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

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

doi:10.1111/age.12797

Cited by 47 publications

(52 citation statements)

References 30 publications

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“…Obtained proportion of ROHs across the genome of Norik of Muran horse is comparable to other local horse breeds, e.g. Austrian Noriker (Grilz-Seger et al, 2019), Bosnian mountain and Haflinger horses (Druml et al, 2018;Grilz-Seger et al, 2018) or Polish Konik horse (Kamiński et al, 2017). Compared to pedigree analysis, the genomic inbreeding showed the same trend (Fig.…”

Section: Resultssupporting

confidence: 55%

Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Kasarda

Moravčíková

Kadlečík

et al. 2019

Acta Univ. Agric. Silvic. Mendelianae Brun.

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The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

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Section: Resultssupporting

confidence: 55%

Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Kasarda

Moravčíková

Kadlečík

et al. 2019

Acta Univ. Agric. Silvic. Mendelianae Brun.

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“…The F ROH statistic proposed by McQuillan et al 83 was then calculated, whereby the total length of ROH covering an individual animal's genome (L ROH ) is divided by the length of the autosomal genome (L AUTO ); F ROH = L ROH / L AUTO . Here, consistent with other equine studies 84,85 we used the length of the equine autosomal genome (assembly EquCab 2) 86 as 2,242,960 kb (www.ncbi.nlm.nih.gov/genome/145?genome_assembly_id=22878).…”

Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

McGivney

Han

Corduff

et al. 2020

Sci Rep

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The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F iS R 2 = 0.942, P = 2.19 × 10 −13 ; F RoH R 2 = 0.88, P = 1.81 × 10 −10 ) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomicsbased methods will be beneficial to actively monitor the population to address the marked inbreeding trend.The Thoroughbred is among the fastest animals selected by humans for sport, originating from "the commingled blood of Arabs, Turks and Barbs" 1 crossed with local British and Irish mares 2 "but selection and training have together made him a very different animal from his parent-stocks" 1 . The Thoroughbred is now a large (N ~ 500,000) global breed but, in the context of modern horse breeds, it has very low genetic diversity 3,4 due to the limited foundation alleles at the establishment of the stud book and restriction of external gene flow subsequent to the closing of the population 5-7 . In Thoroughbred horse breeding selection of potential champion racehorses is a global multi-billion-dollar business, but there is no systematic industry-mediated genomic selection or genetic population management. We hypothesised that the market-driven emphasis on highly valuable pedigrees and the common practice of inbreeding to successful ancestors in attempts to reinforce...

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“…ROH hotspots are not randomly distributed across the genome and are shared by all individuals within a breed [12]. ROH are commonly used to identify genome regions under putative selection in order to map the candidate genes responsible for economically important traits in livestock populations [13][14][15][16][17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Jiang

Han

et al. 2020

Animals

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In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

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

Cited by 47 publications

References 30 publications

Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

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