Genome-wide association analyses reveals copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle.

This study aimed to evaluate the impact of copy number variants (CNVs) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing Log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole genome sequence data from 126 animals, resulting in 870 high-confidence CNV regions (CNVRs) on 12,131 animals. Out of these, 54 CNVRs had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVRs were significantly (p-value < 3.7 × 10-5) associated with at least one of the traits analyzed in this study. Specifically, 2 CNVRs were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and non-return rate), and 2 CNVRs were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVRs harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVRs on the mentioned traits are warranted.

A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.

Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.

Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

BACKGROUND: In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic impact using whole-genome sequence data. RESULTS: Looking at the genetic differences between breeds, the Dutch chicken breeds demonstrated a complex and admixed subdivided structure. The dissection of this complexity highlighted the influence of selection adhering to management purposes, as well as the role of geographic distance within subdivided breed clusters. Identification of signatures of genetic differentiation revealed genomic regions that are associated with diversifying phenotypic selection between breeds, including dwarf size (bantam) and feather color. In addition, with a case study of a recently developed bantam breed developed by crossbreeding, we provide a genomic perspective on the effect of crossbreeding. CONCLUSIONS: This study demonstrates the complex population structure of local traditional Dutch chicken, and provides insight into the genomic basis and the factors involved in the formation of this complexity.

Unravelling the genetics of non-random fertilization associated with gametic incompatibility.

In the dairy industry, mate allocation is dependent on the producer's breeding goals and the parents' breeding values. The probability of pregnancy differs among sire-dam combinations, and the compatibility of a pair may vary due to the combination of gametic haplotypes. Under the hypothesis that incomplete incompatibility would reduce the odds of fertilization, and complete incompatibility would lead to a non-fertilizing or lethal combination, deviation from Mendelian inheritance expectations would be observed for incompatible pairs. By adding an interaction to a transmission ratio distortion (TRD) model, which detects departure from the Mendelian expectations, genomic regions linked to gametic incompatibility can be identified. This study aimed to determine the genetic background of gametic incompatibility in Holstein cattle. A total of 283,817 genotyped Holstein trios were used in a TRD analysis, resulting in 422 significant regions, which contained 2075 positional genes further investigated for network, overrepresentation, and guilt-by-association analyses. The identified biological pathways were associated with immunology and cellular communication and a total of 16 functional candidate genes were identified. Further investigation of gametic incompatibility will provide opportunities to improve mate allocation for the dairy cattle industry.

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

BACKGROUND: Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. RESULTS: Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. CONCLUSION: Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.