NDLI: Genome-wide association studies and functional annotation of pre-weaning calf mortality and reproductive traits in Nellore cattle from experimental selection lines

Content Provider	Springer Nature : BioMed Central
Author	Rodrigues, Gustavo R. D. Brito, Luiz F. Mota, Lúcio F. M. Cyrillo, Joslaine N. S. G. Valente, Júlia P. S. Benfica, Lorena F. Silva Neto, João B. Borges, Marcelo S. Monteiro, Fábio M. Faro, Lenira El Albuquerque, Lucia G. Mercadante, Maria E. Z.
Abstract	Reproductive efficiency is crucial for the long-term economic sustainability of beef cattle production. Pregnancy loss and stillbirth are complex reproductive traits that do not yet have their genomic background fully understood, especially in zebu breeds (Bos taurus indicus). Hence, this study aimed to perform a genome-wide association study (GWAS) and functional annotation for conception success (CS), pregnancy loss (PL), stillbirth (SB), and pre-weaning calf mortality (PWM) in Nellore cattle. In this study, 3,728 cows with 17,094 reproductive records and 11,785 calves were evaluated. A total of 3,351 genotyped animals and 383,739 SNP markers were considered for GWAS analyses. SNP effects were estimated using the weighted single-step GWAS (WssGWAS), which considered two iterations. The top ten genomic windows with the highest contribution to the additive genetic variance of the traits were selected for gene annotation. Candidate genes were then analyzed for Gene Ontology terms (GO) and metabolic pathways. The top ten genomic windows that explained the largest proportion of the direct additive genetic variance ( $\:{{\sigma\:}}_{\text{a}}^{2}$ ) for CS, PL, SB, and PWM accounted for 17.03% (overlapping with 79 genes), 16.76% (57 genes), 11.71% (73 genes), and 12.03% (65 genes) of the total $\:{{\sigma\:}}_{\text{a}}^{2}$ , respectively. For CS, significant GO terms included Somitogenesis (GO:0001756), Somite Development (GO:0061053), and Chromosome Segregation (GO:0007059). Considering PL, the processes annotated were the Regulation of Hormone Secretion (GO:0046883), and Hormone Transport (GO:0009914), along with the Glucagon Signaling Pathway (bta04922). Embryonic Development (GO:0045995), and Cerebellum Development (GO:0021549) were the main biological processes found in the gene enrichment analysis for SB. For PWM, the Regulation of Glucose metabolic processes (GO:0010906), Zinc Ion Homeostasis (GO:0055069), Lactation (GO:0007595), and Regulation of Insulin Secretion (GO:0050796) were the most significant GO terms observed. These findings provide valuable information on genomic regions, candidate genes, biological processes, and metabolic pathways that may significantly influence the expression of complex reproductive traits in Nellore cattle, offering potential contributions to breeding strategies and future genomic selection strategies.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-11113-4.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-11113-4
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-12-18
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Beef cattle Pregnancy loss Reproduction Single nucleotide polymorphism Stillbirth
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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