Runs of Homozygosity and Population History of Three Horse Breeds With Small Population Size

Grilz-Seger, Gertrud; Mesarič, Matjaž; Cotman, Marko; Neuditschko, Markus; Druml, Thomas; Brem, Gottfried

doi:10.1016/j.jevs.2018.09.004

Cited by 36 publications

(46 citation statements)

References 20 publications

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“…The ROHs detected in this study covered 13.17% (295.29 Mb) of the autosomal genome expressed by the SNP loci. The total genome length covered by ROHs is comparable with study of Grilz-Seger et al (2018) and Druml et al (2018) that showed across various breeds the overall genomewide ROH coverage at level 305.1 Mb. But, the study of Grilz-Seger et al (2019a) revealed by use of 700k genotyping array that the genome ROH coverage in Noriker horse depending on the colour variety resulting from different mating strategies.…”

Section: Resultssupporting

confidence: 72%

Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

Moravčíková

Kasarda

Kadlečík

et al. 2019

Acta Univ. Agric. Silvic. Mendelianae Brun.

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The aim of this study was to analyse the genome-wide distribution of runs of homozygosity (ROH) segments in the genome of Norik of Muran horse and to identify the regions under strong selection pressure. Overall, 25 animals genotyped by the GGP Equine70k chip were included in the study. After SNP pruning, 54479 SNPs (75.72%) covering 2.25 Gb of the autosomal genome were retained for scan of ROH segments distribution. The ROHs were present in the genome of all animals and covered in average 13.17% (295.29 Mb) of autosomal genome expressed by the SNP loci. The highest number of ROHs was identified on autosome 1 (404), while the lowest proportion of autosome residing in ROH showed ECA31 (38). The footprints of selection, characterized by SNPs with extreme frequency in ROHs across specific genomic regions, were defined by the top 0.01 percentile of signals. Overall, nine genomic regions located on seven autosomes (3, 6, 9, 11, 15, 23) were identified. The strongest signal of selection showed three autosomes ECA3, ECA9 and ECA11. The protein-coding genes located within these regions suggested that the identified footprints of selection are most likely consequences of intensive breeding for traits of interest during the grading-up process of the Norik of Muran horse.

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Section: Resultssupporting

confidence: 72%

Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

Moravčíková

Kasarda

Kadlečík

et al. 2019

Acta Univ. Agric. Silvic. Mendelianae Brun.

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“…() and Grilz‐Seger et al . (). A further private island on ECA3 was shared by 58.3% of chestnut animals and harbored the genes solute carrier family 39 member 8 ( SLC39A8 ) and B‐cell scaffold protein with ankyrin repeats 1 ( BANK1 ).…”

Section: Resultsmentioning

confidence: 97%

“…Interestingly this ROH island was also found in a previous study in the Bosnian Mountain Horse, the oldest horse breed on the Balkan Peninsula (Grilz‐Seger et al . ). Leopard spotted coat color was detected in 25 000‐year‐old ancient DNA samples originating from wild, pre‐domestic horses of Western and Eastern Europe (Pruvost et al .…”

Section: Resultsmentioning

confidence: 97%

“…The identical HOXB cluster and GO terms were also cited in a recent study for the Posavina horse breed (Grilz‐Seger et al . ). From the manifold functions HOX genes can have, the definition of axial identity on the anterior–posterior axis, morphological regulation and genetic control of body shape represent the most important ones (Pearson et al .…”

Section: Resultsmentioning

confidence: 97%

“…In addition to the Noriker horses, we used SNP data of 28 Posavina horses from a previous study (Grilz‐Seger et al . ). The Posavina horse was sampled to represent family structure of the Slovenian Posavina population.…”

Section: Methodsmentioning

confidence: 97%

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Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

et al. 2019

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Summary Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage ( S ROH ) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity ( S ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size ( ZFAT , LASP1 and LCORL/NCAPG ), coat color ( MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis ( HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.

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Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole‐genome sequencing data

Gmel

Guichard

Dainat

et al. 2023

Ecology and Evolution

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Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole‐genome queen genotypes, from a pool‐seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well‐defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (FROH) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean FROH (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower FROH (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean FROH of 2.33%. Within the breed‐specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh‐BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.

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Runs of Homozygosity and Population History of Three Horse Breeds With Small Population Size

Cited by 36 publications

References 20 publications

Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole‐genome sequencing data

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