Database of NGS results of UPC3 gene of intensive fattening lambs of sheep breeds raised in Latvia in 2022 within the framework of project of the Latvian Council of Science LZP-2021/1-0489 project

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming.”

The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent Feed efficiency status in a training population of lambs when fed the same diet.

Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs.

About the project:

The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two largest components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least amount of feed intake) is a key factor in the sheep industry. Improving FE reduces production costs. Improving Feed efficiency by 5% can bring economic benefits that are up to four times higher than a 5% increase in average daily gain (ADG).

Traditionally, meat breeding programs have focused on outputs, due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program, as well as, according to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyze animal-to-animal variation in live lambs could be used as a cost-effective and rapid tool for genetic selection or management decisions.

As with other complex traits (also referred to as quantitative or polygenic traits), Feed efficiency is controlled by many genes which are involved in several molecular mechanisms and pathways causing animal-to-animal genetic variation in different biological functions. GWAS results suggested genes impacting lipid and energy metabolism as markers of Feed efficiency. Detection of many variants in these genes is necessary to predict or identify efficient animals accurately.

It is also known that genetic factors can also influence the regulation of energy metabolism, body composition and determination of excess weight. Among the genes evolved in these pathways is uncoupling protein 3 (UCP3). Uncoupling protein (UCP) abundance increases at birth in the lung and adipose tissue, then gradually decline, an adaptation that is important in enabling normal tissue function.  The UCP3 gene plays an important role as a mediator in adaptive thermogenesis, in the regulation of mitochondrial fatty acid oxidation and in the prevention of oxidative damage produced by free radicals. It is also known that this gene is involved in the regulation of energy metabolism and control of body weight. Moreover, some studies showed that UCP3 may modulate the use of lipids and glucose as an energy substrate after weight loss, suggesting possible actions in insulin resistance.

About the data of the project:

LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.

Full UCP3 gene (7 exons) were sequenced using Illumina NGS technology (AmpliSeq). The UCP3 gene has been sequenced in lambs of Latvia (in sheep research in Latvia) for the first time.

Information about 137 loci was found compared with the last reference sequences ARS_UI_Ramb_v2.0. Eighty-three (40) loci form ten groups with complete linkage disequilibrium between polymorphisms. Fifteen new SNP (without ID number) were found.

The database contains information on each locus for each lamb and the distribution of alleles and genotypes for each locus across all 76 samples. The data will be used in (1) analysis of Latvian sheep and (2) analysis of association with feed efficiency.

The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.