Genetic heterogeneity at the bovine KIT gene in cattle breeds carrying different putative alleles at the spotting locus

Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations

OBJECTIVE

The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions.

METHODS

A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis.

RESULTS

A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease.

CONCLUSION

Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives

Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.

Resequencing the Yaroslavl cattle genomes reveals signatures of selection and a rare haplotype on BTA28 likely to be related to breed phenotypes

The genomes of local livestock could shed light on their genetic history, mechanisms of adaptations to environments and unique genetics. Herein we look into the genetics and adaptations of the Russian native dairy Yaroslavl cattle breed using 22 resequenced individuals and comparing them with two related breeds (Russian Kholmogory and Holstein), and to the taurine set of the 1000 Bull Genomes Project (Run 9). HapFLK analysis with Kholmogory and Holstein breeds (using Yakut cattle as outgroup) resulted in 22 regions under selection (q‐value < 0.01) on 11 chromosomes assigned to Yaroslavl cattle, including a strong signature of selection in the region of the KIT gene on BTA6. The F_ST (fixation index) with the 1000 Bull Genomes Dataset showed 48 non‐overlapping top (0.1%) F_ST regions of which three overlapped HapFLK regions. We identified 1982 highly differentiated (F_ST > 0.40) missense mutations in the Yaroslavl genomes. These genes were enriched in the epidermal growth factor and calcium‐binding functional categories. The top F_ST intervals contained eight genes with allele frequencies quite different between the Yaroslavl and Kholmogory breeds and the rest of the 1000 Bull Genomes Dataset, including KAT6B, which had a nearly Yaroslavl breed‐specific deleterious missense mutation with the highest F_ST in our dataset (0.99). This gene is a part of a long haplotype containing other genes from F_ST and hapFLK analyses and with a negative association with weight and carcass traits according to the genotyping of 30 phenotyped Yaroslavl cattle individuals. Our work provides the industry with candidate genetic variants to be focused on in breed improvement efforts.

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (F_PED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.

Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours

Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed-specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well-known Protected Designation of Origin Parmigiano-Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome-wide information in comparative F_ST analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% F_ST values, a total of 64 markers were detected in the single-marker analysis. The top F_ST value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window-based analyses, which included 0.5-Mb or 1-Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle.

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal's birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system's possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.

Exploiting within-breed variability in the autochthonous Reggiana breed identified several candidate genes affecting pigmentation-related traits, stature and udder defects in cattle

Autochthonous cattle breeds constitute important reservoirs of genetic diversity. Reggiana is an Italian local cattle breed reared in the north of Italy for the production of a mono‐breed Parmigiano–Reggiano cheese. Reggiana cattle usually have a classical solid red coat colour and pale muzzle. As part of the strategies designed for the sustainable conservation of this genetic resource, we investigated at the genome‐wise level the within‐breed detected variability of three pigmentation‐related traits (intensity of red coat colour, based on three classes – light/diluted, normal and dark; spotted patterns/piebaldism that sometime emerge in the breed; muzzle colour – pink/pale, grey and black), stature, presence/absence and number of supernumerary teats and teat length. A total of 1776 Reggiana cattle (about two‐thirds of the extant breed population) were genotyped with the GeneSeek GGP Bovine 150k SNP array and single‐marker and haplotype‐based GWASs were carried out. The results indicated that two main groups of genetic factors affect the intensity of red coat colour: darkening genes (including EDN3 and a few other genes) and diluting genes (including PMEL and a few other genes). Muzzle colour was mainly determined by MC1R gene markers. Piebaldism was mainly associated with KIT gene markers. Stature was associated with BTA6 markers upstream of the NCAPG–LCORL genes. Teat defects were associated with TBX3/TBX5, MCC and LGR5 genes. Overall, the identified genomic regions not only can be directly used in selection plans in the Reggiana breed, but also contribute to clarifying the genetic mechanisms involved in determining exterior traits in cattle.

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the F_ST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and F_ST parameters. The mean F_ROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Background

A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.

Results

In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color).

Conclusion

Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.

A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama)

Background

The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced.

Results

Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele.

Conclusions

A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-020-00950-3.

