Whole genome detection of sequence and structural polymorphism in six diverse horses

Al-Abri, Mohammed; Holl, Heather M.; Kalla, Sara E.; Sutter, Nathan B.; Brooks, Samantha A.

doi:10.1371/journal.pone.0230899

Cited by 18 publications

(10 citation statements)

References 59 publications

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“…Although detection methods for the former have been developed 11 – 16 , no methods are available for detecting genetic modifications. For this purpose, whole-genome sequencing 17 , which requires a detailed understanding of variations of the Thoroughbred genome, may be useful.…”

Section: Introductionmentioning

confidence: 99%

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Tozaki

Ohnuma

Kikuchi

et al. 2021

Sci Rep

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The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.

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Section: Introductionmentioning

confidence: 99%

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Tozaki

Ohnuma

Kikuchi

et al. 2021

Sci Rep

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“…Previous studies observed a similar trend on the same chromosomes for SNVs and nonsynonymous substitutions [ 7 , 16 ]. Although the exact reason for this is unknown, one reason is thought to be the existence of metabolic and sensory perception regions on chromosome 12, and immune response and antigen-processing regions on chromosome 20 [ 18 , 19 , 20 ]. These genes have several pseudogenes that lose their function because of substitutions, insertions, and deletions in the gene regions.…”

Section: Discussionmentioning

confidence: 99%

Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses

Tozaki

Ohnuma

Kikuchi

et al. 2023

Genes

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Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1–31) and X chromosomes, respectively, while 18 INDELs were identified on the mitochondrial genome, totaling 1,566,414 INDELs. Of those, 779,457 loci (49.8%) were novel INDELs, while 786,957 loci (50.2%) were already registered in Ensembl. The sizes of diallelic INDELs ranged from −286 to +476, and the majority, 717,736 (52.14%) and 220,672 (16.03%), were 1-bp and 2-bp variants, respectively. Numerous INDELs were found to have lower frequencies of alternative (Alt) alleles. Many rare variants with low Alt allele frequencies (<0.5%) were also detected. In addition, 5955 loci were genotyped as having a minor allele frequency of 0.5 and being heterogeneous genotypes in all the horses. While short-read sequencing and its mapping to reference genome is a simple way of detecting variants, fake variants may be detected. Therefore, our data help to identify true variants in Thoroughbred horses. The INDEL database we constructed will provide useful information for genetic studies and industrial applications in Thoroughbred horses, including a gene-editing test for gene-doping control and a parentage test using INDELs for horse registration and identification.

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“…The genetic variants representing the population level polymorphisms were obtained from the following species and their available datasets: Equus caballus (EquCab2 assembly in the EVA study PRJEB9799 [81]), Bos taurus (UMD3.1 assembly in the NextGen project: https://projects.ensembl.org/nextgen/), Ovis aries (Oar v3.1 assembly in the NextGen project), Capra hircus (CHIR1 assembly in the NextGen project), converted to ARS1 assembly with dbSNP identifiers [82]), Chlorocebus sabaeus (ChlSab1.1 assembly in the EVA project PRJEB22989 [83]), Homo sapiens (GRCh38 assembly in the 1000 Genomes Project [84]). In total, we analyzed 28 populations across the 6 different species with polymorphism data.…”

Section: Methodsmentioning

confidence: 99%

Section: Polymorphism Datasetmentioning

confidence: 99%

Estimating the proportion of beneficial mutations that are not adaptive in mammals

Latrille

Hartasánchez

Salamin

2023

Preprint

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Mutations can be beneficial by bringing innovation to their bearer, allowing them to adapt to environmental change. However, mutations can also be beneficial because they are reverting previous deleterious changes, simply restoring pre-existing functions. By integrating phylogenomic and population data in mammals, we estimated the contribution of beneficial back-mutations to molecular evolution, which had remained widely overlooked so far. Applying a mutation-selection model, we estimated amino acid fitness landscapes for mammalian protein-coding genes. Assuming these fitness landscapes do not change, any beneficial mutation is necessarily a back-mutation. We confirmed that these beneficial back-mutations are positively selected in extant populations and demonstrated that a substantial part of ongoing positive selection is not driven by adaptation to environmental change.

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Whole genome detection of sequence and structural polymorphism in six diverse horses

Cited by 18 publications

References 59 publications

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses

Estimating the proportion of beneficial mutations that are not adaptive in mammals

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