Xianglong Li

Genetic variation of chicken MC1R gene in different plumage colour populations.

1. Genetic variation in the chicken MC1R gene was analysed through bioinformatic methods after polymerase chain reaction (PCR) amplification and sequencing of the coding region of MC1R gene from 5 different populations with 4 plumage colours (black, grey plumage with black spots, yellow plumage with black spots, red). 2. A total of 11 novel variations were detected in Hebei chickens, of which 8 were non-synonymous. Allele distribution analysis showed that the wild-type e + (Brown Leghorn) allele was mainly found in Hy-Line Brown and Lohmann Brown, the dominant Extended black E(AY220304) allele was mainly found in Hebei chicken with black plumage, whereas the Buttercup (e bc) allele was rare. 3. Nucleotide diversity (π) within each colour strain of Hebei chickens (0·0047–0·0052) was significantly greater than that of Hy-Line Brown (0·0024) or Lohmann Brown (0·0043). 4. The results indicate that there is abundant polymorphism in the MC1R gene, especially in Hebei chicken, which was associated with its rich plumage colour diversity.

Bioinformatics Analysis of Lactoferrin Gene for Several Species

Much attention has been focused on the study of lactoferrin due to its function in antibacterial, antiviral, antifungal, anti-inflammatory, anti-oxidant, and immunomodulatory activities. A total of 60 lactoferrin (LF) gene sequences with the complete coding regions (CDS) and corresponding amino acids belonging to 11 species were analyzed, and the differentiation within and among the species was also studied. The results showed that most of the species have the stop codon TAA, with the variation of TGA for Mus musculus. The length of the LF gene with the complete CDS varies greatly, from 2,055 to 2,190 bp, due to deletion, insertion, and stop codon mutation resulting in elongation. Observed genetic diversity was higher among species than within species, and Sus scrofa had more polymorphisms than any other species. Novel amino acid variation sites were detected within several species (8 in Homo sapiens, 6 in Mus musculus, 6 in Capra hircus, 10 in Bos taurus, and 20 in Sus scrofa), which might be used to illustrate the functional variation. Differentiation of the LF gene was obvious among species, and the clustering result was consistent with the taxonomy in the National Center for Biotechnology Information.

Polymorphism of the PRNP gene in the main breeds of indigenous Chinese goats

The polymorphism of the PRNP gene plays a key role in susceptibility to prion disease. Scrapie is a neurodegenerative disease affecting sheep and goats and belongs to the group of prion diseases. We isolated DNA from 333 goat samples representing the main local goat breeds in six provinces in China to identify PRNP polymorphisms and to determine whether these breeds were at risk for developing scrapie. Two novel amino acid polymorphisms (R211G and T219I) and a novel silent mutation at codon 125 as well as nine previously reported polymorphisms were observed. Twenty-eight alleles and forty-nine different genotypes were obtained. The codon 142M associated with resistance of goat scrapie was not found in this study. The codon 143R was relatively rare. The codon 222K, a potentially useful candidate site for selecting for scrapie resistance, was also rare in indigenous Chinese goats. These results could provide some useful data for assessing the risk of scrapie in Chinese indigenous goats.

Sequencing of part of the goat agouti gene and SNP identification.

The agouti gene plays an important role in the synthesis and distribution of coat color in domestic animals. Most attention has been focused on the study of sequencing, identification of single nucleotide polymorphisms (SNPs), and association analysis with color variation in a number of animals as well as human beings (Voisey and van Daal 2002; Voisey et al. 2006; Rieder et al. 2001; Vage et al. 1997; Eizirik et al. 2003). Altogether, 10 color patterns have been observed and were postulated to be caused by 10 alleles at the agouti locus, with the allele for white or tan color dominant and the nine others codominant (Adalsteinsson et al. 1994). No more molecular data for the goat agouti gene have been obtained, but it has been shown to be located at 13q22 (Schibler et al. 1998). Earlier we sequenced intron 2 (AY291442) and exon 4 (DQ058664) of the goat agouti gene and found that allele T of 423G[T in DQ058664 might be responsible for the black phenotype or be linked with the causative site in goats (Tang et al. 2008). In this paper, other parts of the goat agouti gene have been sequenced and assembled (EF587236) and some SNPs have been identified in order to provide more useful information for further study of the association between variations and coat colors.

