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CSN1S1 is one of the major genes encoding milk proteins of mammals. In this study we determined allele frequencies of CSN1S1-5' flanking region as well as exon 17 variants and their effects on milk traits in three indigenous cattle breeds Mazandarani, Golpaygani (Bos indicus) and Sarabi (Bos taurus) and Holstein cattle in Iran. CSN1S1*B variant was nearly fixed in Holstein but ranged from 0.40 to 0.66 in indigenous breeds. CSN1S1*C allele had higher frequency in indigenous breeds, especially in Bos indicus. Four genetic variants of the promoter were found in all breeds in different frequencies with allele 2 being the prevalent in all breeds (frequency 0.359 to 0.711) and allele 4 the least frequent (0.074 to 0.011). Allele B of the coding region was found in combination with all four promoter alleles. Allele 4 of the promoter was not found in any cow having the exon 17 allele C in all breeds except Mazandarani. BC / 23 genotype yielded the highest fat percentage (P<0.05) in Holstein but it had no significant effect in Golpaygani. There was not any homozygous CSN1S1*CC cow, to investigate the influence of C variant for fat content. None of the genetic combinations had significant effect on fat yield, although variant '2' of promoter indicated a negative effect. No significant effect among various combined genotypes on milk yield was found, but CSN1S1*B tended to higher milk production. Differences of allelic frequencies and milk production traits found among these breeds might be due to differences in origin of breeds or selection breeding programs. [ABSTRACT FROM AUTHOR]

In the camel tyrosinase gene, a restriction site provoked by the T variant was used in a special restriction fragment length polymorphism analysis (PCR-RFLP) for genotyping of animals from six different Pakistani camel breeds (Marecha, Dhatti, Larri, Kohi, Campbelpuri and Sakrai). For this purpose, four new primer pairs were designed for sequencing the coding region of exon 1 of the tyrosinase gene. PCR reactions were carried out in a total volume of 25 μl using 100 ng genomic DNA to amplify a 474 bp fragment at 56°C. A SNP (T/C) at 200 bps was found and exploited with a Dde I restriction enzyme that resulted in three different genotypes i.e. TT, TC and CC in each studied camel breed. Significant differences in the genotype frequency between the breeds were recorded. The Sakrai breed showed a distinctly higher frequency of heterozygous animals compared to Marecha, Dhatti, Larri and Kohi breeds. Our new designed primers could be used for genotype screening of other camel breeds. However, for understanding the contribution of tyrosinase gene and its antagonist i.e. agouti in the coat colour production, complete sequence of the gene is imperative. [ABSTRACT FROM AUTHOR]

ABSTRACT Mastitis in cattle is often caused by microorganism infections in the udder. The three most common pathogens are esculin‐positive streptococci (SC+), coagulase‐negative staphylococci (CNS), and Escherichia coli (E. coli). In a previous study, 10 SNPs were associated with somatic cell score and mastitis in diverse Holstein populations. We tested these SNPs for their effects on individual pathogen presence. Milk and pathogen samples of 3076 Holstein cows were collected from four farms. Samples were excluded if multiple pathogens were present at the same time. Records of the same pathogen within 14 days of each other were counted as one infection. This resulted in 1129 pathogen‐positive samples. Cases and controls were in ratios of 20:80 for SC+, 8:92 for CNS, and 11:89 for E. coli. The lasso, backward, and forward methods were used to narrow down SNPs associated with pathogen presence. The suitability of the SNPs to separate the samples into cases or controls for each pathogen was indicated using ROC curves. The Cochran‐Armitage (CAT) and the Jonckheere‐Terpstra (JTT) tests evaluated the influence of the SNPs on pathogen presence. Finally, a generalised linear mixed model (GLMM) including fixed environmental effects and a random sire effect was fitted to the binary trait of pathogen presence to test for association. In total, six out of the 10 investigated SNPs showed associations with pathogen presence based on the forward method: Two SNPs each for SC+ (rs41588957, rs41257403) and CNS (rs109934030, rs109441194), and three for E. coli (rs109934030, rs41634110, rs41636878). The CAT and GTT tests linked four SNPs (rs41588957, rs41634110, rs109441194, rs41636878) to pathogen presence, two of which were confirmed with the GLMM (rs41634110, rs109441194), with effects on CNS and E. coli. The SNPs linked to CNS and those linked to E. coli explained 13.2% and 13.8% of the variance, compared to 19% and 18.4%, respectively, of the full model with all 10 SNPs. Half of the SNP genotypes previously linked to lower SCS also decreased the probability for pathogen presence and might therefore be targets not just for lower SCS but for a better pathogen resistance.Trial Registration: Not applicable, no new data were collected for this study. [ABSTRACT FROM AUTHOR]

