Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep.
Ontology highlight
ABSTRACT:
SUBMITTER: Abousoliman I
PROVIDER: S-EPMC8228706 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The most common sheep breeds of Egypt are Ossimi, Rahmani, and Barki breeds. The latter one is well adapted to the challenging desert environment, characterized by food shortage and a high temperature fluctuation. Growth performance of Barki sheep has an important economic value in terms of minimizing the shortage of mutton meat in Egypt. Further, milk production is of great importance for feeding newborn lambs. Eight candidate genes, recently associated with production traits in different breeds, were used to study the effect of genotype on lamb growth and ewe milk traits. The examined genes were LEP, IGF1, DGAT1, STAT5A, PRL, CSN1S2, GHR, and GHRHR, of which one representative single nucleotide polymorphism (SNP) located in the coding region was selected for genotyping. Data from 251 Barki sheep were used in this study. Association analysis between SNPs and lamb growth traits identified rs420693815 of the LEP gene to be significantly associated with weaning weight and average daily gain. In ewes, significant effects on milk yield and composition have been estimated for LEP (rs420693815), STAT5A (rs161082816), PRL (rs422713690), and GHRHR (rs414991449). The results indicated that these genes might be considered as interesting candidates for further investigations to improve growth and milk performance in Barki sheep.
| S-EPMC7070871 | biostudies-literature
Project description:Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (FST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.
| S-EPMC8394750 | biostudies-literature
Project description:The Barki sheep industry is becoming increasingly important in Egypt because of the high quality of their meat and wool. This sheep breed is also commonly known for its resistance to arid and harsh environmental conditions. Such characteristics can be exploited in solving the problematic situation of inadequate animal protein for human consumption, particularly under climatic changes. However, very few studies have investigated aspects of breeding, nutrition, and susceptibility to infectious or non-infectious diseases in Barki sheep. Herein, we propose to unravel the differences in the clinical and biochemical profiles among Barki sheep of different growth rates. We measured clinical and biochemical parameters in stunted (n = 10; test group) and in good body condition (n = 9; control group) Barki sheep. Animals subjected to this experiment were of the same sex (female), age (12 months old), and housed in the same farm with similar conditions of feeding, management practice, and vaccination and deworming regimens. Regarding clinical examination, stunted/tested sheep showed a significantly higher pulse and respiratory rate compared to sheep with a good body condition/control group. The appetite, body temperature, and digestion processes were the same in both groups. In biochemical investigations, nutritional biomarkers were reduced markedly in stunted sheep compared with the control sheep, including total protein (p = 0.0445), albumin (p = 0.0087), cholesterol (p = 0.0007), and triglycerides (p = 0.0059). In addition, the Barki sheep test group suffered from higher levels of urea and blood urea nitrogen than the control group. Consistently, growth and thyroid hormone levels were lower in stunted sheep than the control sheep, although the differences were not statistically significant (p > 0.05). No significant differences were detected in both groups for serum levels of calcium, phosphorus, magnesium, iron, and zinc (p > 0.05). To detect the reasons for emaciation, certain debilitating infections were tested. All tested sheep showed negative coprological tests for gastrointestinal parasites, and had no obvious seropositivity to brucellosis, toxoplasmosis, neosporosis, or Q fever. This study demonstrates the useful biochemical markers for monitoring growth performance in Egyptian Barki sheep and unravels the usefulness of this breed in nationwide breeding and farming.
| S-EPMC10044517 | biostudies-literature
Project description:Insulin-like growth factor-1 gene (IGF-1) is considered as a major candidate gene for the economic traits of animal production. Polymorphism of 5' flanking region of IGF-1 gene in Barki sheep (n = 91) and its association with wool traits were studied using the polymerase chain reaction coupled with single-strand conformation polymorphism technique (PCR-SSCP), PCR-restriction fragment length polymorphism (PCR-RFLP), sequence analysis and different measurements of wool traits (clean fleece weight and fiber diameter). PCR-SSCP analysis revealed three different banding patterns corresponding with three genotypes frequencies GG (0.25), GA (0.58), AA (0.17). PCR-RFLP and corresponding sequence analysis revealed nucleotide transversion from Guanine (G) to Cytosine (C) at nucleotide position 85 and transition from (G) to Adenine (A) at position 87. This is the first study that recorded two SNPs within the 5' flanking region of IGF-1 gene in Egyptian Barki sheep, which were submitted to DNA Data Bank OF Japan (DDBJ) with Accession No. LC151463.1. The genotype GG showed positive significant association (P < 0.001) with clean fleece weight (CFW) trait (Odd Ratio = 2.83). By contrast, genotype AA had negative significant association (P < 0.05) with such trait (Odd Ratio = 0.15). On the other hand, fiber diameter (FD) measurements showed no significant association (P > 0.05) with different IGF-1 genotypes. This study adds evidence of the association between IGF-1 gene polymorphism and CFW of wool in Egyptian Barki sheep. Therefore; it is important to consider IGF-1 gene as a candidate gene marker for wool weight traits and it should be identified before using successful breeding program.
