Genetics and Breeding

A cDNA library from white alpaca (Vicugna pacos) skin was constructed using SMART technology to investigate the global gene expression profile in alpaca skin and identify genes associated with physiology of alpaca skin and pigmentation. A total of 5359 high-quality EST (expressed sequence tag) sequences were generated by sequencing random cDNA clones from the library. Clustering analysis of sequences revealed a total of 3504 unique sequences including 739 contigs (assembled from 2594 ESTs) and 2765 singletons. BLAST analysis against GenBank nr database resulted in 1287 significant hits (E-value < 10−10), of which 863 were annotated through gene ontology analysis. Transcripts for genes related to fleece quality, growth and coat color (e.g. collagen types I and III, troponin C2 and secreted protein acidic and rich in cysteine) were abundantly present in the library. Other genes, such as keratin family genes known to be involved in melanosome protein production, were also identified in the library. Members (KRT10, 14 and 15) of this gene family are evolutionarily conserved as revealed by a cross-species comparative analysis. This collection of ESTs provides a valuable resource for future research to understand the network of gene expression linked to physiology of alpaca skin and development of pigmentation. more »

Melanin plays important roles in the formation of animal hair color, the members of TYR gene family participate in the synthesis of melanin. For exploring the relationship between gene expression of alpaca TYR gene family and alpaca's coat color, the relative expression quantity of TYR,TRP1,TRP2 in alpaca of different colors were analyzed by using real-time quantitative PCR in this research. Results showed that the relative expression quantity of TYR,TRP1,TRP2 in Brown alpaca respectively were 13.669,3.417,8.593 times than that in White alpaca, all results were corrected by the household gene. The findings indicated that gene expression level of TYR gene family in Brown alpaca were higher than that in White alpaca, and the gene expression level of TYR gene family were related with phenotype of alpacas' coat color. more »

Gene expression analysis can aid in prioritising regions or classes of variants for genomic prediction and they increase our understanding of quantitative traits. The number of reads from RNA sequencing that align to a gene can be used to quantify gene expression. We sampled liver and muscle tissues of 150 lambs at slaughter. Their dams had been managed to high, medium, and low body condition scores (BCS) during mid-to-late pregnancy and the lambs were fed three different finishing diets. Differential expression of genes (DEG) was investigated contrasting tissue, BCS, lamb diets, other treatment differences, as well as high and low lamb carcass eye muscle width (CEMW). A large number of DEG were identified between tissues, but only the low versus high BCS comparison resulted in DEG for treatments. DEG were also found when we contrasted high and low CEMW. A strong trend toward down regulation was observed in all tests, except in BCS where all DEG were overexpressed in fatter ewes. more »