Genome-wide analysis of homozygosity regions in european simmental bulls

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (F_ROH ) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) F_ROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.

Intracellular and tissue specific expression of FTO protein in pig: changes with age, energy intake and metabolic status

Genome-wide association studies in the FTO gene have identified SNPs correlating with obesity and type 2 diabetes. In mice, lack of Fto function leads to intrauterine growth retardation and lean phenotype, whereas in human it is lethal. The aim of this study in a pig model was to determine the localization of the FTO protein in different tissues and cell compartments, in order to investigate potential targets of FTO action. To better understand physiological role of FTO protein, its expression was studied in pigs of different age, metabolic status and nutrition, using both microscopic methods and Western blot analysis. For the first time, FTO protein was found in vivo in the cytoplasm, of not all, but specific tissues and cells e.g. in the pancreatic β-cells. Abundant FTO protein expression was found in the cerebellum, salivary gland and kidney of adult pigs. No FTO protein expression was detected in blood, saliva, and bile, excluding its role in cell-to-cell communication. In the pancreas, FTO protein expression was positively associated with energy intake, whereas in the muscles it was strictly age-related. In IUGR piglets, FTO protein expression was much higher in the cerebellum and kidneys, as compared to normal birth body weight littermates. In conclusion, our data suggest that FTO protein may play a number of distinct, yet unknown intracellular functions due to its localization. Moreover, it may play a role in animal growth/development and metabolic state, although additional studies are necessary to clarify the detailed mechanism(s) of action.

On-Target CRISPR/Cas9 Activity Can Cause Undesigned Large Deletion in Mouse Zygotes

Genome engineering has been tremendously affected by the appearance of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-based approach. Initially discovered as an adaptive immune system for prokaryotes, the method has rapidly evolved over the last decade, overtaking multiple technical challenges and scientific tasks and becoming one of the most effective, reliable, and easy-to-use technologies for precise genomic manipulations. Despite its undoubtable advantages, CRISPR/Cas9 technology cannot ensure absolute accuracy and predictability of genomic editing results. One of the major concerns, especially for clinical applications, is mutations resulting from error-prone repairs of CRISPR/Cas9-induced double-strand DNA breaks. In some cases, such error-prone repairs can cause unpredicted and unplanned large genomic modifications within the CRISPR/Cas9 on-target site. Here we describe the largest, to the best of our knowledge, undesigned on-target deletion with a size of ~293 kb that occurred after the cytoplasmic injection of CRISPR/Cas9 system components into mouse zygotes and speculate about its origin. We suppose that deletion occurred as a result of the truncation of one of the ends of a double-strand break during the repair.

MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens)

Small numbers of domestic yak (Bos grunniens) were imported to North America in the late 19th century indirectly from the Qinghai-Tibetan Plateau. Coat color of yak is of interest for fiber production, aesthetics, and as a potential indicator of recent hybridization with cattle. North American yak are classified into 3 major coat color patterns depending upon the presence and extent of white markings. They are further classified by nose pigmentation (black or gray). The aim of this study was to identify loci involved in white patterning and nose pigmentation of North American yak. Genotyping by mass spectrometry of markers identified through Sanger and whole-genome sequencing revealed a 388 kb haplotype of KIT associated in a semi-dominant manner with white coloration in this population of yak. This KIT haplotype is similar to both a haplotype found in white-faced Chinese yak and to haplotypes found in cattle but is divergent from other Bos species such as bison, gaur, and banteng. Melanocortin 1 receptor (MC1R) was implicated as a dominant determinant of black nose color with a single haplotype containing 2 missense mutations perfectly associated with the phenotype. The MC1R haplotype associated with black nose pigment is also similar to cattle haplotypes. No cattle studied, however, shared either of the 2 haplotypes associated with color in yak, suggesting these alleles were introgressed into yak before they were imported to North America. These results provide molecular insight into the history of North American yak and information from which breeders can determine possible color outcomes of matings.