| S-EPMC6296639 | biostudies-literature
Project description:ObjectiveMilk production is one of the most desirable traits in livestock. Recently, the toll-like receptor (TLR) has been identified as a candidate gene for milk traits in cows. So far, there is no information concerning the contribution of this gene in milk traits in sheep. This study was designed to investigate the TLR 4 gene polymorphisms in Barki ewes in Egypt and then correlate that with milk traits in order to identify potential single nucleotide polymorphisms (SNPs) for these traits in sheep.MethodsA part of the ovine TLR 4 gene was amplified in Barki ewes, to identify the SNPs. Consequently; Barki ewes were genotyped using polymerase chain reaction-single strand conformation polymorphism protocol. These genotypes were correlated with milk traits, which were the daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP).ResultsAge and parity of the ewe had a significant effect (p<0.05 or p<0.01) on DMY, FP, and TSP. The direct sequencing identified a missense mutation located in the coding sequence of the gene (rs592076818; c.1710C>A) and was predicted to change the amino acid sequence of the resulted protein (p.Asn570Lys). The association analyses suggested a significant effect (p<0.05) of the TLR genotype on the FP and PP, while the DMY tended to be influenced as well (p = 0.07). Interestingly, the presence of the G allele tended to increase the DMY (+40.5 g/d) and significantly (p<0.05 or p<0.01) decreased the FP (-1.11%), PP (-1.21%), and TSP (-7.98%).ConclusionThe results of this study suggested the toll-like receptor 4 (TLR4) as a candidate gene to improve milk traits in sheep worldwide, which will enhance the ability to understand the genetic architecture of genes underlying SNPs that affect such traits.
| S-EPMC7961266 | biostudies-literature
Project description:Natural selection and domestication have shaped modern sheep populations into a vast range of phenotypically diverse breeds. Among these breeds, dairy sheep have a smaller population than meat sheep and wool sheep, and less research is performed on them, but the lactation mechanism in dairy sheep is critically important for improving animal-production methods. In this study, whole-genome sequences were generated from 10 sheep breeds, including 57 high-milk-yield sheep and 44 low-milk-yield sheep, to investigate the genetic signatures of milk production in dairy sheep, and 59,864,820 valid SNPs (Single Nucleotide Polymorphisms) were kept after quality control to perform population-genetic-structure analyses, gene-detection analyses, and gene-function-validation analyses. For the population-genetic-structure analyses, we carried out PCA (Principal Component Analysis), as well as neighbor-joining tree and structure analyses to classify different sheep populations. The sheep used in our study were well distributed in ten groups, with the high-milk-yield-group populations close to each other and the low-milk-yield-group populations showing similar classifications. To perform an exact signal-selection analysis, we used three different methods to find SNPs to perform gene-annotation analyses within the 995 common regions derived from the fixation index (FST), nucleotide diversity (Ɵπ), and heterozygosity rate (ZHp) results. In total, we found 553 genes that were located in these regions. These genes mainly participate in the protein-binding pathway and the nucleoplasm-interaction pathway, as revealed by the GO- and KEGG-function-enrichment analyses. After the gene selection and function analyses, we found that FCGR3A, CTSK, CTSS, ARNT, GHR, SLC29A4, ROR1, and TNRC18 were potentially related to sheep-milk-production traits. We chose the strongly selected genes, FCGR3A, CTSK, CTSS, and ARNT during the signal-selection analysis to perform a RT-qPCR (Reale time Quantitative Polymerase Chain Reaction) experiment to validate their expression-level relationship with milk production, and the results showed that FCGR3A has a significant negative relationship with sheep-milk production, while other three genes did not show any positive or negative relations. In this study, it was discovered and proven that the candidate gene FCGR3A potentially contributes to the milk production of dairy sheep and a basis was laid for the further study of the genetic mechanism underlying the strong milk-production traits of sheep.
| S-EPMC10215608 | biostudies-literature
Project description:Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
| S-EPMC6478285 | biostudies-literature
Project description:The importance and unique biological traits, as well as the growing financial value, of milk from small Greek ruminants is continuously attracting interest from both the scientific community and industry. In this regard the construction of a reference dataset of the milk of the Greek sheep breeds is of great interest. In order to obtain such a dataset we employed cutting-edge proteomics methodologies to investigate and characterize, the proteome of milk from the three indigenous Greek sheep breeds Mpoutsko, Karagouniko and Chios. In total, more than 1300 protein groups were identified in milk whey from these breeds, reporting for the first time the most detailed proteome dataset of this precious biological material. The present results are further discussed in the research paper "Milk of Greek sheep and goat breeds; characterization by means of proteomics" (Anagnostopoulos et al. 2016) [1].
| S-EPMC4957575 | biostudies-literature
Project description:Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.
| S-EPMC5430420 | biostudies-literature
Project description:Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the genetic mechanisms underlying the phenotypic differences among Chinese indigenous sheep with tails of three different types, we used ovine high-density 600K SNP arrays to detect genome-wide copy number variation (CNV). In large-tailed Han sheep, Altay sheep, and Tibetan sheep, 371, 301, and 66 CNV regions (CNVRs) with lengths of 71.35?Mb, 51.65?Mb, and 10.56?Mb, respectively, were identified on autosomal chromosomes. Ten CNVRs were randomly chosen for confirmation, of which eight were successfully validated. The detected CNVRs harboured 3130 genes, including genes associated with fat deposition, such as PPARA, RXRA, KLF11, ADD1, FASN, PPP1CA, PDGFA, and PEX6. Moreover, multilevel bioinformatics analyses of the detected candidate genes were significantly enriched for involvement in fat deposition, GTPase regulator, and peptide receptor activities. This is the first high-resolution sheep CNV map for Chinese indigenous sheep breeds with three types of tails. Our results provide valuable information that will support investigations of genomic structural variation underlying traits of interest in sheep.
| S-EPMC4901276 | biostudies-literature