Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (<i>Capra</i> species) breeds for the production of dairy, cashmere, and meat

Bao, Zhenan; Chang, Liao; Lan, Xianyong; Nadeem, Asif; Guan, Fanglin; Fu, Deliang; Li, Bo; Yan, Cheng; Zhang, Xiaoyan; Huang, Yongzhen; Chen, Hong; Yu, Jun; Li, Shengbin

doi:10.1093/gigascience/giy105

Cited by 35 publications

(30 citation statements)

References 55 publications

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“…For instance, the causal factor of the white color typical of many sheep breeds is the ubiquitous expression of a duplicated copy of the ASIP coding sequence, which is regulated by a duplicated promoter corresponding to the itchy E3 ubiquitin protein ligase gene [6,39]. Although some studies proposed that the ASIP CNV might be associated with different pigmentation patterns in goats [8,17,37], no functional assay has verified an association of ASIP copy number with ASIP mRNA levels. Another interesting shared copy number variable gene is ADAMTS20, which was also identified in two previous CNV surveys [17,18].…”

Section: Discussionmentioning

confidence: 99%

A genome-wide analysis of copy number variation in Murciano-Granadina goats

et al. 2020

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Background: In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. Results: Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 Bead-Chip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10 −10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10 −04) and bile secretion (foldenrichment = 3.90, q-value = 5.70 × 10 −03). Conclusions: A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by nonallelic homologous recombination.

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Section: Discussionmentioning

confidence: 99%

A genome-wide analysis of copy number variation in Murciano-Granadina goats

et al. 2020

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“…There are several reasons for addressing these associations. First, a region on chromosome 3 was reported to show the highest intensity signal effect on meat traits in goats, which includes the HIAT1, SLC35A3, and SASS6 genes [19,21]. The same region spanning 43.3 to 43.8 Mb on chromosome 3 of water buffalo was shown to affect milk fat and protein percentages, and this region harbors the HIAT1, SLC35A3, and PALMD genes [21].…”

Section: Discussionmentioning

confidence: 99%

“…The HIAT1 gene, which is also known as MFSD14A (major facilitator superfamily domain containing 14A), plays a role in transmembrane transport and the molecular function of transporter activity [18]. Our previous genome resequencing study of goats revealed that a set of genes play critical roles in meat goats compared with wool and dairy breeds, including the HIAT1 gene [19]. In addition, HIAT1 was identified as a novel candidate gene for milk production in buffaloes and was localized to a bovine QTL (quantitative trait locus) affecting the milk fat yield and protein yield [20,21].…”

Section: Introductionmentioning

confidence: 99%

Detection of rs665862918 (15-bp Indel) of the HIAT1 Gene and its Strong Genetic Effects on Growth Traits in Goats

Gao

Song

et al. 2020

Animals

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The hippocampus abundant transcript 1 (HIAT1) gene, which was detected by the genome-wide identification of selective sweeps among elite goat breeds and water buffalo, is proposed to play an important role in meat characteristics. Four indels of the HIAT1 gene selected from the NCBI and Ensembl databases were detected via a pooling and sequencing strategy. A 15 bp insertion (rs665862918) in the first intron of HIAT1 was selected and classified on an electrophoresis platform in the Shaanbei white cashmere goat (SBWC) population. The correlation analysis revealed that rs665862918 is significantly highly associated with chest width (p = 1.57 × 10−5), chest depth (p = 8.85 × 10−5), heart girth (p = 1.05 × 10−7), body length (p = 0.022), and height at hip cross (p = 0.023) in the SBWC population (n = 1013). Further analysis revealed that individuals with a genotype insertion/insertion (II) of the rs665862918 locus exhibited better growth trait performance than individuals with an insertion/deletion (ID) or deletion/deletion (DD). These findings verify that HIAT1 affects the body size of goats and that rs665862918 could be a potential molecular marker for growth traits in goat breeding.

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“…For example, the growth hormone (GH) gene influences the expression of growth and milk characteristics. The vital candidate genes for goat play a significant role in the production, reproduction, metabolism, sex determination, and disease resistance [4,[12][13][14][15][16]. A study of the candidate genes for major economic traits could be applied for a direct search of QTL in terms of planning future breeding program.…”

Section: Introductionmentioning

confidence: 99%

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

Siddiki

Miah

Islam

et al. 2020

International Journal of Genomics

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Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

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Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat

Cited by 35 publications

References 55 publications

A genome-wide analysis of copy number variation in Murciano-Granadina goats

A genome-wide analysis of copy number variation in Murciano-Granadina goats

Detection of rs665862918 (15-bp Indel) of the HIAT1 Gene and its Strong Genetic Effects on Growth Traits in Goats

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

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