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The complete sequences of mtDNA D-loops from 362 individuals were analyzed in order to investigate the genetic diversity and differentiation of their lineages. The results indicated that all of the analyzed sequences were differentiated into four clear lineages (A, B, C, and D). Lineages C and D might originate from Lineages B and A, respectively. The genetic diversity of complete mtDNA D-loop of four lineages was very abundant. The 76 bp insertion and the 17 bp deletion were detected in the longest and the shortest sequences, respectively. The 76 bp insertion was a repeat like motif found in many other animals. Lineages C and D were differentiated into two subclades (C1 and C2) and (D1 and D2), respectively. Lineage C might originate from Asia, and Lineage D might originate from Fertile Crescent.

In order to investigate its distribution in different goat populations, one SNP (184C→T, corresponding to AY850925) of goat callipyge (CLPG) gene recognized by Fork I was identified after sequencing 23 individuals from 10 breeds. PCR-RFLP was carried out according to the variation site in 584 goats of 14 populations from 11 provinces and autonomous regions in China. An interesting result was found that the Boer goat having the characteristics of double muscle had significantly higher T allele (0.2465) frequency and lower C allele (0.7535) frequency compared to other breeds. It could be inferred that the 184C→T mutation might be related to the double muscle characteristics of the Boer goat. The general linear model analysis showed that parental genotype had significant effect on the body weight of their offspring at different ages. It could be inferred that transition of 184C→T might be a paternal imprinting form, a polar over-dominance, in which only individuals that received the allele from their mother expressed the callipyge phenotype. The double muscle characteristics of the Boer goat might be related to its maternal genotype. More data with detailed information need to be investigated in order to confirm this assumption.

A total of 436 goat samples from twenty-six populations were scanned for single nucleotide polymorphisms (SNPs) in 5′UTR of goat MSTN gene using sequencing and the polymerase chain reaction technique combined with restriction enzyme fragment length polymorphism (PCR-RFLP). The deletion of TTTTA found in 5′UTR of goat MSTN gene was conserved in different species and might be a unique mutation in goats. The Foreign Group and the Boer Goat backcrossed offspring had the highest and smallest genetic diversity of this mutation respectively, and also with the smallest and highest heterozygosity deficiency respectively. The genetic diversity of this mutation for the South Group of Chinese indigenous goat breeds was higher than that of the North Group, and the South Group had the smaller heterozygosity deficiency than the North Group. The estimated marginal means based on the modified population marginal mean and pairwise comparison between significant pairs showed that there was a trend that genotype AA had a significant effect on body weight and size from birth to four-month old (P

Part of intron 2 of the myostatin (MSTN) gene of 140 goats from 24 populations and 38 sheep from 8 breeds were sequenced, and similar sequences of different species from Gene bank were also obtained to study MSTN diversity within and among species. The results indicated that there were seven polymorphic sites in the sequenced region of goat, which have not been separated by recombination (or recurrent mutation), presented complete linkage disequilibrium, and could be sorted into three haplotypes. There was no polymorphic site in the sequenced region of sheep. The haplotype diversity, nucleotide diversity, and average number of single nucleotide polymorphism (SNP) differences of goats from the South group are higher than those of North group, and the corresponding value of the Foreign group is also higher than that of Chinese. The genetic differentiation (0.7558) between the Foreign and Chinese group is significant. There are two main haplotypes of the MSTN intron 2 in the goat, which may represent two ancestral types, in support of the theory that domestic goats in the world mainly originated from two ancestors based on morphology, history, archaeology, and molecular markers. The sequence differences of the MSTN intron 2 among species are greater than those within species.

The melanophilin (MLPH) gene has been characterized as the candidate gene for dilute coat color in some species, but little is known about it in the goat. In this study, part of the genomic DNA sequence (19,289 bp) containing the whole coding region of the MLPH gene from goat, as well as from sheep, was determined. We found 16 exons and 15 introns; the coding region was 1767 bp distributed in 15 exons (2-16). In sheep, the length of part of the genomic DNA sequence was 16,988 bp, with 16 exons and 15 introns, and the coding region was 1833 bp, distributed in 15 exons (2-16). Dozens of SNPs as well as some noticeable motifs in the goat MLPH gene were found during the process of sequencing and polymorphism screening. Based on the SSR Tool, three simple sequence repeat motifs were detected in the goat and sheep DNA sequences. Compared with cattle, we found insertions of 4 amino acids in goats and 26 amino acids in sheep.

Coat color offers some prospects for evolutionary studies due to its large amount of presumably adaptive coat color variation and conserved genetic mechanisms of generating different coat colors in different species. Melanocyte-stimulating hormone receptor (MSHR) gene is responsible for intraspecific and interspecific color variation in mammals and birds. A total number of 206 MSHR gene sequences belonging to 84 species, 58 genera, and 20 families were analyzed to investigate its evolution and differentiation in different species. Most of the species have 954 bp and stop codon TGA. Species in Callithrix and Callimico have a stop codon mutation from TGA to TGG and elongate 81 bp with TAG as stop codon. Species in Phasianidae, Fringillidae, and Lemuridae also use TAG as stop codon. The Sus scrofa had an insertion of AACCAGACC encoding Asn-Gln-Thr from 85 to 93 bp. In Bovidae, a brown strain of cow with 966 bp due to the 12-bp duplication of GGCATTGCCCGG from 670 to 681 bp encoding for Gly-Ile-Ala-Arg was found. Teiidae has the smallest number of total mutations (6), silent mutations (3), nonsynonymous mutations (3), average number of nucleotide differences (1.519), synonymous nucleotide diversity (pi(s) = 0.0030), and nonsynonymous nucleotide diversity (pi(a) = 0.0029), and Hominidae, Lemuridae, Canidae, and Teiidae have higher ratio of pi(a)/pi(s) (0.537-0.973). The reconstructed phylogenetic tree of MSHR gene of families is basically consistent with the taxonomy of National Center for Biotechnology Information.