Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results

被引:0
作者
Ogunbawo, Adebisi R. [1 ]
Mulim, Henrique A. [1 ]
Campos, Gabriel S. [1 ]
Oliveira, Hinayah R. [1 ]
机构
[1] Purdue Univ, Dept Anim Sci, W Lafayette, IN 47907 USA
关键词
candidate genes; genomic region; over-representation; prioritization; QTL; ENRICHMENT ANALYSIS; DNA-DAMAGE; EXPRESSION; CATTLE; UBIQUITINATION; INTEGRATION; PROTEINS; SERVER;
D O I
10.3390/genes15091131
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of 8569 positional candidate genes were annotated for reproduction, 11,195 for carcass, 5239 for growth, and 3483 for morphological traits, and used in an over-representation analysis. The significant genes (adjusted p-values < 0.05) identified in the over-representation analysis underwent prioritization analyses, and enrichment analysis of the prioritized over-represented candidate genes was performed. The prioritized candidate genes were GFRA4, RFWD3, SERTAD2, KIZ, REM2, and ANKRD34B for reproduction; RFWD3, TMEM120A, MIEF2, FOXRED2, DUSP29, CARHSP1, OBI1, JOSD1, NOP58, and LOXL1-AS1 for the carcass; ANKRD34B and JOSD1 for growth traits; and no genes were prioritized for morphological traits. The functional analysis pinpointed the following genes: KIZ (plays a crucial role in spindle organization, which is essential in forming a robust mitotic centrosome), DUSP29 (involved in muscle cell differentiation), and JOSD1 (involved in protein deubiquitination, thereby improving growth). The enrichment of the functional candidate genes identified in this study highlights that these genes play an important role in the expression of reproduction, carcass, and growth traits in Nellore cattle.
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页数:19
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共 83 条
  • [1] STATISTICAL TEST FOR THE COMPARISON OF SAMPLES FROM MUTATIONAL SPECTRA
    ADAMS, WT
    SKOPEK, TR
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1987, 194 (03) : 391 - 396
  • [2] GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets
    Aguirre-Plans, Joaquim
    Pinero, Janet
    Sanz, Ferran
    Furlong, Laura, I
    Fernandez-Fuentes, Narcis
    Oliva, Baldo
    Guney, Emre
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2019, 431 (13) : 2477 - 2484
  • [3] Albuquerque L. G., 2017, Proceedings of the 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics (AAABG), Townsville, Queensland, Australia, 2-5 July 2017, P255
  • [4] Alliance of Genome Resources, 2022, Solute Carrier Family 27 Member 1 (SLC27A1)
  • [5] Alliance of Genome Resources, 2022, Dual Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2)
  • [6] Alliance of Genome Resources, 2022, Ankyrin Repeat Domain 34B (ANKRD34B)
  • [7] Alliance of Genome Resources, 2022, ORC Ubiquitin Ligase 1(OBI1)
  • [8] Alliance of Genome Resources, 2022, Josephin Domain Containing 1 (JOSD1)
  • [9] Alliance of Genome Resources, 2022, Synaptosome Associated Protein 47 (SNAP47)
  • [10] Alliance of Genome Resources, 2022, Calcium Regulated Heat Stable Protein 1 (CARHSP1)