Next-Generation Sequencing in Equine Genomics

Petersen, Jessica L.; Coleman, Stephen J.

doi:10.1016/j.cveq.2020.03.002

Cited by 9 publications

(6 citation statements)

References 63 publications

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“…As EquCab2.0 contained many gaps, the genome of Twilight was re-sequenced and assembled in 2018 using high-throughput sequencing technologies, thus resulting in the new reference genome: EquCab3.0. The new assembly contains 3771 gaps comprising 9 Mb (0.34% of the genome) with a scaffold N50 of 86 Mb ( Table 1 ) [ 87 , 90 ].…”

Section: The Horse Genomementioning

confidence: 99%

Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

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Section: The Horse Genomementioning

confidence: 99%

Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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“…Todavia, não há contraindicações de ser realizado após este período, porém os benefícios serão menores comparados à uma investigação mais precoce. Este teste é um exame não invasivo, que utiliza a técnica de Sequenciamento de Nova Geração (NGS) para analisar o DNA da criança e consiste na coleta de uma amostra de saliva do interior da boca do bebê com auxílio de um cotonete (SWAB), sendo uma coleta rápida e indolor que tem a função de complementar os testes de triagem neonatal convencionais (PETERSEN & COLEMAN, 2020).…”

Section: Triagem Neonatal Molecularunclassified

Triagem Neonatal

MAGALHÃES DOS SANTOS,

NOGUEIRA DUARTE,

SILVEIRA BRANDÃO

et al. 2023

Fundamentos E Práticas Pediátricas E Neonatais - Edição XIV

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“…Horse genomics has progressed rapidly since the establishment of the horse reference genome [ 5 , 6 ] and advancements in genomics technology. The genetic mechanisms of many horse traits have been investigated using single nucleotide polymorphism (SNP) chips and resequencing of the whole genome [ 7 ]. In contrast to SNP chips, whole-genome sequencing can repeatedly cover the entire genome, resulting in greater resolution and accuracy.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide

Chen

Zhu

Tang

et al. 2023

Genes

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In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies.

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Next-Generation Sequencing in Equine Genomics

Cited by 9 publications

References 63 publications

Unlocking Horse Y Chromosome Diversity

Unlocking Horse Y Chromosome Diversity

Triagem Neonatal

Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide

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