In German Holstein population a very signifi cant QTL with effects on milk yield trait (MY) was mapped on chromosome 6 and 20 to the interval BM143–ILSTS97 and AGLA29–ILSTS72, respectively. Where, three markers BM143, FBN13 and ILSTS97 on chromosome 6 and two markers AGLA29 and ILSTS72 on chromosome 20 were associated with highly signifi cant effects (P

Four dominant coat color phenotypes are found in fallow deer ( Dama dama ). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP , MC1R , TYR , and SLC45A2 genes. In ASIP , two mutations (ASIP-M-E2, located at the boundary from exon 2 to intron 2; and ASIP-M-E3, an InDel of five nucleotides) were found, leading to black fallow deer being either homozygous or heterozygous in combination. There were also two mutations found in MC1R . Whereby the mutation MC1R-M1 (leucine to proline, L48P) homozygous leads to a white coat, while the mutation MC1R-M2 (glycine to aspartic acid, G236D) homozygous is associated with the menil phenotype. When both mutations occur together in a heterozygous character state, it results in a menil coat. Since the mutations in the two genes are only present alternatively, 36 genotypes can be identified that form color clusters to which all animals can be assigned. No mutations were found in the TYR and SLC45A2 genes. Our investigations demonstrate that the four dominant coat colors in fallow deer can be explained by ASIP and MC1R mutations only.

American Bashkir Curly Horses are claimed to be hypoallergenic, but this has not been clinically proven. In the present study, the effect of exposure to Curly Horses was investigated in 141 patients allergic to horses by measuring their lung function and nasal patency during Curly Horse contact. Continuous contact with Curly Horses, including riding and brushing, decreased the allergic riders' reactivity as measured by FEV 1 , PEF, and PNIF. Subsequent visits (up to 40 or more hours of riding) further reduced reactivity to the Curly Horses. Allergic events to horses occurred only in 72 out of 1312 riding hours, mainly in the first ten riding hours.In 41 out of the 141 patients, it was further investigated whether repeated exposure to Curly Horses could induce tolerance to other horses. Patients in the tolerance induction study were tested annually for horse allergy using a nasal provocation test. The tolerance induction study showed that exposure to Curly Horses induced immune tolerance to other horses in 88% of patients who completed the study.To understand the mechanism causing hypoallergenicity, we performed IgE immunoblots to determine whether Curly Horse hairs contain IgE binding proteins. However, no differences in IgE reactivity were found between Curly and non-Curly Horses. Moreover, the immune tolerance induction study patients did not show decreased IgE reactivity to hairs from Curly or non-Curly Horses even though patients had developed tolerance. However, we did find increasing levels of anti-horse IgG antibodies in the study patients.Overall, our data strongly suggests that continuous exposure to Curly Horses can induce immune tolerance, rendering these patients non-reactive to horses. The reason for the reduced clinical allergenicity of Curly Horses remains unclear, but the data suggest that blocking IgG antibodies may be of importance for immune tolerance development., Competing Interests: The authors declare that they have no conflict of interest., (Thieme. All rights reserved.)

RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses ( Equus caballus ) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1 , CCL5 , CD40LG , FOS , IL1R2 , IL20RA , and IL22RA2 , on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2 , GYG1 , HIF1A , MOGAT1 , PFKFB3 , PLIN5 , SIK1 , and STBD1 .

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists., (© 2023. L’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).)

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity., (© 2023. The Author(s).)

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log 10 ( p ) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (-log 10 ( p ) = 11.93, MAF = 0.23, substitution effect of the minor allele (ß MA ) = -0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (-log 10 ( p ) = 8.47, MAF = 049, ß MA = -0.055%) and the GNG2 region (-log 10 ( p ) = 10.48, MAF = 0.34, ß MA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.

