Genetic basis investigation of wattle phenotype in goat using genome-wide sequence data.

In domestic goats, wattles often appear in even numbers, mostly on the neck and a few under the ear. Goat wattle is composed of ectopic cartilage tissue covered by skin and was reported as a dominant inheritance. Thirty-eight goats from two Southwest Chinese breeds were studied to elucidate the genetic basis of wattle phenotype in goat. Their genomes were sequenced for wide-genome selective sweep analysis (WGSA) and a genome-wide association study (GWAS). The WGSA results revealed 500 candidate genes identified by fixation index and π ratio and 261 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with 195 genes and 38 significantly enriched KEGG items. In particular, three chondrogenesis-related pathways (Wnt, Hippo and MAPK signaling pathways) were found. Among the 500 genes, 474 were enriched to 2855 Gene Ontology items, and four (BMP2, BMP4, RARA and MSX1) were annotated in the regulation and development of chondrogenesis. Four chondrogenesis-related genes (GREM1, NEDD4, ATG7 and ITGA1) were identified from 519 single-nucleotide polymorphisms (SNPs) with a GWAS above the threshold. Six and 11 SNPs on chromosome 10 are located on GREM1 and NEDD4 respectively, and the highest numbers of SNPs on chromosomes 20 and 22 are located on ITGA1 and ATG7 respectively. All of these genes are related to cartilage development. This study identified a series of genes related to chondroplasia by GWAS and WGSA and presented the possibility that wattle inheritance may be influenced by multiple genes. This work provides a new theoretical understanding of the hereditary basis of wattle phenotype.

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA.

The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.

[Animal gene pyramiding in cross populations].

Gene pyramiding aims at producing individuals with one superior economic trait according to the optimal breeding scheme involving selection of favorable target alleles or linked markers after crossing basal populations and pyramiding them into a single individual. In consideration of animal traditional cross program along with the features of animal segregating population, four types of cross programs and two types of selection strategies for gene pyramiding are performed from practice perspective of view, two population cross for pyramiding two genes (denoted II), three populations cascading cross for pyramiding three genes (denoted III), four population symmetrical (denoted IV-S) and cascading cross for pyramiding four genes (denoted IV-C), and various schemes (denoted cross program-A-E) were designed for each cross program with different levels of initial favorable allele frequencies, basal population sizes, and trait heritabilities. The process of gene pyramiding for various schemes were simulated and compared based on the population hamming distance, average superior genotype frequencies, and average phenotypic values. By simulation, the results showed that larger base population size and higher initial favorite allele frequency resulted in higher efficiency of gene pyramiding. The order of parent crossing was shown to be the most important factor in cascading cross, but had no significant influence on the symmetric cross. The results also showed that genotypic selection strategy was superior to phenotypic selection in accelerating gene pyramiding. The method and corresponding software would be used to compare different cross schemes and selection strategies. Moreover, our study would help to build the optimal gene pyramiding simulation platform.

[Relationship between microsatellite DNA polymorphism and hind-quarter development in sheep chromosome 18].

Ten highly polymorphic microsatellite loci possibly linked to or correlated with the Callipyge gene were selected, according to the genetic map and linkage map of sheep chromosome 18. They were ILSTS54, TGLA337, HH47, TGLA122, BP33, OB2, BM3413, MCM38, MCMA26 and CSSM18. Polymorphisms of these microsatellites were detected in 61 Dorset (male) x Xinjiang fine wool sheep (female) samples and 76 Suffolk (male) x Xinjiang fine wool sheep (female) samples. Results showed that the number of alleles for the 10 microsatellite loci, heterozygosity and PIC (polymorphism information content) in the Dorset population were 8-16, 0.8370-0.9252, and 0.8221-0.9167, respectively. The same parameters in the Suffolk population were 5-10, 0.7603-0.8913 and 0.7176-0.8809, respectively. The effect of these loci on hindquarter width was analyzed in a generalized linear model. Results showed that, in the Dorset group, BM3413, MCMA26 and CSSM18 each had a significant effect on hindquarter width (P<0.05), while the other seven loci had no effect on it (P>0.05). In the Suffolk group, TGLA122, BM3413, MCM38 and CSSM18 had a significant effect on hindquarter width (P<0.05), while the other six loci did not (P>0.05). Our results also indicated that the cause of hindquarters hypertrophy in Xinjiang meat sheep may be different from the A-to-G mutation between the region of DLK1 and GTL2 . There may be other genes or QTL (quantitative trait loci) that affect hindquarter muscle development on chromosome 18 in Xinjiang meat sheep.

