A PstI polymorphism at 3'UTR of goat POU1F1 gene and its effect on cashmere production

Association analysis for SNPs of BAAT and COL1A1 genes with cashmere production performance and other production traits in Liaoning cashmere goats

This study aimed to investigate the relationship between the polymorphism of bile acid-CoA: amino acid N-acyltransferase (BAAT) and collagen type I alpha 1 chain (COL1A1) genes and the production performance of Liaoning Cashmere goat (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence comparison of BAAT and COL1A1 genes and PCR-Seq polymorphism, and the effect of SNPs on production performance was analyzed by SPSS software. The results showed that three SNPs loci were detected in BAAT gene: G7900A, T7967C, C7998T, and one SNP locus T6716C was detected in COL1AL gene. At G7900A locus, the dominant genotype for cashmere performance was GG, and the dominant genotype for body measurement traits and milk production traits was AG. At T7967C locus, the dominant genotype for cashmere performance was TT, and the dominant genotype for body measurement traits and milk production traits was CC. At C7998T locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. At the T6716C locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. H1H1: AACC is the dominant haplotype combination. Therefore, this study will provide a reliable reference for future research on cashmere production performance, body measurement traits, and milk production traits of LCG.

Landmark native breed of the Orenburg goats: progress in its breeding and genetics and future prospects

This paper reviews information about a unique and iconic breed of the Orenburg Oblast, the homeland and the only place where the best herds of Orenburg down-hair goats in Russia are concentrated. Three types of these small ruminant animals are widespread on the territory of the region: Orenburg purebred gray goats, Orenburg purebred white goats, as well as crossbred white goats of F1 White Don × White Orenburg. Currently, at the farms of the Orenburg region, animals are selected according to their phenotype, with selected traits being color, weight and length of down hair. In recent years, the Orenburg goat breed has become an object of genetic research using various marker systems including immunogenetic, microsatellite, mtDNA and SNP markers. Overall, these studies evidence about the uniqueness of the allele pool in the landmark native breed of the Orenburg goats, which is a complex dynamic genetic system, prioritizing its further in-depth genome research and breeding applications.

Characterization of third exonic region of POU1F1 gene in the Osmanabadi breed of goat

The POU1F1 gene has been identified as one of the major gene for productivity, and its polymorphism is known to be associated with important production traits of various livestock. The present study was designed to investigate POU1F1 (exon-3) gene polymorphism and its association with body weight in Osmanabadi goat (n=217). The PCRSSCP and DNA sequencing revealed single ‘C’ > ‘T’ transition at nucleotide position 42 in the third exonic region (225 bp) POU1F1 gene of Osmanabadi goat. Genotyping revealed ‘TT’ and ‘CC’ genotypes with predominance of ‘C’ allele in the Osmanabadi goat population. Though no association between the said SNP and body weight was observed, these findings can be extended to find the genetic variability of POU1F1 gene associated with growth traits of various Indian goat breeds.

Associations between genetic variants of the POU1F1 gene and production traits in Saanen goats

This study was conducted to determine the polymorphisms of the POU1F1 gene and their relationships with milk yield and components, litter size, birth weight, and weaning weight in goats. For this purpose, a total of 108 Saanen goats from two different farms (Bornova and Manisa) were used as animal materials. Polymorphisms at the exon 6 and the 3' flanking region of the POU1F1 gene were determined by using PCR-RFLP with PstI and AluI restriction enzymes and DNA sequencing analyses. Two alleles and three genotypes were identified by AluI or PstI digestions of the POU1F1 gene. The genotypes frequencies of TT, TC, and CC were 64.8 %, 31.5 % and 3.7 % for the PstI locus; 54.6 %, 31.5 % and 13.9 % for the AluI locus, respectively. T allele frequencies (0.56 and 0.88 for the AluI locus, 0.80 and 0.81 for the PstI locus, respectively) were predominant in both loci at the Bornova and Manisa farms. In terms of POU1F1-AluI and POU1F1-PstI loci, two populations were found to be in Hardy-Weinberg equilibrium. In the POU1F1-AluI locus, significant associations were found between genotypes and lactation milk yield and litter size. Similarly, a significant relationship between genotypes and birth weight in the POU1F1-PstI locus ( p < 0.05 ) was determined. The TC and CC genotypes were observed to be higher than the TT genotype for lactation milk yield and litter size at the POU1F1-AluI locus. Birth weight was found to be higher in animals that have the CC genotype at the POU1F1-PstI locus. In conclusion, the POU1F1 gene can be used as a molecular marker for economic features like reproduction, growth, milk content and yield in Saanen goats.