The improvement of milk production of indigenous Sudanese cattle such as Bos indicus Butana and its cross with Holstein is a major goal of the Sudanese government to ensure sufficient healthy nutrition in the country. In this study, we investigated the K232A polymorphism of diacylglycerol acyltransferase (DGAT1), a well-known modulator of milk production in other breeds. We determined allele frequencies and the allele effects on milk production. Therefore, 93 purebred Butana and 203 Butana × Holstein crossbred cattle were genotyped using competitive allele-specific PCR assays. Association analysis was performed using a linear mixed model in R. In purebred Butana cattle, the lysine DGAT1 protein variant K232, which is found to be associated with higher fat and protein contents, as well as higher fat yield was highly frequent at 0.929, while its frequency in Butana × Holstein crossbred cattle was 0.394. Significant effects were found on milk yield (P = 7.6 × 10 -20 ), fat yield (P = 2.2 × 10 -17 ), protein yield (P = 2.0 × 10 -19 ) and lactose yield (P = 4.0 × 10 -18 ) in crossbred cattle. As expected, the protein variant K232 was disadvantageous since it was decreasing milk, protein, and lactose yields by 1.741 kg, 0.063 kg and 0.084 kg, respectively. No significant effects were found for milk fat, protein, and lactose contents. The high frequency of the lysine DGAT1 protein variant K232 in Butana cattle could contribute to their high milk fat content in combination with low milk yield. In Butana × Holstein crossbred cattle, the DGAT1 marker can be used for effective selection and thus genetic improvement of milk production., (© 2022. The Author(s).)

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.

The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, P BF  = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: P BF  = 0.003, Butana × Holstein: P BF  = 6.2 × 10 -16 ). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci., (© 2022. The Author(s).)

Background: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement., Results: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%., Conclusion: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future., (© 2021. The Author(s).)

Background: Individuals' ideals and aspirations are considered to constitute a central reference frame for subjective evaluations of their perceived reality, and, thus, to be crucial for individual quality of life (QoL) outcomes. By examining individual values and spirituality in very old people, the aim of this study was to describe two constructs representing the aspirations of the individual, as well as the relation of these constructs to both hedonic and eudaimonic QoL outcomes in very old age (VOA)., Material and Methods: Cross-sectional data from a representative survey of people in VOA (NRW80+, n = 1863) were used. Individual values were assessed based on the Portrait Value Questionnaire. A revised questionnaire was developed drawing on the Spiritual Health and Life-Orientation Measure. Individual values and spirituality were studied using descriptive statistics, and hierarchical linear regression models were used to analyze their predictive value for two QoL outcomes: 1) affective well-being as an indicator of hedonic QoL, which was assessed using the positive affect subscale of the short form of the Positive and Negative Affect Schedule, and 2) engagement with life, which captures eudaimonic aspects and which was measured with a subscale of the Valuation of Life Scale., Results: The most important values were both protection and growth-oriented values with a social focus. However, only values representing strivings for growth had a positive association with QoL outcomes. Spirituality was of high relevance to very old people, although not in the sense of religious institutions or practices. Rather, it predominantly consisted in environmental, interpersonal, and transcendental connectedness, all of which were positively connected to QoL outcomes., Conclusion: Individual values and spirituality can be an important resource for hedonic as well as eudaimonic QoL; however, age-related losses may lead to an emphasis of protective values that are not beneficial in terms of QoL. To support older people on their spiritual journey, a broad concept of spirituality needs to be established among researchers as well as practitioners., (© 2021. The Author(s).)

Background: People in very old age (VOA) are expected to be confronted with particularly negative stereotypes. These influence societally shared behavior towards and judgements about them. Such external evaluations of individuals' lives are considered a crucial part of their quality of life (QoL)., Objective: The present study elaborated a) the societal appreciation perceived by people in VOA and b) the stereotypes about people in VOA held by stakeholders from key societal areas. The aim was to discuss possible connections between these external standards and individual life results., Material and Methods: A parallel mixed methods design was employed. Cross-sectional data from a representative survey of people aged 80 years and older (n = 1863) were analyzed by means of χ 2 -tests and Kruskal-Wallis tests to examine differences in perceived societal appreciation (PSA) by characteristics of the person, their biography, and current lifestyle. Linear regression models were used to investigate the impact of these characteristics on PSA. Regarding stereotypes about people in VOA, semi-structured interviews with stakeholders from key societal areas (n = 22) were analyzed using qualitative content analysis. The quantitative and qualitative findings were juxtaposed for comparison., Results: PSA was predicted by health-related variables and productive activities. Several societal stakeholders highlighted that age-related losses pose challenges on very old individuals, their families, and society, whereas remaining potentials in VOA can and should be used for the benefit of others; however, stakeholders' perceptions differed by the extent of their professional contact with (very) old people. Different pathways were proposed through which the observed stereotypes and determinants of PSA might be connected (e.g., stereotype internalization)., Conclusion: Our study illustrates the relevance of external standards for individual QoL and highlights the need for a normative perspective in the discussion about QoL and its enhancement., (© 2021. The Author(s).)