Estimation of genetic parameters of defective appearances in Japanese Black heifer calves in Kagoshima

Defective appearances, including white spotting (WS), tongue defect (TD), and nipple defect (ND), in Japanese Black cattle potentially lead to economic losses to farmers in Japan. We estimated genetic parameters of defective appearances using 553,433 records of Japanese Black heifer calves housed in the Kagoshima Prefecture. Variance and covariance were estimated using the Gibbs sampling algorithm. The estimated heritability ranged from 0.29 for TD to 0.76 for WS. Percent breeding value (%BV) estimates indicated high variation in WS and ND among sires, reflecting higher heritability. Furthermore, there was a positive linear relationship between the %BV estimate of a sire and the mean incidence rate of each defect in his female offsprings. TD was positively associated with other defects. Therefore, genetic factors strongly affect the incidence of defective appearances in Japanese Black cattle.

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

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.

A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population

Background

Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene. For this purpose, samples of one white hind and her brown calf were available for whole genome sequencing to identify the single nucleotide polymorphism(s) responsible for the white phenotype. Subsequently, samples from 194 brown and 11 white animals were genotyped.

Results

Based on a list of colour genes of the International Federation of Pigment Cell Societies, a non-synonymous mutation with exchange of a glycine residue at position 291 of the tyrosinase protein by arginine was identified as the cause of dilution of the coat colour. A gene test led to exactly matching genotypes in all examined animals. The study showed that 14% of the brown animals carry the white gene. This provides a simple and reliable way of conservation for the white animals. However, results could not be transferred to another, unrelated red deer population with white animals. Although no brown animals with a white tyrosinase genotype were detected, the cause for the white colouring in this population was different.

Conclusions

A gene test for the conservation of white red deer is available for the population of the Reinhardswald. While mutations in the tyrosinase are commonly associated with oculocutaneous albinism type 1, the amino acid exchange at position 291 was found to be associated with coat colour dilution in Cervus elaphus.

A large interactive visual database of copy number variants discovered in taurine cattle

BACKGROUND

Copy number variants (CNVs) contribute to genetic diversity and phenotypic variation. We aimed to discover CNVs in taurine cattle using a large collection of whole-genome sequences and to provide an interactive database of the identified CNV regions (CNVRs) that includes visualizations of sequence read alignments, CNV boundaries, and genome annotations.

RESULTS

CNVs were identified in each of 4 whole-genome sequencing datasets, which together represent >500 bulls from 17 breeds, using a popular multi-sample read-depth-based algorithm, cn.MOPS. Quality control and CNVR construction, performed dataset-wise to avoid batch effects, resulted in 26,223 CNVRs covering 107.75 unique Mb (4.05%) of the bovine genome. Hierarchical clustering of samples by CNVR genotypes indicated clear separation by breeds. An interactive HTML database was created that allows data filtering options, provides graphical and tabular data summaries including Hardy-Weinberg equilibrium tests on genotype proportions, and displays genes and quantitative trait loci at each CNVR. Notably, the database provides sequence read alignments at each CNVR genotype and the boundaries of constituent CNVs in individual samples. Besides numerous novel discoveries, we corroborated the genotypes reported for a CNVR at the KIT locus known to be associated with the piebald coat colour phenotype in Hereford and some Simmental cattle.

CONCLUSIONS

We present a large comprehensive collection of taurine cattle CNVs in a novel interactive visual database that displays CNV boundaries, read depths, and genome features for individual CNVRs, thus providing users with a powerful means to explore and scrutinize CNVRs of interest more thoroughly.

Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese production system

Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that characterise Reggiana and define the diversity of this local cattle breed. A total of 168 Reggiana sires (all bulls born over 35 years for which semen was available) and other 3321 sires from 3 cosmopolitan breeds (Brown, Holstein and Simmental) were genotyped with the Illumina BovineSNP50 panel. ADMIXTURE analysis suggested that Reggiana breed might have been influenced, at least in part, by the other three breeds included in this study. Selection signatures in the Reggiana genome were identified using three statistical approaches based on allele frequency differences among populations or on properties of haplotypes segregating in the populations (fixation index (FST); integrated haplotype score; cross-population extended haplotype homozygosity). We identified several regions under peculiar selection in the Reggiana breed, particularly on bovine chromosome (BTA) 6 in the KIT gene region, that is known to be involved in coat colour pattern distribution, and within the region of the LAP3, NCAPG and LCORL genes, that are associated with stature, conformation and carcass traits. Another already known region that includes the PLAG1 gene (BTA14), associated with conformation traits, showed a selection signature in the Reggiana cattle. On BTA18, a signal of selection included the MC1R gene that causes the red coat colour in cattle. Other selection sweeps were in regions, with high density of quantitative trait loci for milk production traits (on BTA20) and in several other large regions that might have contributed to shape and define the Reggiana genome (on BTA17 and BTA29). All these results, overall, indicate that the Reggiana genome might still contain several signs of its multipurpose and non-specialised utilisation, as already described for other local cattle populations, in addition to footprints derived by its ancestral origin and by its adaptation to the specialised Parmigiano-Reggiano cheese production system.

