| The homology of chromosomes among cattle, sheep and goat was analyzed using Phylogenetic Computer Tools and Phylip software based on markers that exist in GOATMAP DATABASE and NCBI biological database located at their autosomes. The results indicated that similarity of homologous chromosomes among three species was between 0.0000～1.0000. The chromosomal homology of cattle and goat is higher than that of sheep and goat, and that of cattle and sheep, which further confirmed that sheep chromosome 1, 2 and 3 came from chromosomal reorganization of goat chromosome 1 and 3, goat chromosome 2 and 8, and goat chromosome 5 and 11, respectively.Part of CLPG gene sequences of Ovis aries, Capra hircus, Bos taurus, Canis familiaris, Equus caballus, Oryctolagus cuniculus, Sus scrofa and Rattus norvegicus was analyzed using the method of comparative genomics and bioinformatics and the Genetic diversity and genetic differentiation were analyzed. The results showed that a total of 176 polymorphic sites were detected from 12 sequences, more genetic diversity of the CLPG gene existed within and among species.9 haplotypes were derived from the 12 CLPG gene sequences, which indicated that rich genetic variation existed among species. The average number of nucleotide differences among species(k), nucleotide diversity(π) and haplotype diversity(Hd) are 28.045, 0.15935 and from 0.881 to 0.997, respectively. The partial CLPG gene sequences from different species were clustered. Results showed that Ovis aries, Aoudad and Bharal were clustered together firstly, followed by cattle, then by goat, which was consistent with the biological classification of bovine.The goat CLPG gene was predicted at chromosome 21 by bioinformatics analysis among species. Most of goat chromosomes are telocentric in metaphase (2n=60). Via fluorescent in situ hybridization (FISH), physical location of CLPG gene was set, which showed that CLPG gene located at the 21th chromosome of goat, having enriched the physical map and integration map of goat chromosome 21. The coat color candidate genes of goat, Myo5a, Brca1, Sox10, Zic2, kit, Snai2, Wnt3a and Tyrp1, were predicted at chromosome 10, 17, 5, 12, 6, 14, 7 and 8.According to the reported sheep Callipyge gene sequence (AF401294) and cattle chromosome 21 genomic contig (NW001494068), pairs of primers were designed and P0, P1, P2 and P3 fragments of CLPG gene were amplified. 2709bp sequence was got after connecting these fragments. Then we identified two SNPs (A316G and C372G) in the P2 fragment from Liaoning Cashmere Goat, Jining gray goat, Tangshan dairy goat, Nanjiang brown goat, Leizhou black goat and Boar goat. PCR-RFLP analysis of A316G showed that allele G had lower frequency in each of the analyzed populations, with Liaoning cashmere goat the lowest (0.2000) and Tangshan dairy goat the highest (0.5000). GG genotype was mainly found in Tangshan diary goat, Jining gray goat, Leizhou black goat and Nanjiang brown goat (fast grow strain), but not found in Liaoning cashmere goat and Boer goat. Hardy-Weinberg equilibrium test (chi-square) showed that all these involved populations were in equilibrium for A316G (P>0.05). General linear model analysis showed that the individual genotype had no significant effect (P=0.121>0.05) on birth weight of Boer goat.
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