Genomic insights into racing camels: inbreeding levels and positive selection linked to athletic traits
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ABSTRACT:
PROVIDER: PRJEB82798 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR14244207_1.fastq.gz | Fastqsanger.gz | |||
| ERR14244207_2.fastq.gz | Fastqsanger.gz | |||
| ERR14244208_1.fastq.gz | Fastqsanger.gz | |||
| ERR14244208_2.fastq.gz | Fastqsanger.gz |
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Project description:Genome diversity and signatures of selection for production and performance traits in dromedary camels
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Project description:The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidence for purging in the population that might have improved racing performance over time. Over 80% of inbreeding in the contemporary population is accounted for by a small number of ancestors from the foundation of the breed. Inbreeding to these ancestors has variable effects on fitness, demonstrating that an understanding of the distribution of genetic load is important in improving the phenotypic value of a population in the future. Our findings hold value not only for Thoroughbred and other domestic breeds, but also for small and endangered populations where such comprehensive information is not available.
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Project description:The deleterious mutation model proposes that quantitative trait variation should be dominated by rare, partially recessive, deleterious mutations. Following artificial selection on a focal trait, the ratio of the difference in inbreeding effects between control and selected populations (ΔB), to the difference in trait means caused by directional selection (ΔM), can inform the extent to which deleterious mutations cause quantitative trait variation. Here, we apply the ΔB/ΔM ratio test to two quantitative traits (male mating success and body size) in Drosophila melanogaster. For both traits, ΔB/ΔM ratios suggested that intermediate-frequency alleles, rather than rare, partially recessive alleles (i.e. deleterious mutations), caused quantitative trait variation. We discuss these results in relation to viability data, exploring how differences between regimens in segregating (measured through inbreeding) and fixed (measured through population crosses) mutational load could affect the ratio test. Finally, we present simulations that test the statistical power of the ratio test, providing guidelines for future research.
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Project description:Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding (FROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of FROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.
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Project description:Dromedary camels (Camelus dromedarius) are single-humped animals found throughout the deserts of Africa, the Arabian Peninsula, and the southwest of Asia. This well-adapted species is mainly used for milk and meat production, although some specific types exhibit superior running performance and are used in racing competitions. However, neither performance nor production camels are bred under intensive genomic selection programs with specific aims to improve these traits. In this study, the full genome sequence data of six camels from the Arabian Peninsula and the genotyping-by-sequencing data of 44 camels (29 packing and 15 racing) from Sudan were analyzed to assess their genome diversities, relationships, and candidate signatures of positive selection. Genome ADMIXTURE and principle component analyses indicate clear geographic separation between the Sudanese and the Arabian Peninsula camels, but with no population-specific genetic distinction within populations. Camel samples from the Arabian Peninsula show higher mean heterozygosity (0.560 ± 0.003) than those from Sudan (0.347 ± 0.003). Analyses of signatures of selection, using pooled heterozygosity (Hp) approach, in the Sudanese camels revealed 176, 189, and 308 candidate regions under positive selection in the combined and packing and racing camel populations, respectively. These regions host genes that might be associated with adaptation to arid environment, dairy traits, energy homeostasis, and chondrogenesis. Eight regions show high genetic differentiation, based on Fst analysis, between the Sudanese packing and racing camel types. Genes associated with chondrogenesis, energy balance, and urinary system development were found within these regions. Our results advocate for further detailed investigation of the genome of the dromedary camel to identify and characterize genes and variants associated with their valuable phenotypic traits. The results of which may support the development of breeding programs to improve the production and performance traits of this unique domesticated species.
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Project description:Australian racing greyhound
| PRJEB53922 | ENA
Project description:Purpose: RNA-seq method was used to identify differentially expressed genes in whole blood involved in bone remodelling during racing training in young Arabian horses. Methods: The comparisons of transcriptomes of whole blood between GI (6 untrained horses) and GII (4 horses after 24 weeks of flat racing training) has been performed. The RNA was isolated using MagMAX™-96 Total RNA Isolation Kit and 400ng were directed to cDNA libraries construction Illumina deep sequencing (75 single-end cycles on Illumina HiScan SQ platform). The bioinformatics analysis include the RSEM and STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes were detected by DESeq2.The validation of RNA-seq results were performed by qPCR. Results: After comparison of whole blood transcriptomes from control and trained horses, we identified 1290 training induced genes. Among significant deregulated molecules we recognized twelve genes potentially involved in metabolism of bone (BGLAP, CTSK, TYROBP, PDLIM7, SLC9B2, TWSG1, NOTCH2, IL6ST, VAV3, NFATC1, CLEC5A, TXLNG). Within significantly deregulated pathways one from the most overrepresented was associated with osteoclast differentiation. Conclusions: In the presented study, we identified a panel of DEGs which should be evaluated as candidate biomarkers for bone homeostasis indicators in Arabians performed racetrack. In our results, we pinpointed that intense training has itself effect on immature skeletal system. Thus, further studies are essential to establish biomarkers which could be used in assessment of bone remodelling state during training for race track competition.
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