SNP genotypes reveal breed substructure,selection signatures and highly inbred regions in Piétrain pigs

The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F_ST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population-specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.     

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (S_ROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (S_ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.     

Taking advantage from phenotype variability in a local animal genetic resource: identification of genomic regions associated with the hairless phenotype in Casertana pigs

Casertana is an endangered autochthonous pig breed (raised in south‐central Italy) that is considered to be the descendant of the influential Neapolitan pig population that was used to improve British breeds in the 19th century. Casertana pigs are characterized by a typical, almost complete, hairless phenotype, even though a few Casertana pigs are normal haired. In this work, using Illumina PorcineSNP60 BeadChip data, we carried out a genome‐wide association study and an F_ST analysis with this breed by comparing animals showing the classical hairless phenotype (n = 81) versus pigs classified as haired (n = 15). Combining the results obtained with the two approaches, we identified two significant regions: one on porcine chromosome (SSC) 7 and one on SSC15. The SSC7 region contains the forkhead box N3 (FOXN3) gene, the most plausible candidate gene of this region, considering that mutations in another gene of the same family (forkhead box N1; Foxn1 or FOXN1) are responsible for the nude locus in rodents and alopecia in humans. Another potential candidate gene, rho guanine nucleotide exchange factor 10 (ARHGEF10), is located in the SSC15 region. FOXN3 and ARHGEF10 have been detected as differentially expressed in androgenetic and senescent alopecia respectively. This study on an autochthonous pig breed contributes to shed some light on novel genes potentially involved in hair development and growth and demonstrates that local animal breeds can be valuable genetic resources for disclosing genetic factors affecting unique traits, taking advantage of phenotype variability segregating in small populations.     

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

A dataset consisting of 787 animals with high‐density SNP chip genotypes (346 774 SNPs) and 939 animals with medium‐density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F_PED and F_ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F_ROH estimates from medium‐density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make‐up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.     

Signatures of Diversifying Selection in European Pig Breeds

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.     

A genome‐wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry‐cured hams

Intermuscular fat content in protected designations of origin dry‐cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome‐wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance‐tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome‐wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E?04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; P_FDR < 0.05), included in the largest QTL region which spanned about 6.8 Mb on SSC1, is located within the glutamate ionotropic receptor kainate type subunit 2 (GRIK2) gene. Functional annotation of all genes included in QTL regions for VIF suggested that intermuscular fat in the Italian Large White breed is a complex trait apparently influenced by complex biological mechanisms also involving obesity‐related processes. These QTL target mainly chromosome regions different from those affecting subcutaneous and intramuscular fat deposition.     

Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I^d allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I^p), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th–19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.     

Four loci differentially expressed in muscle tissue depending on water-holding capacity are associated with meat quality in commercial pig herds

Four genes, VTN, KERA, LYZ, and a non-annotated EST (Affymetrix probe set ID: Ssc.25503.1.S1_at), whose candidacy for traits related to water-holding capacity of meat arises from their trait-dependent differential expression, were selected for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing and used to genotype animals of 4 pig populations including 3 commercial herds of Pietrain (PI), Pietrain × (German Large White × German Landrace) (PIF1), German Landrace (DL) and 1 experimental F₂ population Duroc × Pietrain (DUPI). Comparative and genetic mapping established the location of VTN on SSC12, of LYZ and KERA on SSC5 and of UN on SSC7, coinciding with QTL regions for meat quality traits. VTN showed association with pH1, pH24 and drip loss. LYZ revealed association with conductivity 24, pH1 and drip loss. KERA was associated with pH. UN showed association with pH24 and drip loss, respectively. However, none of the candidate genes showed significant associations for a particular trait across all populations. This may be due to breed specific effects that are related to the differences in meat quality of theses pig breeds. The studies revealed statistic evidence for a link of genetic variation at these loci or close to them and promoted those four candidate genes as functional and/or positional candidate genes for meat quality traits.     

Genes with expression levels correlating to drip loss prove association of their polymorphism with water holding capacity of pork

Six genes that were known to exhibit expression levels that are correlated to drip loss BVES, SLC3A2, ZDHHC5, CS, COQ9, and EGFR have been for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing, and used for genotyping. The SNPs were genotyped in about 1,800 animals from six pig populations including commercial herds of Pietrain (PI) and German Landrace (DL), different commercial herds of Pietrain × (German Large White × German Landrace) (PIF1(a/b/c)), and one experimental F₂-population Duroc × Pietrain (DUPI). Comparative and genetic mapping established the location of BVES on SSC1, of SLC3A2 and ZDHHC5 on SSC2, of CS on SSC5, of COQ9 on SSC6 and of EGFR on SSC9, respectively, coinciding with QTL regions for carcass and meat quality traits. BVES, SLC3A2, and CS revealed association at least with drip loss and with several other measures of water holding capacity (WHC). Moreover, COQ9 and EGFR were associated with several meat quality traits such as meat color and/or thawing loss. This study reveals statistic evidence in addition to the functional relationship of these genes to WHC previously evidenced by expression analysis. This study reveals positional and genetic statistical evidence for a link of genetic variation at these loci or close to them and promotes those six candidate genes as functional and/or positional candidate genes for meat quality traits.     

Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome

The Göttingen Minipig (GMP) developed at the University of Göttingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism (SNP) genotypes from the Illumina Porcine SNP60 BeadChip using two methods: the extended haplotype homozygosity (EHH) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome‐wide breed composition were tested with a permutation‐based empirical test. Results for a comprehensive whole‐genome scan for both methods are presented. Several regions showing the highest P‐values in the EHH test are related to breeding goals relevant in the GMP, such as growth (SOCS2, TXN, DDR2 and GRB10 genes) and white colour (PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree‐based expectations and the genome average. The results provide a genome‐wide map of selection signatures in the GMP, which leads to a better understanding of selection that took place over the last decades in GMP breed development.     

A genome-wide association study for feed efficiency-related traits in a crossbred pig population

Feed efficiency (FE) is one of the most important traits in pig production. However, it is difficult and costly to measure it, limiting the collection of large amount of data for an accurate selection for better FE. Therefore, the identification of single-nucleotide polymorphisms (SNPs) associated with FE-related traits to be used in the genetic evaluation is of great interest of pig breeding programs for increasing the prediction accuracy and the genetic progress of these traits. The objective of this study was to identify SNPs significantly associated with FE-related traits: average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR). We also aimed to identify potential candidate genes for these traits. Phenotypic information recorded on a population of 2386 three-way crossbreed pigs that were genotyped for 51 468 SNPs was used. We identified three loci of quantitative trait (QTL) regions associated with ADG and three QTL regions associated with ADFI; however, no significant association was found for FCR. A false discovery rate (FDR) ≤ 0.005 was used as the threshold for declaring an association as significant. The QTL regions associated with ADG on Sus scrofa chromosome (SSC) 1 were located between 177.01 and 185.47 Mb, which overlaps with the QTL regions for ADFI on SSC1 (173.26 and 185.47 Mb). The other QTL region for ADG was located on SSC12 (2.87 and 3.22 Mb). The most significant SNPs in these QTL regions explained up to 3.26% of the phenotypic variance of these traits. The non-identification of genomic regions associated with FCR can be explained by the complexity of this trait, which is a ratio between ADG and ADFI. Finally, the genes CDH19, CDH7, RNF152, MC4R, PMAIP1, FEM1B and GAA were the candidate genes found in the 1 Mb window around the QTL regions identified in this study. Among them, the MC4R gene (SSC1) has a well-known function related to ADG and ADFI. In this study, we identified three QTL regions for ADG (SSC1 and SSC12) and three for ADFI (SSC1). These regions were previously described in purebred pig populations; however, to our knowledge, this is the first study to confirm the relevance of these QTL regions in a crossbred pig population. The potential use of the SNPs and genes identified in this study in prediction models that combine genomic selection and marker-assisted selection should be evaluated for increasing the prediction accuracy of these traits in this population.     

Identifying candidate positive selection genes in Korean imported pig breeds

Domestication and artificial selection have modified the genome landscape of the pig. The identification of selection signatures in the genome can help to elucidate the selection mechanisms and uncover the causal genes related to the phenotypic variations between domestic pig breeds. We scanned the genomes of Korean imported pig breeds against native breeds using Z-transformed Fst (ZF_ST) and Heterozygosity (ZH_p) statistics to search for the signatures of positive selection. We identified 411 (ZF_ST?=?175; ZH_p?=?256) putatively selected genes in commercial breeds. The gene regions identified were harboring those related to immunity, coat color, reproduction function and other traits. Several genes (e.g., PLSCR4, AGTR1 and CORIN) were related to reproduction traits such as fertility, ovulation rate, and uterine function. This study revealed genes which improve our understanding of the biological mechanisms of higher litter sizes, the phenotype of interest, in higher litter pig breeds.     

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The F_ST‐outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual‐purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.     

