Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep.
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ABSTRACT:
SUBMITTER: Zlobin AS
PROVIDER: S-EPMC8002146 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundVariants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles.ResultsWhereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles.ConclusionsWe detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
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Project description:The aim of the present research was to analyze the variability of 45 SNPs from different genes involved in metabolism and innate immunity to perform an association analysis with the milk yield, composition and milk coagulation traits. A population of 1112 Sarda breed sheep was sampled. Genotyping was generated by a TaqMan Open ArrayTM. Thirty out of the 45 SNPs were polymorphic, and 12 displayed a minor allele frequency higher than 0.05. An association analysis showed that the variability at genes PRKAG3 and CD14 was significantly associated with the daily milk yield. The variability at PRKAG3 was also associated with the protein and casein content, somatic cell score and bacterial score. The variation at the PRKAA2 gene was associated with the milk lactose concentration. The SNPs at CD14 were also associated with the traditional milk coagulation properties, while the SNPs at GHR and GHRHR were associated with kSR, a derived coagulation parameter related to the rate of syneresis. The information provided here is new and increases our knowledge of genotype-phenotype interactions in sheep. Our findings might be useful in appropriate breeding schemes to be set up for the Sarda sheep breed, but these should be confirmed by further studies, possibly performed on independent populations.
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Project description:BackgroundGrowth and meat production traits are significant economic traits in sheep. The aim of the study is to identify candidate genes affecting growth and meat production traits at genome level with high throughput single nucleotide polymorphisms (SNP) genotyping technologies.Methodology and resultsUsing Illumina OvineSNP50 BeadChip, we performed a GWA study in 329 purebred sheep for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers, chest girth, and shin circumference). After quality control, 319 sheep and 48,198 SNPs were analyzed by TASSEL program in a mixed linear model (MLM). 36 significant SNPs were identified for 7 traits, and 10 of them reached genome-wise significance level for post-weaning gain. Gene annotation was implemented with the latest sheep genome Ovis_aries_v3.1 (released October 2012). More than one-third SNPs (14 out of 36) were located within ovine genes, others were located close to ovine genes (878bp-398,165bp apart). The strongest new finding is 5 genes were thought to be the most crucial candidate genes associated with post-weaning gain: s58995.1 was located within the ovine genes MEF2B and RFXANK, OAR3_84073899.1, OAR3_115712045.1 and OAR9_91721507.1 were located within CAMKMT, TRHDE, and RIPK2 respectively. GRM1, POL, MBD5, UBR2, RPL7 and SMC2 were thought to be the important candidate genes affecting post-weaning gain too. Additionally, 25 genes at chromosome-wise significance level were also forecasted to be the promising genes that influencing sheep growth and meat production traits.ConclusionsThe results will contribute to the similar studies and facilitate the potential utilization of genes involved in growth and meat production traits in sheep in future.
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