High polymorphism at microsatellite loci in the Chinese donkey.

To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

Analysis of POU1F1 gene DdeI polymorphism in Chinese goats.

As a member of the POU-domain family, the POU1F1 is a positive regulator for growth hormone, prolactin and thyroid-stimulating hormone b, by binding to target DNA promoters as a dimer in mammals. This study described the polymorphisms at the goat POU1F1-DdeI locus and analyzed the distribution of alleles in 15 indigenous Chinese goat breeds. The PCR-RFLP analysis showed a predominance of the D1D1 genotype and the D1 allele, with average frequencies of 0.550 and 0.790, respectively, irrespective of goat utility type. The D1D2 genotype was the second most frequent, with a mean frequency of 0.371. The distributions of genotypic and allelic frequencies at this locus were found to be significantly different among populations based on a Chi square test (P < 0.001), suggesting that the breed factor significantly affected the molecular genetic character of the POU1F1 gene. The genetic diversity analysis revealed that Chinese indigenous populations had a wide spectrum of genetic diversity at the goat POU1F1-DdeI locus. However, an ANOVA analysis revealed no significant differences in gene homozygosity, gene heterozygosity, effective allele numbers, or polymorphism information content among meat, dairy, and cashmere utility types (P > 0.05). This suggests that the goat utility types had no significant effect on the spectrum of genetic diversity.

Frequency of gray coat color in native Chinese horse breeds.

Gray horses are born colored, and they then gradually lose their hair pigmentation. Tremendous progress has been made in identifying the genes responsible for graying with age in horses in recent years. Results show that gray coat color in horses is caused by a 4.6-kb duplication in intron 6 of the syntaxin 17 gene (STX17), which constitutes a cis-acting-regulatory mutation. However, little is known about the gray phenotype in native Chinese horses. This study was conducted to explore the frequency distribution of the gray mutation in native Chinese horse breeds. A total of 489 samples from 14 native Chinese horse breeds were genotyped for the STX17 duplication using a simplified conventional PCR-based method. The results show that the gray mutation was present in 12 native Chinese horse breeds, except the Balikun and Guanzhong breeds. The Chakouyi and Hequ breeds had the highest frequency of the gray mutation (P(G) = 0.367 and P(G) = 0.274, respectively). There was no significant geographical difference in the distribution of gray coat color across native Chinese horse breeds. Our results suggest that gray is a common coat color in Chinese horses.

Y-STR INRA189 polymorphisms in Chinese yak breeds.

To further explore Y-STR INRA189 polymorphisms in the yak, and to determine the genetic differences among yak breeds, genotyping analysis of INRA189 in 102 male yak individuals from three yak breeds in Qinghai Province of China was performed. Genotyping revealed the presence of four alleles, with sizes of 149, 155, 157, and 159 bp, respectively. Of these, the 157-bp allele, which was found with the highest frequency in the three yak breeds, was the dominant allele. Interestingly, the 149-bp allele was only detected in the Gaoyuan breed, and the 159-bp allele was only found in the Huanhu and Datong breeds. Only the 157- and 155-bp alleles were found in all three yak breeds. Taking the three yak breeds as a single population, the frequency of these four alleles was 0.0294, 0.0686, 0.8628, and 0.0392, respectively. The average polymorphism information content in the three yak breeds was 0.2379, indicating that the INRA189 was a low polymorphic Y-STR marker in yak.

Polymorphism in the 5ꞌ-UTR of the insulin-like growth factor I gene associated with production traits in Chinese cattle.

The insulin-like growth factor I (IGF-1) gene plays important roles in the growth and body composition of animals. Serum IGF1 concentration has been associated with growth traits in many livestock species. We found a polymorphism of cattle IGF1-TasI locus and analyzed the distribution of alleles in three cattle breeds, including Qinchuan, Nanyang, and Chinese Holstein. PCR-RFLP analysis showed that allele A was the dominant allele. The frequencies of allele A varied from 0.84 to 0.97. Distributions of genotypic and allelic frequencies were significantly different among breeds. Polymorphism of the IGF1 gene was significantly affecting hucklebone width at 6 months in the Nanyang breed and protein and fat yield of the third lactation in Chinese Holstein cattle. Individuals with allele C had a significantly higher performance in production traits.

Impacts of single nucleotide polymorphisms and haplotypes in the bovine Dapper1 gene on body weight.

The Dapper1 protein plays important role in multiple developmental processes via negative modulation of the Wnt signaling pathway. We detected variations in Dapper1 in 1185 individuals from 5 Chinese cattle breeds and determined their effects on bovine body weight. Two silent mutations (g.8344C>T and g.8428C>T) in exon 6 along with two substitutions (g.10513A>G and g.10765C>G) in the 3'-untranslated region were detected with DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism. Haplotype variability and the extent of linkage disequilibrium of the 4 single nucleotide polymorphisms (SNPs) were analyzed, and the results revealed 16 haplotypes and 7 combined haplotypes in the 5 cattle breeds. Statistical analyses indicated that genotypes CC and AA in the g.8344C>T and g.10513A>G loci were associated with heavier body weight at 6 months in the Nanyang cattle population (P < 0.05), and the combined haplotype had consistent significant effects on body weight with a single SNP. Cattle with haplotype combinations H1H5 (CCCTAACC) displayed the heaviest body weight at 6 months compared with that of other haplotypes (P < 0.05). Our results provide evidence that 4 SNPs and haplotypes in Dapper1 may be used for marker-assisted selection in beef cattle breeding programs.