Relationship between SNPs of POU1F1 Gene and Litter Size and Growth Traits in Shaanbei White Cashmere Goats

POU (Pit-Oct-Unc) class 1 homeobox 1 (POU1F1, or Pit-1) is a transcription factor that directly regulates pituitary hormone-related genes, as well as affects the reproduction and growth in mammals. Thus, POU1F1 gene was investigated as a candidate gene for litter size and growth performance in goats. In the current study, using direct DNA sequencing, c.682G > T, c.723T > G and c.837T > C loci were genotyped in Shaanbei white cashmere (SBWC) goats (n = 609), but c.876 + 110T > C was monomorphic. Besides, the c.682G > T locus was first identified by HinfI (Haemophilus influenzae Rf) restriction endonuclease. Association analysis results showed that the c.682G > T, c.837T > C loci and diplotypes were significantly associated with goat litter size (p < 0.05). The positive genotypes were GT and TT for the two SNPs, respectively, and the optimal diplotype was H3H7 (GTTT-TTTT). On the other hand, the c.682G > T, c.723T > G and c.837T > C strongly affected growth traits and body measurement indexes in SBWC goats (p < 0.05). The positive genotypes or allele of these SNPs were GT, G and TT, respectively. Additionally, the goats with H3H7 diplotype also had a greater growth status than others (p < 0.05). Here, individuals with same genotype had both a better litter size and growth traits, showing a positive correlation between these economic traits. Meanwhile, the positive genotypes of four SNPs were combined to obtain the optimal diplotype, which was also H3H7. These SNPs, especially the diplotype, could be used for the genomic selection of excellent individuals with a greater litter size and better growth status in goat breeding.

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.

Associations of six SNPs of POU1F1-PROP1-PITX1-SIX3 pathway genes with growth traits in two Chinese indigenous goat breeds

In the process of anterior pituitary gland development and maturation, numerous transcription factors were involved in the pituitary organogenesis. To date, the lack of knowledge on POU1F1-PROP1-PITX1-SIX3 pathway genes affecting growth traits was reported in Chinese goat breeds. The objective of this work was to identify genetic variants of the POU1F1, PROP1, PITX1 and SIX3 genes, as well as to evaluate their associations with growth traits in goats. The results showed that one novel and five reported single nucleotide polymorphisms (SNP) were confirmed in above four genes. The novel SNP (NC_019460.2:g.1100T>A) was located in intron 1 of SIX3 gene. Among these loci, DQ826397.1:g.102T>G (SNP1), DQ826397.1:g.279T>C (SNP2) and NC_019460.2:g.1100T>A (SNP6) were associated with growth traits. In details, the SNP1 locus had significant association with hucklebone width (P<0.05) and hucklebone width index (P<0.05) in the Guanzhong dairy goat. The SNP2 locus was associated with body weight (P<0.05), chest circumference (P<0.01), chest width (P<0.05), hucklebone width (P<0.05), cannon circumference (P<0.01) and trunk index (P<0.01) in the Hainan black goat. The SNP6 locus was significantly associated with hucklebone width index (P<0.05) and chest width (P<0.05) in the Guanzhong dairy goat and Hainan black goat, respectively. These findings indicated that goat POU1F1-PROP1-PITX1-SIX3 pathway genes were important genetic factors, which could affect growth traits. Three SNPs detected in this study may be useful for potential marker-assisted selection programs in goat breeding and production.

Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits

The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZH_p and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.

Association of pituitary specific transcription factor-1 (POU1F1) gene polymorphism with growth and biometric traits and blood metabolites in Iranian Zel and Lori-Bakhtiari sheep

