DOI: 10.5281/zenodo.8146756
title: Database of NGS results of PPARG gene of intensive fattening of sheep breeds raised in Latvia in 2022 within the framework of project of the Latvian Council of Science LZP-2021/1-0489 project

description: 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 Feed efficiency 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 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.


Peroxisomes are cytoplasmic organelles having important roles in modulating lipid homeostasis in mammals. The receptors found on peroxisomes were initially identified as the master regulators of adipose cell development, but are also involved with other cellular events such as inflammation, cell growth and steroidogenesis. The peroxisome proliferator-activated receptor gamma (PPARG, also called NR1C3) is a nuclear receptor of the peroxisome proliferator-activated receptor family (PPAR). PPARs are involved in the regulation of apoptosis, cell cycle, estradiol and progesterone synthesis, and metabolism. The PPARG, a nuclear receptor of the PPAR family, is activated after binding to natural ligands such as polyunsaturated fatty acids (PUFAs) and prostaglandin metabolites.


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.


Exons (6) of the PPARG gene and their flanking intron regions were sequenced using Illumina NGS technology (AmpliSeq). The PPARG gene has been sequenced in lambs of Latvia (in sheep research in Latvia) for the first time.


Information about 31 loci were found compering with the last reference sequences ARS_UI_Ramb_v2.0. Seven (7) loci form two groups with complete linkage disequilibrium between polymorphisms. Two 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.