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle

Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.

Cdrom Archive: A Gateway to Study Camel Phenotypes

Camels are livestock that exhibit unique morphological, biochemical, and behavioral traits, which arose by natural and artificial selection. Investigating the molecular basis of camel traits has been limited by: (1) the absence of a comprehensive record of morphological trait variation (e.g., diseases) and the associated mode of inheritance, (2) the lack of extended pedigrees of specific trait(s), and (3) the long reproductive cycle of the camel, which makes the cost of establishing and maintaining a breeding colony (i.e., monitoring crosses) prohibitively high. Overcoming these challenges requires (1) detailed documentation of phenotypes/genetic diseases and their likely mode of inheritance (and collection of related DNA samples), (2) conducting association studies to identify phenotypes/genetic diseases causing genetic variants (instead of classical linkage analysis, which requires extended pedigrees), and (3) validating likely causative variants by screening a large number of camel samples from different populations. We attempt to address these issues by establishing a systematic way of collecting camel DNA samples, and associated phenotypic information, which we call the "Cdrom Archive." Here, we outline the process of building this archive to introduce it to other camel researchers (as an example). Additionally, we discuss the use of this archive to study the phenotypic traits of Arabian Peninsula camel breeds (the "Mezayen" camels). Using the Cdrom Archive, we report variable phenotypic traits related to the coat (color, length, and texture), ear and tail lengths, along with other morphological measurements.

Genetic background of coat colour in sheep

Abstract. The coat colour of animals is an extremely important trait that affects their behaviour and is decisive for survival in the natural environment. In farm animal breeding, as a result of the selection of a certain coat colour type, animals are characterized by a much greater variety of coat types. This makes them an appropriate model in research in this field. A very important aspect of the coat colour types of farm animals is distinguishing between breeds and varieties based on this trait. Furthermore, for the sheep breeds which are kept for skins and wool, coat/skin colour is an important economic trait. Until now the study of coat colour inheritance in sheep proved the dominance of white colour over pigmented/black coat or skin and of black over brown. Due to the current knowledge of the molecular basis of ovine coat colour inheritance, there is no molecular test to distinguish coat colour types in sheep although some are available for other species, such as cattle, dogs, and horses. Understanding the genetic background of variation in one of the most important phenotypic traits in livestock would help to identify new genes which have a great effect on the coat colour type. Considering that coat colour variation is a crucial trait for discriminating between breeds (including sheep), it is important to broaden our knowledge of the genetic background of pigmentation. The results may be used in the future to determine the genetic pattern of a breed. Until now, identified candidate genes that have a significant impact on colour type in mammals mainly code for factors located in melanocytes. The proposed candidate genes code for the melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), microphthalmia-associated transcription factor MITF, and v-kit Hardy–Zuckerman 4 feline sarcoma viral oncogene homologue (KIT). However, there is still no conclusive evidence of established polymorphisms for specific coat colour types in sheep.

Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat

The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.

Climate Adaptation of Tropical Cattle

There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.