The pituitary-specific positive transcription factor 1 (POU1F1) gene has been the subject of many recent studies because of its important roles in growth and development of mammals. In this study, we investigated the single nucleotide polymorphisms (SNPs) at the third exon of POU1F1 gene and its association with growth and biometric traits and blood metabolites in two Iranian sheep breeds, Zel and Lori-Bakhtiari. Blood samples from 90 Lori-Bakhtiari and 90 Zel sheep were collected to extract DNA and the 295-bp fragment of the POU1F1 gene was amplified and the restriction fragment length polymorphism (RFLP) technique was adopted for genotyping. A SNP was identified in both Lori-Bakhtiari and Zel sheep breeds, which represents a non-synonymous single base mutation at restriction site for endonuclease AciI. The results revealed differential frequencies of alleles between the two studied breeds, where A allele was more frequent in Lori-Bakhtiari breed, while G allele was more frequent in Zel breed. When POU1F1 genotypes were tested, the animals with AA genotype had a higher weaning weight than those with GG genotype (p < 0.05), however there were not significant association between genotypes and birth weight, biometric traits (body length, body height, heart girth, thigh girth and abdominal girth) and blood metabolites (triglyceride and cholesterol) of the studied breeds (p > 0.05). These findings imply that the POU1F1 polymorphism may affect weaning weight, thus can be used as a molecular marker for this production trait.

Identification of novel SNPs in the Sarda breed goats POU1F1 gene and their association with milk productive performance

The aim of the study was to detect polymorphism in the POU1F1 gene in Sarda breed goat, as well as to establish if SNPs could be associated with milk productive traits. The research was conducted on 129 Sarda breed goats from 4 to 5 years old, multiparous, lactating and in their third to fifth lactation. We report nine exonic and seven non-coding regions SNPs within the Sarda goat POU1F1 gene, namely, Ex 1 61 G>C; Ex 1 108 G>A; Ex 3 C>T; Ex 3 92 C>T; Ex 4 110 A>G; Ex 5 34 G>A resulting in Arg213Lys change; IVS4 641 G>A, IVS4 643 A>C, IVS4 659 G>A, IVS4 677 A>C, IVS4 G699Del, IVS4 709 C>G, Ex 6 17 G>A resulting in Arg228Ser change, Ex 6 58 G>T, Ex 6 172 T>C, 3'UTR 110 T>C. A statistically significant association was found between genotype TT, in position 17 of the exon 6 (3.1 % of frequency), and increased milk yield (P < 0.01) while genotype GT (25.6 % of frequency) was associated with a higher fat content. Genotype TT in position 58 of the exon 6 (3.9 % of frequency) was found to be associated with a higher fat (P < 0.01) and protein content (P < 0.05). Twenty-eight haplotypes were detected, but no significant association between the haplotypes and the milk production traits have been found. Our data, as well as providing new SNPs extending the POU1F1 gene characterization, evidence a relationship between polymorphism and milk production traits in Sarda goat breed.

Polymorphisms of caprine POU1F1 gene and their association with litter size in Jining Grey goats

Seven pairs of primers were designed to amplify 5' promoter region, six exons and partial introns and to detect the polymorphisms of POU1F1 gene in five goat breeds with different prolificacy. The results showed that six mutations were identified in caprine POU1F1 gene including C256T in exon 3, C53T and T123G in intron 3, and G682T (A228S), T723G and C837T in exon 6. The former four mutations were novel SNPs in goat POU1F1 gene. The 53 and 123 loci were in complete linkage disequilibrium in five caprine breeds. Regarding the 256 locus, the Jining Grey goat does with genotype CT had 0.66 kids more than those with genotype CC (P < 0.05), while does with genotype GT had 0.63 (P < 0.05) kids more than those with genotype GG at the 682 locus. The present study preliminarily showed an association between allele T at the 256 and 682 loci of POU1F1 gene and high litter size in Jining Grey goats. Totally 16 haplotypes and 50 genotypes were identified at the above six loci in POU1F1 gene of five goat breeds. Three common haplotypes (hap2, hap3 and hap4) were identified in five goat breeds joined. Four specific haplotypes (hap7, hap9, hap11 and hap13) were detected in Jining Grey goats. The predominant haplotype was hap1 (35.29% and 48.25%) in both Jining Grey and Guizhou White goats, while hap4 (50%) in Boer goats, and hap2 (42.86% and 38.75%) in both Wendeng Dairy and Liaoning Cashmere goats. The most frequent genotypes at six loci in the above five goat breeds were hap1/hap2 (14.38%) and hap1/hap4 (14.38%), hap1/hap2 (38.60%), hap4/hap4 (40.91%), hap2/hap4 (26.53%), hap2/hap5 (20.00%), respectively. The Jining Grey goat does with nine genotypes analyzed of POU1F1 gene showed no obvious difference in litter size.