To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed

The cat (Felis silvestris catus) shows significant variation in pelage, morphological, and behavioral phenotypes amongst its over 40 domesticated breeds. The majority of the breed specific phenotypic presentations originated through artificial selection, especially on desired novel phenotypic characteristics that arose only a few hundred years ago. Variations in coat texture and color of hair often delineate breeds amongst domestic animals. Although the genetic basis of several feline coat colors and hair lengths are characterized, less is known about the genes influencing variation in coat growth and texture, especially rexoid – curly coated types. Cornish Rex is a cat breed defined by a fixed recessive curly coat trait. Genome-wide analyses for selection (d_i, Tajima’s D and nucleotide diversity) were performed in the Cornish Rex breed and in 11 phenotypically diverse breeds and two random bred populations. Approximately 63K SNPs were used in the analysis that aimed to localize the locus controlling the rexoid hair texture. A region with a strong signature of recent selective sweep was identified in the Cornish Rex breed on chromosome A1, as well as a consensus block of homozygosity that spans approximately 3 Mb. Inspection of the region for candidate genes led to the identification of the lysophosphatidic acid receptor 6 (LPAR6). A 4 bp deletion in exon 5, c.250_253_delTTTG, which induces a premature stop codon in the receptor, was identified via Sanger sequencing. The mutation is fixed in Cornish Rex, absent in all straight haired cats analyzed, and is also segregating in the German Rex breed. LPAR6 encodes a G protein-coupled receptor essential for maintaining the structural integrity of the hair shaft; and has mutations resulting in a wooly hair phenotype in humans.     

Genomic regions affecting backfat thickness and cannon bone circumference identified by genome‐wide association study in a Duroc pig population

We performed a genome‐wide association study using the porcine 60K SNP array to detect QTL regions for nine traits in a three‐generational Duroc samples (n = 651), viz. generations 1, 2 and 3 from a population selected over five generations using a closed nucleus breeding scheme. We applied a linear mixed model for association mapping to detect SNP effects, adjusting for fixed effects (sex and season) and random polygenic effects (reflecting genetic relatedness), and derived a likelihood ratio statistic for each SNP using the efficient mixed‐model association method. We detected a region on SSC6 for backfat thickness (BFT) and on SSC7 for cannon bone circumference (CANNON), with a genome‐wide significance of P < 0.01 after Bonferroni correction. These regions had been detected previously in other pig populations. Six genes are located in the BFT‐associated region, while the CANNON‐associated region includes 66 genes. In the future, significantly associated SNPs, derived by sequencing the coding regions of the six genes in the BFT region, can be used in marker‐assisted selection of BFT, whereas haplotypes constructed from the SSC7 region with strong LD can be used to select for the CANNON trait in our resource family.     

Genomic signatures reveal selection of characteristics within and between Meishan pig populations

The Chinese Meishan pig breed is well known for its high prolificacy. Moreover, this breed can be divided into three types based on their body size: big Meishan, middle Meishan (MMS) and small Meishan (SMS) pigs. Few studies have reported on the genetic signatures of Meishan pigs, particularly on a genome‐wide scale. Exploring for genetic signatures could be quite valuable for revealing the genetic architecture of phenotypic variation. Thus, we performed research in two parts based on the genome reducing and sequencing data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection signatures among all Meishan pigs studied using the relative extended haplotype homozygosity test. Second, we detected the selection signatures between MMS and SMS pigs using the cross‐population extended haplotype homozygosity and F_ST methods. A total of 111 398 SNPs were identified from the sequenced genomes. In the population analysis, the most significant genes were associated with the mental development (RGMA), reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross‐population analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant. This study may have achieved consistency between selection signatures and characteristics within and between Meishan pig populations. These findings can provide insight into investigating the molecular background of high prolificacy and body size in pig.     

Genome‐wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome‐wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two‐end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white‐spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.     

Genome‐wide variability and selection signatures in Italian island cattle breeds

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo‐Bruna and Sardo‐Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within‐breed genetic heterogeneity. The F_ST comparison revealing the largest number of significant SNPs was Sardo‐Bruna vs. Sardo‐Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo‐Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo‐Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi‐dimensional scaling and the admixture analysis the Sardo‐Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo‐Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.     

Genomic regions influencing coat color saturation and facial markings in Fleckvieh cattle

Genomic regions associated with coat color and pigmented areas of the head were identified for Fleckvieh (dual‐purpose Simmental), a red‐spotted and white‐headed cattle breed. Coat color was measured with a chromameter, implementing the CIELAB color space and resulting in numerical representation of lightness, color intensity, red/green and blue/yellow color components, rather than subjective classification. Single marker regression analyses with fixed effects of the sex and barn were applied, and significant regions were determined with the local false discovery rate methodology. The PMEL and ERBB3 genes on chromosome 5 were in the most significant region for the color measurements. In addition to the blue/yellow color component and color intensity, the AP3B2 gene on chromosome 21 was identified. Its function was confirmed for similar traits in a range of model species. The KIT gene on chromosome 6 was found to be strongly associated with the inhibition of circum‐ocular pigmentation and pigmented spots on the cheek.