BREEDING AND GENETICS SYMPOSIUM:Breeding heat tolerant dairy cattle: the case for introgression of the "slick" prolactin receptor variant into dairy breeds

Increasing environmental temperatures are a threat to the sustainability of livestock production and, because of the high metabolic demands of lactation, to dairy production in particular. Summer heat waves in temperate climates reduce feed intake, milk production, and cow comfort. In extreme heat events, there is an increase in cow mortality. In tropical climates, dairy cattle are mostly (zebu) type or zebu crossbred with temperate dairy breeds. Crossbreeding is undertaken to combine the heat tolerance and tick resistance of zebu with the productivity of temperate dairy breeds. In the absence of improved heat tolerance, milk production and fertility of temperate cattle is severely impaired. We have recently identified a key role for the prolactin pathway in regulating heat tolerance. A de novo mutation in prolactin that impairs prolactin activity was discovered in hairy and heat intolerant, New Zealand dairy cattle. The phenotypes produced were remarkably similar to those seen in fescue toxicosis, a syndrome seen in grazing cattle in the U.S. where ingestion of ergovaline, a fungal toxin from infected pasture, inhibits prolactin secretion. Recognition of the role of prolactin in hairy cattle led us to identify a deletion in exon 10 of the long-form of the prolactin receptor in Senepol cattle that causes truncation of the protein and determines the slick coat and heat tolerance traits found in this , beef breed. The short form of the prolactin receptor is predicted to be unaffected by the deletion. Knowledge of this dominant mutation has provided the impetus to begin a crossbreeding program to investigate performance and heat tolerance of temperate dairy cattle carrying the slick, prolactin receptor variant. The perceived opportunity is to introgress this variant into temperate dairy cattle to enable performance and welfare improvement in hot climates. Heat tolerance of cattle with slick coats appears to be mostly associated with coat type although sweating ability may also be enhanced. Further investigation is required of performance traits in cows homozygous for the slick variant because the published data are almost exclusively from heterozygous animals. Combination of the slick mutation with other favorable genes for heat tolerance, especially those for coat color, will be particularly enabled by gene editing technologies, offering opportunities for further improvement in bovine thermotolerance.

Detection of selection signatures in dairy and beef cattle using high-density genomic information

Background

Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs.

Results

Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (F_ST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the F_ST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global F_ST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection.

Conclusions

This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0127-3) contains supplementary material, which is available to authorized users.

Investigation of inherited diseases in cats: genetic and genomic strategies over three decades

PRACTICAL RELEVANCE

The health of the cat mirrors a complex interaction between its environment (nurture) and its genetics (nature). To date, over 70 genetic mutations (variants) have been defined in the cat; many involve diseases, structural anomalies, coat color and texture, including numerous that are clinically relevant. This trend will continue as more of the feline genome is deciphered. Genetic testing, and eventually whole-genome sequencing, should become routine diagnostic tools in feline healthcare within the foreseeable future.

GLOBAL IMPORTANCE

Cat breeds have dispersed around the world. Thus, feline medicine clinicians should be aware of breeds common to their region and common mutations found within those regional populations. Random-bred populations of domestic cats can also have defined genetic characteristics and mutations, which are equally worthy of understanding by feline medicine clinicians.

OUTLINE

This article reviews the chronology and evolution of genetic and genomic tools pertinent to feline medicine. Possible strategies for mapping genetic traits and defects, and how these impact on feline health, are also discussed. The focus is on three historical periods: (1) research conducted before the availability of the cat genome; (2) research performed immediately after the availability of sequences of the cat genome; and (3) current research that goes beyond one cat genome and utilizes the genome sequences of many cats.

EVIDENCE BASE

The data presented are extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning heritable traits and/or diseases. The authors draw upon their personal experience and expertise in feline genetics.

The melanocyte lineage in development and disease

Melanocyte development provides an excellent model for studying more complex developmental processes. Melanocytes have an apparently simple aetiology, differentiating from the neural crest and migrating through the developing embryo to specific locations within the skin and hair follicles, and to other sites in the body. The study of pigmentation mutations in the mouse provided the initial key to identifying the genes and proteins involved in melanocyte development. In addition, work on chicken has provided important embryological and molecular insights, whereas studies in zebrafish have allowed live imaging as well as genetic and transgenic approaches. This cross-species approach is powerful and, as we review here, has resulted in a detailed understanding of melanocyte development and differentiation, melanocyte stem cells and the role of the melanocyte lineage in diseases such as melanoma.

Summary: This Review discusses melanocyte development and differentiation, melanocyte stem cells, and the role of the melanocyte lineage in diseases such as melanoma.

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.

