Exome sequencing in genomic regions related to racing performance of Quarter Horses

Pereira, Guilherme Luís; Malheiros, Jessica Moraes; Ospina, Alejandra Maria Toro; Chardulo, Luis Artur Loyola; Curi, Rogério Abdallah

doi:10.1007/s13353-019-00483-1

Cited by 9 publications

(14 citation statements)

References 20 publications

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“…In the studies of Pereira et al (2018Pereira et al ( , 2019, who used the single-step GBLUP method to estimate the effect of thousands of SNPs and genomic regions on SImax in the same racing Quarter Horses as used in the present study, one of the regions/windows on ECA15 found to be associated with the trait of interest harbors the SLC3A1 gene whose variant was also related to racing performance of Quarter Horses in the present study. In addition to this coincidence, these authors also found other regions that were relatively close (distance of 1.6 Mb) to the CCN6 (ECA10).…”

Section: Discussionmentioning

confidence: 95%

“…Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5 0 and 3 0 UTRs sequenced. A detailed description of the sample used, and the processes of SNPs genotyping, estimation of genomic breeding values (GEBVs), selection of the extreme samples for the GEBVs and the exome sequencing are available in Pereira et al (2019).…”

Section: Introductionmentioning

confidence: 99%

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Exome analysis and functional classification of identified variants in racing Quarter Horses

et al. 2020

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Summary The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5′ and 3′ UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.

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Section: Discussionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Exome analysis and functional classification of identified variants in racing Quarter Horses

et al. 2020

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“…Exome sequencing has been used in the horse to identify variants relative to racing performance in quarter horses. 28 In each of these examples, the sequence generated was aligned to the reference genome and variants differing between affected horses and the reference sequence, or compared with healthy controls, were identified. As part of this process, after variants that either fit the hypothesized mode of inheritance or are found in candidate genes are identified, the possible function of each can be predicted using the genome annotation.…”

Section: Applicationsmentioning

confidence: 99%

Next-Generation Sequencing in Equine Genomics

Petersen

Coleman

2020

Veterinary Clinics of North America: Equine Practice

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Next-generation sequencing of both DNA and RNA represents a second revolution in equine genetics following publication of the equine genome sequence.• Technological advancements have resulted in a wide selection of next-generation sequencing platforms capable of completing small targeted experiments or resequencing complete genomes.• DNA and RNA sequencing have applications in clinical and research environments.• Standards for the validation and sharing of next-generation sequencing data are critical for the widespread application of the technology and applications discussed herein.• As researchers and clinicians develop a better understanding of how genetic variation and phenotypic variation are linked, next-generation sequencing could help pave the way to personalized and precision management of horses.

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“…For example, the American Quarter Horse (Petersen et al 2014a; Avila et al 2018; Marchiori et al. 2019; Pereira et al 2019), the Hanoverian and other German Warmblood breeds (Nanaei et al. 2019; Nolte et al 2019), the Arabian and related Middle Eastern breeds (Almarzook et al 2017; Sadeghi et al.…”

Section: Ancient Genomics and Natural History Of The Horsementioning

confidence: 99%

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post‐genome era

et al. 2019

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Summary The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite-free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past ~2300 years due to selective breeding. The high-quality reference genome has led to the development of three different SNP arrays and whole genome sequences (WGS) of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits, continues to benefit the health and performance of the horse while also serving as a model for complex disease across species.

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Exome sequencing in genomic regions related to racing performance of Quarter Horses

Cited by 9 publications

References 20 publications

Exome analysis and functional classification of identified variants in racing Quarter Horses

Exome analysis and functional classification of identified variants in racing Quarter Horses

Next-Generation Sequencing in Equine Genomics

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post‐genome era

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