Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Mastrangelo, Salvatore; Jemaa, Slim Ben; Sottile, Gianluca; Casu, Sara; Portolano, Baldassare; Ciani, Elena; Pilla, Fabio

doi:10.1111/jbg.12422

Cited by 11 publications

(14 citation statements)

References 49 publications

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“…Despite the phenotypic differences, the two populations share a common genetic background [5][6][7]. This leads to minimize the confounding effects due to genetic divergence and population structure [15,20]. Moreover, some candidate genes identified here, such TYR, are consistent with results reported from previous studies on chicken plumage color.…”

Section: Discussionsupporting

confidence: 87%

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Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Mastrangelo

Cendron

Sottile

et al. 2020

Animals

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Simple Summary: In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait.Abstract: Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (F ST ) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and F ST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

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Section: Discussionsupporting

confidence: 87%

“…Potentially, there is much unrecognized beneficial genetic variation in local autochthonous animal breeds and populations [15]. As visual characteristics of animals, pigmentation traits are often used for breed identification, and represent an important phenotype of interest for breeding and research [16].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Mastrangelo

Cendron

Sottile

et al. 2020

Animals

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“…However, the possible function of other genes responsible for the presence of white coat parts in the SB pig is not entirely excluded in the breed standard [61][62][63]. The development of Single-Nucleotide Polymorphism (SNP) panels has allowed for the identification of highly differentiated genomic regions increasing the potency of genome-wide association studies (GWASs) [64]. SNPs represent the primary functional basis of genetic variability, which is reflected in phenotypic differences between and within breeds.…”

Section: Genetic and Genomic Characterizationmentioning

confidence: 99%

“…SNPs represent the primary functional basis of genetic variability, which is reflected in phenotypic differences between and within breeds. In the event that the polymorphisms identified represent exclusive selective footprints of the breed under consideration, these markers can be effectively applied to identify the most favorable genetic variants for the improvement of quantitative traits of zootechnical interest, or in the identification and traceability of products [63,64]. Muñoz et al [65] analyzed the genomic diversity of 20 European autochthonous pig breeds, including SB, using high-density SNP chips.…”

Section: Genetic and Genomic Characterizationmentioning

confidence: 99%

Sicilian Black Pig: An Overview

Zumbo

Sutera

Tardiolo

et al. 2020

Animals

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The Sicilian black pig (SB) (Nero Siciliano), also known as the Nero dei Nebrodi, Nero delle Madonie, or Nero dell’Etna pig ecotype, is an autochthonous Italian breed. The origins of this breed date back to Greek and Carthaginian dominations. In ancient times, its breeding was fairly common throughout Sicily, registering only a temporary reduction during the Arab domination. This breed is known primarily for its distinctive black coat, although some individuals display wattles and a partially or wholly white face. The SB pig has a birth rate with an average per sow of 7.6 piglets, each of 1.4 kg live body weight, showing an average daily gain (ADG) of 346 g/day during the fattening period. Slaughter generally takes place at an average age of 390 days, with an average live weight of 95 kg. This breed also appears to withstand adverse climatic conditions and resist disease. The purpose of this manuscript is to offer a general overview regarding the Sicilian Black pig and to consider the recent findings related to genome investigation. The recent application of Next Generation Sequencing (NGS) technologies in the study of the genome of autochthonous breeds showed that polymorphisms of some candidate genes for production performance and phenotypic traits represent important information for selection processes. The protection of autochthonous breeds, intended as sources of genomic diversity for the further improvements of pigs for commercial use, constitutes a valuable opportunity to create new sustainable pig chains.

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“…Studies that compare populations with similar production aptitudes can be considered highly informative to investigate their genetic variability for breeding purpose (Mastrangelo et al, 2019; Sorbolini et al, 2015). The main objective of the present study was to identify putative genomic regions under selection that may explain the phenotypic differences among the three Valdostana cattle populations.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

Mastrangelo

Jemaa

Ciani

et al. 2020

J Animal Breeding Genetics

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The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.

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Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Cited by 11 publications

References 49 publications

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Sicilian Black Pig: An Overview

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

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