[Polymorphism analysis of genes associated with hindquarters muscular development on chromosome 18 in Xinjiang meat sheep].

Through polymorphism analysis of genes associated with hindquarters development on chromosome 18 in Xinjiang meat sheep, we sought genes that are associated with increased hindquarters musculature in the hope to provide theoretical guidance to molecular marker-assisted selection of meat sheep. The polymorphism of Callipyge (CLPG) gene was analyzed by PCR-SSCP and PCR-RFLP in populations of Dorset and Suffolk breeds and their F1 and F2 crosses with local Xinjiang Fine Wool sheep. Results showed that there was no PCR-RFLP polymorphism at 103849 bp in the region between DLK1 and GTL2 on chromosome 18, which suggested that hindquarters over-development was not controlled by the callipyge gene (CLPG) in Xinjiang meat sheep group. In addition, single nucleotide polymorphisms (SNPs) were detected at the Meg3.9 locus on chromosome 18 by PCR-SSCP. Based on the polymorphism, three genotypes AA, AB and AC could be discerned in this locus, with AA being the major one. The relationship between the genotypes and hindquarters hypertrophy was also investigated in the same group. Results indicated that the AC genotype had a significant impact on the hindquarters hypertrophy while the other two were not related to the muscling trait. In F1 crosses between Dorset and local fine wool sheep breeds, there was a significant difference in carcass weight and slaughter rate between the AC genotype and the other two genotypes (P<0.05), but there was not significant difference in the monthly live weight among the three genotypes (P<0.05). Based on the above, we found the muscling trait did not result from the mutation in at the 9571-268.3 site of the CLPG locus. Thus it may be under the influence of other genes or multiple linked QTL.

The developmental changes and effect on IMF content of H-FABP and PPARgamma mRNA expression in sheep muscle.

Male Kazak sheep and Xinjiang fine wool sheep of different ages were selected to investigate the developmental changes and effect on intramuscular fat (IMF) content of heart fatty acid-binding protein (H-FABP) and peroxisome proliferator-activated receptor gamma (PPARgamma) mRNA expression in muscle. Longissimus dorsal muscle was sampled to measure IMF content; and total RNA was extracted to determine H-FABP and PPARgamma mRNA expression levels by real-time PCR. The results showed that: (1) The IMF content increased continuously with growing and showed significant differences (P<0.05) between ages in male Kazak sheep, but no such differences (P>0.05) existed in Xinjiang fine wool sheep. Furthermore, the IMF content in Kazak sheep was very much higher (P<0.01) than that of the other breed from day 30 to 90; (2) H-FABP mRNA expression level was the highest on day 2 and showed significant differences (P<0.05) between ages in male Kazak sheep as well as in Xinjiang fine wool sheep. In the former breed, the expression reached the lowest point at day 30, and then rose continuously. But in the latter breed, it declined continuously from day 2 to 90, and then increased; (3) Significant differences (P<0.05) of PPARgamma mRNA expression between ages occurred in both breeds. In male Kazak sheep, PPARgamma mRNA expression declined from day 2 to 90, while in the other breed it increased continuously from day 2 to 60, but reached the lowest level at day 90, then increased; (4) In male Kazak sheep, the mRNA expression level of H-FABP was highly positively correlated (r=0.737, P<0.01) with IMF content from day 30 to 90, but that of PPARgamma was highly negatively correlated (r=-0.835, P<0.01) with IMF content from day 2 to 90.