Identification of SNPs within the sheep PROP1 gene and their effects on wool traits

Regarding mutations of PROP1 (Prophet of POU1F1) gene significantly associating with combined pituitary hormone deficiency (CPHD) in human patients and animals, PROP1 gene is a novel important candidate gene for detecting genetic variation and growth, reproduction, metabolism traits selection and breeding. The aim of this study was to detect PROP1 gene mutation of the exon 1-3 and its association with wool traits in 345 Chinese Merino sheep. In this study, on the basis of PCR-SSCP and DNA sequencing methods, ten novel SNPs within the sheep PROP1 gene, namely, AY533708: g.45A>G resulting in Glu15Glu, g.1198A>G, g.1341G>C resulting in Arg63Ser, g.1389G>A resulting in Ala79Ala, g.1402C>T resulting in Leu84Leu, g.1424A>G resulting in Asn91Ser, g.1522C>T, g.1556A>T, g.1574T>C, g.2430C>G were reported. In addition, association analysis showed that three genotypes of P4 fragment were significantly associated with fiber diameter in the analyzed population (P=0.044). These results strongly suggested that polymorphisms of the PROP1 gene could be a useful molecular marker for sheep breeding and genetics through marker-assisted selection (MAS).

A novel SNP of the ATP1A1 gene is associated with heat tolerance traits in dairy cows

PCR low ionic strength single-strand conformation polymorphism (PCR-LIS-SSCP) and DNA sequencing methods were used to analyze the polymorphisms within the coding region of bovine ATP1A1 gene. A novel C/A mutation was identified at the nucleotide position 2789 of the ATP1A1 mRNA, but it was silent with respect to the amino acid sequence of the protein. The LIS-SSCP banding pattern could be divided into three kinds of genotypes, named CC, CA, and AA. Also, the association of the novel SNP of ATP1A1 gene with heat tolerance traits was studied, we found that the individuals with genotype CC showed significantly higher heat resistance than those of genotype CA (P<0.05). Further, the mRNA levels of ATP1A1 gene in lymphocytes of peripheral blood in dairy cows among various temperature groups and genotypes were analyzed by using real-time RT-PCR. Results showed that the expression of ATP1A1 mRNA was highest in heat-stressed cows with CC genotype among the three genotypes (P<0.01), and the ATP1A1 mRNA level at temperature 32.5°C was higher than that at optimal temperature 12.5°C in dairy cows (P<0.01). Simultaneity, the plasma potassium (K+, mmol/l) and sodium (Na+, mmol/l) declined when the temperature dropped (P<0.05). Our findings implied that the novel SNP here could be a potential genetic marker for anti-heat stress trait in dairy cow breeding.

A novel missense (A79V) mutation of goat PROP1 gene and its association with production traits

As a paired class homeodomain transcription factor, mutations of PROP1 (Prophet of POU1F1) are responsible for deficiencies of GH, PRL, TSH, LH and FSH. Regarding mutations of GH, PRL, and POU1F1 genes significantly associating with different production traits, PROP1 gene is a novel important candidate gene for detecting genetic variation and association analysis in marked-assist selection (MAS) program. Therefore, the objective of this study is to detect goat PROP1 gene mutation and its association with production traits. Herein, a novel mutation (AF453512:g.1795C>T) within PROP1 gene is revealed by PCR-SSCP and DNA sequencing methods, and genotyped by Hin6I PCR-RFLP method in 1,344 individuals belonging to eight goat breeds. Only two genotypes (CC and CT) are revealed and the frequencies of allele C go from 0.9014 to 1.000 in analyzed populations. The genetic diversity analysis reveals that all PIC values are less than 0.1619, implying that the Hin6I locus within PROP1 gene possesses low genetic diversity in goat. Furthermore, nucleotide sequence analysis shows that AF453512:g.1795C>T results in a missense amino acid (A79V). But, association analysis demonstrates no significant differences between different genotypes and production traits (such as body weight, cashmere yield, fiber length and wool thickness) of Inner Mongolia White Cashmere goat (P > 0.05), as well as no significant relationship between different genotypes and average milk yield (P > 0.05). Although Hin6I polymorphism can not be used as a molecular marker for production traits in MAS, the present work presents preliminary novel missense mutation which extends the spectrum of genetic variations of goat PROP1 gene and may benefit for considering its association with other biophysical and biochemical indexes.