliding window across the autosomes. The two-dashed horizontal lines indicate threshold values for the top 0.1% (top) or 0.5% (bottom) of CSS values.

Figure 6

Functional annotation groups for genes associated with hunting ability. See Table S12 for details.