The KIT gene is associated with the english spotting coat color locus and congenital megacolon in Checkered Giant rabbits (Oryctolagus cuniculus)

The English spotting coat color locus in rabbits, also known as Dominant white spotting locus, is determined by an incompletely dominant allele (En). Rabbits homozygous for the recessive wild-type allele (en/en) are self-colored, heterozygous En/en rabbits are normally spotted, and homozygous En/En animals are almost completely white. Compared to vital en/en and En/en rabbits, En/En animals are subvital because of a dilated (“mega”) cecum and ascending colon. In this study, we investigated the role of the KIT gene as a candidate for the English spotting locus in Checkered Giant rabbits and characterized the abnormalities affecting enteric neurons and c-kit positive interstitial cells of Cajal (ICC) in the megacolon of En/En rabbits. Twenty-one litters were obtained by crossing three Checkered Giant bucks (En/en) with nine Checkered Giant (En/en) and two en/en does, producing a total of 138 F1 and backcrossed rabbits. Resequencing all coding exons and portions of non-coding regions of the KIT gene in 28 rabbits of different breeds identified 98 polymorphisms. A single nucleotide polymorphism genotyped in all F1 families showed complete cosegregation with the English spotting coat color phenotype (θ = 0.00 LOD  = 75.56). KIT gene expression in cecum and colon specimens of En/En (pathological) rabbits was 5–10% of that of en/en (control) rabbits. En/En rabbits showed reduced and altered c-kit immunolabelled ICC compared to en/en controls. Morphometric data on whole mounts of the ascending colon showed a significant decrease of HuC/D (P<0.05) and substance P (P<0.01) immunoreactive neurons in En/En vs. en/en. Electron microscopy analysis showed neuronal and ICC abnormalities in En/En tissues. The En/En rabbit model shows neuro-ICC changes reminiscent of the human non-aganglionic megacolon. This rabbit model may provide a better understanding of the molecular abnormalities underlying conditions associated with non-aganglionic megacolon.

Selection for complex traits leaves little or no classic signatures of selection

Background

Selection signatures aim to identify genomic regions underlying recent adaptations in populations. However, the effects of selection in the genome are difficult to distinguish from random processes, such as genetic drift. Often associations between selection signatures and selected variants for complex traits is assumed even though this is rarely (if ever) tested. In this paper, we use 8 breeds of domestic cattle under strong artificial selection to investigate if selection signatures are co-located in genomic regions which are likely to be under selection.

Results

Our approaches to identify selection signatures (haplotype heterozygosity, integrated haplotype score and F_ST) identified strong and recent selection near many loci with mutations affecting simple traits under strong selection, such as coat colour. However, there was little evidence for a genome-wide association between strong selection signatures and regions affecting complex traits under selection, such as milk yield in dairy cattle. Even identifying selection signatures near some major loci was hindered by factors including allelic heterogeneity, selection for ancestral alleles and interactions with nearby selected loci.

Conclusions

Selection signatures detect loci with large effects under strong selection. However, the methodology is often assumed to also detect loci affecting complex traits where the selection pressure at an individual locus is weak. We present empirical evidence to suggests little discernible ‘selection signature’ for complex traits in the genome of dairy cattle despite very strong and recent artificial selection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-246) contains supplementary material, which is available to authorized users.

Identification of a major locus interacting with MC1R and modifying black coat color in an F₂ Nellore-Angus population

Background

In cattle, base color is assumed to depend on the enzymatic activity specified by the MC1R locus, i.e. the extension locus, with alleles coding for black (E^D), red (e), and wild-type (E⁺). In most mammals, these alleles are presumed to follow the dominance model of E^D > E⁺ > e, although exceptions are found. In Bos indicus x Bos taurus F₂ cattle, some E^DE⁺ heterozygotes are discordant with the dominance series for MC1R and display various degrees of red pigmentation on an otherwise predicted black background. The objective of this study was to identify loci that modify black coat color in these individuals.

