Dataset Information

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.

ABSTRACT: The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.

SUBMITTER: Szmatola T

PROVIDER: S-EPMC9736150 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.

Szmatoła Tomasz T Gurgul Artur A Jasielczuk Igor I Oclon Ewa E Ropka-Molik Katarzyna K Stefaniuk-Szmukier Monika M Polak Grazyna G Tomczyk-Wrona Iwona I Bugno-Poniewierska Monika M

Animals : an open access journal from MDPI 20221125 23

The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding ...[more]

PMID: 36496815

Similar Datasets

Project description:Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.

Project description:Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.

Project description:Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.

Project description:BackgroundGoat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity, especially as we are facing important climate and agriculture challenges. To this aim the genomic architecture of 480 goats belonging to five breeds (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits. Inbreeding, runs of homozygosity (ROH) and runs of heterozygosity (ROHet) were identified. Finally, candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.ResultsIn total, we detected 10,341 ROH in the SAA genome, 11,063 ROH in the CAM genome, 12,250 ROH in the MUR genome, 8,939 ROH in the MAL genome, and 18,441 ROH in the SAR genome. Moreover, we identified 4,087 ROHet for SAA, 3,360 for CAM, 2,927 for MUR, 3,701 for MAL, and 3,576 for SAR, with SAR having the highest heterozygosity coefficient. Interestingly, when computing the inbreeding coefficient using homozygous segment (FROH), SAA showed the lowest value while MAL the highest one, suggesting the need to improve selecting strategies to preserve genetic diversity within the population. Among the most significant candidate genes, we identified several ones linked to different physiological functions, such as milk production (e.g., DGAT1, B4GALT1), immunity (GABARAP, GPS2) and adaptation to environment (e.g., GJA3, GJB2 and GJB6).ConclusionsThis study highlighted the genetic diversity within and among five goat breeds. The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation, which might negatively impact the animal population. Conversely, high levels of ROHet might indicate regions of the genetic diversity, beneficial for breed health and resilience. Therefore, these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.

Dataset Information

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.

Publications

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.

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