Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Gathering and Editing
2.2. Trait Groups
- Reproduction traits: scrotal circumference, age at puberty, early pregnancy, early puberty, precocity, age at first calving, heifer rebreeding, number of calving, testicular hypoplasia, gestation length, preweaning calf mortality rate, antral follicle count, stayability, anti-Müllerian hormone, gestation length, calving interval, calving ease, and post-natal mortality.
- 1.a.
- Subgroup: Sexual precocityIncluded traits: scrotal circumference, early pregnancy, early puberty, age at first calving, antral follicle count, calving interval, and calving ease.
- Carcass traits: backfat thickness, rib eye area, rump fat thickness, hot carcass weight, subcutaneous fat thickness, intramuscular fat content, longissimus muscle area, marbling, tenderness, shear force tenderness, and meat color.
- 2.a.
- Subgroup: Meat qualityIncluded traits: marbling, tenderness, shear force tenderness, and meat color.
- Growth-related traits: residual body weight gain, average daily gain, accumulated productivity, birth weight, weaning weight, yearling weight, adult cow weight, weight gain from birth to weaning, weight gain from weaning to yearling, yearling height, residual feed intake, dry matter intake, feed efficiency, and feed conversion ratio.
- 3.a.
- Subgroup: EfficiencyIncluded traits: residual feed intake, dry matter intake, feed efficiency, and feed conversion ratio.
- Morphological traits: body conformation, muscularity, precocity, feet and leg deformation, and feet and leg conformation.
- 4.a.
- Subgroup: Visual scoresIncluded traits: conformation, precocity, and muscling.
2.3. Over-Representation and Prioritization Analyses
- Reproduction and sexual precocity traits: “Fertility”, “implantation”, “preimplantation”, “endometrium”, “embryonic development”, “primordial follicles”, “uterus”, “luteal”, “gestation”, “embryo”, “ovulation”, “estrogen”, “estradiol”, “endocrine hormone”, “gamete, mammary glands”, “lactation”, “pregnancy”, “oocyte”, “fetus”, “zygote”, “ovary”, “amniotic”, “cervical mucosa follicle”, “Gonad”, “antral follicles”, “pre-eclampsia”, “placenta”, “testes”, “sperm”, “scrotal circumference”, “scrotal, testicular”, “testis”, “semen”, “spermatozoa”, “spermatogenesis”, “testicular hypoplasia”, and “hypogonadism”.
- Carcass and meat quality traits: “Longissimus muscle”, “Backfat thickness”, “Myosin”, “Actin”, “Fibroblast”, “Tissue deposition”, “Fat deposition”, “Muscle, Subcutaneous fat”, “Biceps femoris”, “Carcass weight”, and “Skeletal muscle”.
- Morphological and visual score traits: “body development”, “muscle mass”, “skeletal muscle”, “subcutaneous fat”, “conformational structure”, “adipose tissue”, “body depth”, “feet and leg”, “foot angle”, “tendon”, “joints”, “mobility aplomb”, “osteogenic differentiation”, “articular cartilage”, and “fat deposition”.
- Growth-related and efficiency traits: “body weight”, “birth weight”, “adult weight”, “weight gain”, “body size”, “average daily gain”, “body weight gain”, “daily gain”, “stature”, “growth”, “adipose tissue”, “dry matter intake”, “metabolism”, “maternal behavior”, “maternal ability”, “feed conversion”, “feed efficiency”, “dry matter”, “milk composition”, and “muscle development”.
2.4. Functional Analysis
2.5. Venn Diagrams and Gene Network Integration
3. Results and Discussion
3.1. Gene Annotation and Prioritization Analysis
3.2. Enrichment and Gene Integration Analysis of the Functional Candidate Genes Identified within Groups
3.2.1. Reproduction and Sexual Precocity Traits
3.2.2. Carcass and Meat Quality Traits
3.2.3. Growth-Related and Efficiency Traits
3.2.4. Morphological and Visual Score Traits
3.3. Genes Shared among Groups
3.3.1. Over-Represented Genes
3.3.2. Prioritized Genes
3.4. Genes Shared between Groups and Subgroups
4. Limitations of This Study and Future Directions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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1 Trait Groups | Studies | Genomic Regions | Candidate Genes |
---|---|---|---|
Reproduction | 23 | 605 | 8569 |
Sexual precocity | 19 | 387 | 5412 |
Carcass | 14 | 607 | 11,195 |
Meat quality | 8 | 294 | 6646 |
Growth | 12 | 360 | 5239 |
Efficiency | 7 | 217 | 3319 |
Morphological | 5 | 189 | 3483 |
Visual scores | 3 | 132 | 2114 |
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Ogunbawo, A.R.; Mulim, H.A.; Campos, G.S.; Oliveira, H.R. Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results. Genes 2024, 15, 1131. https://doi.org/10.3390/genes15091131
Ogunbawo AR, Mulim HA, Campos GS, Oliveira HR. Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results. Genes. 2024; 15(9):1131. https://doi.org/10.3390/genes15091131
Chicago/Turabian StyleOgunbawo, Adebisi R., Henrique A. Mulim, Gabriel S. Campos, and Hinayah R. Oliveira. 2024. "Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results" Genes 15, no. 9: 1131. https://doi.org/10.3390/genes15091131