Results

Reddening was classified with a subjective scoring system. Interval analyses identified chromosome-wide suggestive (P < 0.05) and significant (P < 0.01) QTL on bovine chromosomes (BTA) 4 and 5, although these were not confirmed using single-marker association or Bayesian methods. Evidence of a major locus (F = 114.61) that affects reddening was detected between 60 and 73 Mb on BTA 6 (Btau4.0 build), and at 72 Mb by single-marker association and Bayesian methods. The posterior mean of the genetic variance for this region accounted for 43.75% of the genetic variation in reddening. This region coincided with a cluster of tyrosine kinase receptor genes (PDGFRA, KIT and KDR). Fitting SNP haplotypes for a 1 Mb interval that contained all three genes and centered on KIT accounted for the majority of the variation attributed to this major locus, which suggests that one of these genes or associated regulatory elements, is responsible for the majority of variation in degree of reddening.

Conclusions

Recombinants in a 5 Mb region surrounding the cluster of tyrosine kinase receptor genes implicated PDGFRA as the strongest positional candidate gene. A higher density marker panel and functional analyses will be required to validate the role of PDGFRA or other regulatory variants and their interaction with MC1R for the modification of black coat color in Bos indicus influenced cattle.

Identification of large selective sweeps associated with major genes in cattle

Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits.

Molecular genetics of coat colour variations in White Galloway and White Park cattle

White Galloway cattle exhibit three different white coat colour phenotypes, that is, well marked, strongly marked and mismarked. However, mating of individuals with the preferred well or strongly marked phenotype also results in offspring with the undesired mismarked and/or even fully black coat colour. To elucidate the genetic background of the coat colour variations in White Galloway cattle, we analysed four coat colour relevant genes: mast/stem cell growth factor receptor (KIT), KIT ligand (KITLG), melanocortin 1 receptor (MC1R) and tyrosinase (TYR). Here, we show that the coat colour variations in White Galloway cattle and White Park cattle are caused by a KIT gene (chromosome 6) duplication and aberrant insertion on chromosome 29 (Cs29 ) as recently described for colour-sided Belgian Blue. Homozygous (Cs29 /Cs29 ) White Galloway cattle and White Park cattle exhibit the mismarked phenotype, whereas heterozygous (Cs29 /wt29 ) individuals are either well or strongly marked. In contrast, fully black individuals are characterised by the wild-type chromosome 29. As known for other cattle breeds, mutations in the MC1R gene determine the red colouring. Our data suggest that the white coat colour variations in White Galloway cattle and White Park cattle are caused by a dose-dependent effect based on the ploidy of aberrant insertions and inheritance of the KIT gene on chromosome 29.

The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos)

White-spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white (BEW) phenotype is characterized by 2 blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing gray fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals, we identify an abundance of an allele (bew1) in gray animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.

Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks

To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F(2) population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.

Melanocortin 1 receptor (MC1R) gene polymorphisms in three Italian cattle breeds

The Melanocortin 1 receptor (MC1R) is one of the main genes implicated in the determination of the coat colour in mammals. This locus showed a relevant genetic variation between breeds that can be exploited for breed traceability of the animal productions. Modicana, Cinisara and Sardo-Modicana are three Italian endangered cattle breeds. Genetic characterisation by molecular markers is a fundamental prerequisite for managing genetic resources and for developing potential genetic traceability protocols. In order to improve the knowledge on Modicana, Cinisara and Sardo-Modicana breeds and to evaluate the possibility to develop DNA-based protocols for their mono-breeds products traceability, the genetic structure of MC1R gene was analysed. Four main alleles were observed in a representative sample of 162 animals. In the black coated Cinisara breed (n = 42), the ED and E+ alleles segregated with a frequency of 0.93 for ED allele. In the red coated Modicana (n = 60) and Sardo-Modicana (n = 60) breeds the E+ and E1 alleles segregated with frequencies of 0.42, 0.57 and 0.52, 0.47, respectively. The recessive allele e showed a low frequency (0.01) in both breeds. Sequencing a subsample of 34 animals the rare E2 allele was found only in Modicana and Sardo-Modicana at a good frequency (0.50). A new PCR-RFLP test, based on BstOI restriction endonuclease, was devised to assay for this allele. Results of the work indicate that red coat in Modicana and Sardo-Modicana cattle is genetically determined by the E+ and E1 alleles instead of the e allele at homozygote status, as occurs in other red European breeds. In these three Italian breeds of local importance, MC1R polymorphisms can be used to discriminate Cinisara from Modicana and Sardo-Modicana, but it was not able to distinguish between the two red coat populations.