Genetic diversity of five goat breeds in China based on microsatellite markers

The genetic diversity of five goat breeds in China was surveyed using 15 microsatellites. The five goat breeds included Tangshan dairy goat (TSD), Liaoning cashmere goat (LNC), Nanjiang yellow goat (NJY), Chengde polled goat (CDP) and Leizhou black goat (LZB). The mean polymorphism information content value (PIC) of the populations ranged from 0.6606 to 0.8405. The mean heterozygosity (H) of the populations ranged from 0.7936 to 0.8202. The mean number of effective allele (Ne) of the populations ranged from 5.3373 to 5.8812 and the coefficient of genetic differentiation between breeds was 0.0620. It was suggested that the five goat populations have abundant genetic diversity and extensive genetic basis, with limited inbreeding, especially in Leizhou black goat. The unweighted pair-group method with arithmetic averages (UPGMA) dendrogram based on the Neis standard genetic distance indicated that Tangshan dairy goat, Chengde polled goat and Liaoning cashmere goat breeds / populations clustered together. The Nanjiang yellow goat and Leizhou black goat populations clustered together, consistent with the geographical distribution of goat breeds.

Genetic variation of major histocompatibility complex BLB2 gene exon 2 in Hebei domestic chicken.

Genetic variation of MHC BLB2 gene exon 2 in Hebei domestic chicken was investigated, after PCR and sequencing of a 374bp fragment (containing entire exon 2 (270bp) of BLB2 gene) in 76 individuals. The results showed that along this fragment, there were 69 variable sites, of which 18 were novel variations, and 82 estimated haplotypes with the diversity of 0.960. In Hebei domestic chicken, the nucleotide diversity (π), the average number of nucleotide differences (k), the average number of nucleotide diversity of synonymous substitution (π(s)) and non-synonymous substitution (π(a)) in BLB2 gene exon 2 were 0.098, 24.688, 0.075, and 0.106, respectively; nine non-synonymous substitutions was exclusively found in the peptide-binding sites (PBS) region of BLB2 gene exon 2, inferring that these unique substitutions might be helpful to resist some special bacteria and pathogens. The higher genetic diversity of MHC BLB2 gene exon 2 in Hebei domestic chicken might be consistent with its more robust disease resistance.

Sequence Analysis of the Lactoferrin Gene and Variation of g.7605C→T in 10 Chinese Indigenous Goat Breeds

Much attention has been focused on the study of lactoferrin at the protein or nucleotide level in mice, humans, and cattle, but little is known about it in goats. The goat LF gene from 5′ UTR to exon 17 was amplified, and the variation of g.7605C→T in 10 Chinese indigenous goat breeds was analyzed. Among the three ruminant species (cattle, sheep, and goats), the intron–exon distribution pattern was similar, and all the exons had the same length, but the length of introns varied greatly due to insertions or deletions. The frequency of allele T at g.7605C→T (50.12%) was a little higher than that of allele C (49.88%), and the genotype distribution differed greatly between goat populations. The g.7605C→T site showed higher genetic diversity in goat populations. The genetic differentiation was 0.0783, and gene flow was 2.9433 among the 10 Chinese indigenous goat populations.

Erratum to: Bioinformatics Analysis of Lactoferrin Gene for Several Species

Regarding the report in ‘‘Bioinformatics analysis of lactoferrin gene for several species’’ (J.-F. Kang, X.-L. Li, R.-Y. Zhou, L.-H. Li, F.-J. Feng, and X.-L. Guo, Biochemical Genetics 46, Nos. 5/6, June 2008) that Trp 8 is unique to cows, undergraduate Memori Otsuka and Dr. Justen Whittall of Santa Clara University have pointed out that Trp 8 is also found in the buffalo sequence. The authors have examined the data and agree with Otsuka and Whittall that the shared presence of Trp 8 in cow and buffalo (and likely several other closely related yet unsampled bovids) suggests that buffalo also produces lactoferrin proteins with antimicrobial activity. The authors therefore suggest that the sentence ‘‘By analyzing 15 amino acid residues within and among species, it was found that Trp 6 was conserved among all species except Camelus dromedarius (Phe6), and Trp 8 existed only in Bos taurus, which is why cow lactoferricin was more effective against microbes than the others,’’ appearing on page 318, be changed to ‘‘By analyzing 15 amino acid residues within and among species, it was found that Trp 6 was conserved among all species except Canis familiaris (Phe6), and Trp 8 existed only in Bos taurus and Bubalus bubalis, which is why cow lactoferricin was more effective against microbes than the others.’’