Genome-Wide Specific Selection in Three Domestic Sheep Breeds

Wang, Huihua; Zhang, Lili; Cao, Jiaxve; Wu, Mingming; Ma, Xiongfeng; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Wei, Caihong; Du, Lixin

doi:10.1371/journal.pone.0128688

Cited by 50 publications

(47 citation statements)

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“…The regions displaying autozygosity in dairy sheep breeds were linked mostly with genes involved in reproduction, such as the CCNB2 gene, which affects oocyte development (Wang et al . ). Other candidate genes detected within these ROH islands were TYRP1 , which is involved in controlling coat pigmentation in sheep and has a homolog on bovine chromosomes 2 and 8, on which the location of QTL for milk traits has been reported (Ashwell et al .…”

Section: Resultsmentioning

confidence: 97%

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

et al. 2018

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Summary 18The availability of dense single-nucleotide polymorphism (SNP) assays allows for the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 F o r P e e r R e v i e wThe abundance of single-nucleotide polymorphisms (SNPs) throughout the genome and the 44 availability of dense SNP assays, makes these markers particularly suitable for the detection of 45 genomic regions where a reduction in heterozygosity occurred (Kim et al. 2013). Runs of 46 homozygosity (ROH) are contiguous segments of homozygous genotypes that are present in an 47 individual due to parents transmitting identical haplotypes to their offspring (Gibson et al. 2006). 48In animal genetics, ROH are used as predictors of whole genome inbreeding levels (Purfield et 49 al. 2012; Marras et al. 2015; Mastrangelo et al. 2016), to characterize the genomic distribution of 50 inbreeding depression on a phenotype (Biscarini et al. 2014; Pryce et al. 2014), and to identify 51 genes associated with traits of economic interest present in these regions (Zhang et al. 2015; 52 Szmatola et al. 2016; Purfield et al. 2017). Selection pressure and mating schemes can be 53 disentangled by ROH; therefore, ROH detection can also be used to minimize inbreeding and to 54 improve mating systems (Bosse et al. 2012; Zhang et al. 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Runs of homozygosity definition 106Runs of homozygosity were estimated for each animal using PLINK (Purcell et al. 2007). No where L ROH is the total length of all ROH in the genome of an individual, and L aut the specified 118 length of the autosomal genome covered by SNPs on the chip (2 452.06 Mb). 119Each ROH was categorized based on its physical length into 1 to <5 Mb, 5 to <10 Mb, 10 to <15 and averaging this per breed. 123The genomic inbreeding coefficient based on the difference between observed vs. expected 124 number of homozygous genotypes (F HOM ) was also estimated using PLINK (Purcell et al. 2007). 125Pearson's correlation between the two measures of inbreeding was calculated. 127Detection of common runs of homozygosity 128To identify the genomic regions most commonly associated with ROH for the meta-population, 129and for groups on the basis of production purposes (milk, meat, wool and "milk and meat"), the 136Genomic coordinates for all the identified ROH islands were used for the annotation of genes 137 that were fully or partially contained within each selected region using the UCSC Genome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59...

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Section: Resultsmentioning

confidence: 97%

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

et al. 2018

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“…It is responsible for remodeling proteins that maintain the structure of skeletal muscle [16,17]. Another PCR study has reported significant genetic variants in Myocyte enhancer binding factor 2B (MEF2B) and Thyrotropin releasing hormone degrading enzyme (TRHDE) genes affecting body weight and growth in sheep [18][19][20]. For instance, SNPs have been detected in MEF2B and TRHDE genes associated with sheep body weight and chest girth [20].…”

Section: Genes Associated With Growth and Body Weightmentioning

confidence: 99%

“…In addition to growth and body weight traits, body mass index and body size traits are also an important sheep production traits. A genome wide specific selection study has identified Fat mass and obesity-associated protein (FTO) and Apolipoprotein B Receptor (APOBR) genes affecting body mass index in German mutton merino, CMF, and African white dorper sheep breeds [18]. FTO is part of the alpha-ketoglutarate-dependent hydroxylase gene family, which is a non-heme iron-containing protein.…”

Section: Genes Associated With Growth and Body Weightmentioning

confidence: 99%

“…It encodes a ribosomal protein and belongs to the L30P family of ribosomal proteins [28][29][30][31]. Regarding with the post-weaning gain trait, a GWAS study has reported three genes (POL, Complex Subunit 1 (MSL1) and Shisa Family Member 9 (SHISA9)) in sheep breeds [18,26]. Generally, all the genes discussed on the above have been playing a great role directly or indirectly in cell growth, embryonic development, differentiation of muscle tissue and nervous system.…”

Section: Genes Associated With Growth and Body Weightmentioning

confidence: 99%

“…PRLR is one of the member of class 1 cytokine receptors gene family [54]. Furthermore, a GWAS study has reported molecular variants in Cyclin B2 (CCNB2) and Solute Carrier Family 8 Member A3 (SLC8A3) genes associated with oocyte development in Chinese mongolian fat-tailed, German mutton merino and African white dorper sheep breeds [18]. The gene SLC8A3 increases the availability of L-alanine and L-histidine for gap junctional transfer in oocytes [55].…”

Section: Genes Associated With Sheep Fertility Traitsmentioning

confidence: 99%

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Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

Gebreselassie

Berihulay

Jiang

et al. 2019

Animals

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Simple Summary: Sheep is one of the most economically important animals used as a source of meat, milk, wool, and fur for human society. These commodities are essential for human being. Body growth, body weight, carcass quality, fat percent, fertility, milk yield, wool, horn type and coat color are essential and useful sheep traits. Understanding the genetic background of these traits is paramount to increase the production and productivity of domestic animals. The availability of genomic data, development of molecular breeding techniques, and genome technologies have come to play a vital role in understanding the genetic background of different animal traits. This is directly or indirectly helpful for the practice of genetic improvement of economically important traits in sheep. The identification of genomic regions, genes associated with phenotypic traits, and description of gene function are some of the applied research activities to understand the genetics of livestock species. The aim of this review is to discuss and summarize different reported research findings on identified genomic regions and candidate genes related with economically important traits as well as gene annotation in sheep.Abstract: Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.

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Applications of Omics Technologies in Livestock Production, Improvement and Sustainability

Maru,

Kumar

2024

Sustainable Agriculture Reviews

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Genome-Wide Specific Selection in Three Domestic Sheep Breeds

Cited by 50 publications

References 91 publications

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

Applications of Omics Technologies in Livestock Production, Improvement and Sustainability

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