A novel genetic variant of the goat Six6 gene and its association with production traits in Chinese goat breeds.

We looked for novel genetic variations within the Six6 gene by PCR-SSCP, DNA sequencing and forced RFLP-PCR and estimated their associations with production traits in 2132 goats of eight indigenous Chinese breeds. A novel single nucleotide polymorphism (NM_001104993.1: g.232T>C) within the goat Six6 gene was identified. The frequencies of allele "C" varied from 0.8621 to 1.000, which were in Hardy-Weinberg equilibrium. Genotype and allele frequencies were found to be significantly different in the breeds. Association analysis revealed a significant relationship between genotypes and cannon circumference in Hainan black goats (P = 0.047); adult individuals with genotype CT showed higher cannon circumference than those with genotype CC. Another significant association of genotypes with five-year-old fiber length was found in Inner Mongolia white cashmere goats (P = 0.002). In addition, individuals with genotype CT had longer fiber length than those with genotype CC. The data revealed that the Six6 gene positively affects growth traits and cashmere traits. Polymorphism of Six6-PstI could be useful as a DNA marker for goat breeding and genetics via marker-assisted selection.

AGPAT6 polymorphism and its association with milk traits of dairy goats.

As one of the eight members in the 1-acylglycerol-3-phosphate-O-acyltransferase (AGPATs) family, AGPAT6 is a crucial enzyme for the biosynthesis of glycerolipids and triacylglycerol in eukaryotes, as well as catalyzing the conversion from lysophosphatidic acid to phosphatidic acid. AGPAT6 can be considered as a candidate gene for regulating milk composition. DNA sequencing and PCR-RFLP methods were applied to detect genetic variation in the AGPAT6 gene in 549 Chinese dairy goats. Four polymorphisms (NC_007328.3:g.152G>C, 8124G>A, 9263C>G, 16436G>A) were detected in 5'UTR, intron 2, exon 4, and 3'UTR, respectively. For the KpnΙ locus, the frequencies of the AGPAT6-G allele were 0.955 and 0.936 for SN (Xinong Sannen) and GZ (Guanzhong) dairy goat breeds, respectively. In the PCR-RFLP analysis for KpnΙ, EcoRII, NcoΙ, and BglΙ, the frequencies of the G allele of AGPAT6 were 0.955 and 0.936, 0.694 and 0.819, 0.206 and 0.254, 0.729 and 0.623 for SN and GZ dairy goat breeds, respectively. The 9263C>G mutation revealed a synonymous genetic code of Thr (threonine). Associations between the four mutations and milk traits were analyzed in two dairy goat breeds. At the 9263C>G locus, genotype GG and CG individuals showed significantly better milk performance than genotype CC individuals (P < 0.05). Therefore, the G allele is suggested to be a molecular marker for milk production in dairy goats.

Lack of association of single nucleotide polymorphisms of the bovine Flt-1 gene with growth traits in Chinese cattle breeds.

We analyzed 20 exons, with their intron-exon boundaries, of the bovine Flt-1 gene, using a strategy combining PCR amplification and single-strand conformational polymorphism analysis (PCR-SSCP), followed by nucleotide sequence analysis, in 675 cattle. We then looked for associations between polymorphisms and growth traits. Twelve novel SNPs (ss#184956516, ss#184956517, ss#184956518, ss#184956519, ss#251343993, ss#251343994, ss#251343995, ss#251343996, ss#251343997, ss#251343998, ss#251343999, and ss#251344000) were detected in the bovine Flt-1 gene in all three breeds. We observed no significant associations between these polymorphisms and birth weight, body weight and average daily gain during different growth periods (6, 12, 18, and 24 months old) (P > 0.05), or in body height, body length, heart girth, or height at the hip in Nanyang cattle breeds.

A novel polymorphism of the lactoferrin gene and its association with milk composition and body traits in dairy goats.

Milk composition and body measurement traits, influenced by genes and environmental factors, play important roles in value assessments of efficiency and productivity in dairy goats. Lactoferrin (LF), involved in the efficient expression of protein in milk, is also an anabolic factor in skeletal tissue and a potent osteoblast survival factor. Therefore, it is an important candidate gene for milk composition and body measurement trait selection in marker-assisted selection. We employed PCR-SSCP and DNA sequencing to screen the genetic variations of the LF gene in 549 Chinese dairy goats. A novel single-nucleotide polymorphism (SNP) (G198A in exon II) of the LF gene was detected. The frequencies of the AA genotype were 0.0285 and 0.0261 in GZ and SN populations, respectively. Both populations were found to have low levels of polymorphism and were in Hardy-Weinberg disequilibrium (P < 0.05). We found significant (P < 0.05) associations of the SNP marker with milk protein and acidity in the total population; animals with the AA genotype had higher mean values for milk protein than those with the GA genotype. Animals with genotype AA had higher mean values for withers height than those with genotype GG (P < 0.05). We concluded that this SNP of the LF gene has potential as a genetic marker for milk composition and body traits in dairy goat breeding.