Genetic variations in the four casein genes CSN1S1 , CSN2 , CSN1S2 , and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [ Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats ( CSN1S1 ∗ C1), Bezoar ibex ( CSN1S1 ∗ J), and Alpine ibex ( CSN1S1 ∗ K), for beta and kappa caseins in Alpine ibex ( CSN2 ∗ F and CSN3 ∗ X), and for alpha S2 casein in all domesticated and wild goats ( CSN1S2 ∗ H), in Nubian and Desert goats ( CSN1S2 ∗ I), or in Nubian ibex only ( CSN1S2 ∗ J and CSN1S2 ∗ K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Rahmatalla, Arends, Said Ahmed, Hassan, Krebs, Reissmann and Brockmann.)

Non-communicable diseases, such as the metabolic syndrome and inflammatory bowel disease, constitute serious public health threats in developed countries. Besides environmental factors, genetic predispositions contribute to the onset and progression of the disease. State-of-the-art mouse models recently highlight the involvement of Toll-like receptor 5 (TLR5)-driven microbiota composition in the development of metabolic disorders. Here, we discuss the causes and consequences of an altered enteric microbiota and provide information on a similar mechanism in another species, the pig. We show for the first time that a single nucleotide polymorphism in the porcine TLR5 gene conferring impaired functionality is associated with changes in the intestinal microbiota in adult sows and neonatal piglets. Changes in the developing adaptive cellular immune response support the concept of TLR5-driven changes of the microbe-host interplay also in the pig. Together, these findings suggest that pigs with impaired TLR-functionality might represent a model for TLR5-driven diseases in humans.

Although the European roe deer ( Capreolus capreolus ) population of North-West Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and 2039 bp of ASIP were sequenced in 24 specimens and several SNPs were detected. But only the ASIP -SNP c.33G>T completely segregated both phenotypes leading to the amino acid substitution p.Leu11Phe. The SNP was further evaluated in additional 471 samples. Generally, all black specimens ( n = 33) were homozygous TT, whereas chestnut individuals were either homozygote GG ( n = 436) or heterozygote GT ( n = 26). Considering the fact that all melanistic animals shared two mutated alleles of the strongly associated SNP, we concluded that melanism is inherited in a recessive mode in European roe deer.

The aim of the present study was to assess genetic variation that is characteristic for Sudanese goat breeds in the milk whey protein genes (LALBA and BLG). Four Sudanese goat breeds were screened for variability in LALBA and BLG genes at the DNA level by comparative sequencing of five animals per breed. Sixteen SNPs were identified in LALBA: seven in the upstream region, six synonymous, and three in the 3´-UTR. Three novel synonymous SNPs in exon 2 (ss5197800003, ss5197800012, and ss5197800004) were found in Nubian, Desert, and Nilotic, but not in Taggar goats. One SNP in the promoter of LALBA (rs642745519) modifies a predicted transcription factor binding site for Tcfe2a. The SNPs in the 3'-UTR (rs657915405, rs641559728, and rs664225585) affect predicted miRNA target sites. With respect to haplotypes in the exonic region, haplotype LALBA-A is most frequent in Nubian, Desert, and Nilotic goats, while haplotype LALBA-D is prevalent in Taggar goats. In BLG, 30 SNPs were detected: eight in the upstream gene region, two synonymous, 17 intronic, and three in the 3'-UTR. Among the 30 identified SNPs, 15 were novel. Four of these novel SNPs were located in the upstream gene region, one was synonymous, and ten were intronic. The novel synonymous SNP (ss5197800017), located in exon 2, was only found in Nubian and Nilotic goats. The SNPs ss5197800010 and rs635615192 in the promoter are located in predicted binding sites of transcription factors (M6097, Elk3, Elf5, and GABPA). Among seven haplotypes detected in the coding region, haplotype BLG-A is most frequent in Nubian and Nilotic goats while haplotype BLG-B is most frequent in Desert and Taggar goats. The high variability in regulatory gene regions among Sudanese goats could potentially affect the quality and yield of whey proteins in goat milk and provide a wide resource for genetic improvement of milk production and milk technology characteristics.