Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis
Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-07-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.710613/full |
| _version_ | 1818651659918639104 |
|---|---|
| author | Seyed Mehdi Esmaeili-Fard Mohsen Gholizadeh Seyed Hasan Hafezian Rostam Abdollahi-Arpanahi |
| author_facet | Seyed Mehdi Esmaeili-Fard Mohsen Gholizadeh Seyed Hasan Hafezian Rostam Abdollahi-Arpanahi |
| author_sort | Seyed Mehdi Esmaeili-Fard |
| collection | DOAJ |
| description | Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin. |
| first_indexed | 2024-12-17T02:09:38Z |
| format | Article |
| id | doaj.art-476031c26e7647d9818389156ca42adc |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-17T02:09:38Z |
| publishDate | 2021-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-476031c26e7647d9818389156ca42adc2022-12-21T22:07:36ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-07-011210.3389/fgene.2021.710613710613Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment AnalysisSeyed Mehdi Esmaeili-Fard0Mohsen Gholizadeh1Seyed Hasan Hafezian2Rostam Abdollahi-Arpanahi3Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, IranDepartment of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, IranDepartment of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, IranDepartment of Animal and Dairy Science, University of Georgia, Athens, GA, United StatesEwe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.https://www.frontiersin.org/articles/10.3389/fgene.2021.710613/fullmaternal genesmaternal pathwaysGWASgene-set analysisewe productivity |
| spellingShingle | Seyed Mehdi Esmaeili-Fard Mohsen Gholizadeh Seyed Hasan Hafezian Rostam Abdollahi-Arpanahi Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis Frontiers in Genetics maternal genes maternal pathways GWAS gene-set analysis ewe productivity |
| title | Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis |
| title_full | Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis |
| title_fullStr | Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis |
| title_full_unstemmed | Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis |
| title_short | Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis |
| title_sort | genes and pathways affecting sheep productivity traits genetic parameters genome wide association mapping and pathway enrichment analysis |
| topic | maternal genes maternal pathways GWAS gene-set analysis ewe productivity |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.710613/full |
| work_keys_str_mv | AT seyedmehdiesmaeilifard genesandpathwaysaffectingsheepproductivitytraitsgeneticparametersgenomewideassociationmappingandpathwayenrichmentanalysis AT mohsengholizadeh genesandpathwaysaffectingsheepproductivitytraitsgeneticparametersgenomewideassociationmappingandpathwayenrichmentanalysis AT seyedhasanhafezian genesandpathwaysaffectingsheepproductivitytraitsgeneticparametersgenomewideassociationmappingandpathwayenrichmentanalysis AT rostamabdollahiarpanahi genesandpathwaysaffectingsheepproductivitytraitsgeneticparametersgenomewideassociationmappingandpathwayenrichmentanalysis |