Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits

Sweet-Jones, James; Yurchenko, Andrey A.; Igoshin, Alexander V.; Yudin, N. A.; Swain, Martin; Larkin, Denis M.

doi:10.1111/age.13015

Cited by 8 publications

(7 citation statements)

References 31 publications

(33 reference statements)

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“…For the interbreed CNVRs present either in Baikal or Tuva breeds, almost all (except for two gain events in the Tuva breed) regions were detected in the resequencing set from Sweet‐Jones et al . (2020) (Table ).…”

Section: Resultsmentioning

confidence: 99%

“…We also used CNVs of Tuva and Baikal breeds detected from whole‐genome sequencing data (Sweet‐Jones et al . 2020) to check our CNVRs. We performed a simple overlap (1 bp minimum) of coordinates of our interbreed CNVRs (Table ) with Tuva and Baikal breed CNVs detected in the resequencing set.…”

Section: Methodsmentioning

confidence: 99%

“…Simple overlap of interbreed CNVRs with CNVseq data (Sweet‐Jones et al . 2020; CNVRs overlapping with CNVseq/All CNVRs in group). Table S11.…”

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confidence: 99%

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Copy number variants in genomes of local sheep breeds from Russia

et al. 2021

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Summary Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed‐specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Copy number variants in genomes of local sheep breeds from Russia

et al. 2021

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“…Fabp9 is typically expressed in the testis (Selvaraj et al 2010), but previous findings have also suggested a role in skin homeostasis in Artiodactyls (Jiang et al 2014). Aadacl3 , although poorly studied, appears to be related with epidermal fat deposition (Lu et al 2020; Sweet-Jones et al 2021). Additionally, analysis of the Human Protein Atlas (www.proteinatlas.org) shows a very specific pattern with expression noted only in skin, breast, and placenta (not shown).…”

Section: Resultsmentioning

confidence: 99%

Convergent Decay of Skin-specific Gene Modules in Pangolins

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Caramelo

et al. 2022

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The Mammalia skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a key deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation - Awat1/2, show patterns of inactivation in the stem pangolin branch; while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function, is intact and expressed in the skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated, convergent and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes

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“…Three remaining Welsh sheep resequenced genomes for Welsh Hardy-Speckled Faced, Dolgellau Welsh Mountain, and Talybont Welsh Mountain were downloaded from the National Centre for Biotechnology Information Sequence Read Archive, PRJNA160933 (Heaton et al, 2014). A dataset of resequenced Russian sheep samples (n = 40) adapted to a contrasting environment was used as an outgroup in this study (Sweet-Jones et al, 2021).…”

Section: Data Source and Variant Callingmentioning

confidence: 99%

Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

et al. 2021

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BackgroundAdvances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.ResultsHaplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).ConclusionWe found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.

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Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits

Cited by 8 publications

References 31 publications

Copy number variants in genomes of local sheep breeds from Russia

Copy number variants in genomes of local sheep breeds from Russia

Convergent Decay of Skin-specific Gene Modules in Pangolins

Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

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