Signatures of selection in Nelore cattle revealed by whole-genome sequencing data

Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2022-03, Vol.114 (2), p.110304-110304, Article 110304
Main Authors: Maiorano, Amanda Marchi, Cardoso, Diercles Francisco, Carvalheiro, Roberto, Júnior, Gerardo Alves Fernandes, de Albuquerque, Lúcia Galvão, de Oliveira, Henrique Nunes
Format: Article
Language:English
Subjects:
Adaptation
Allele frequency
Alleles
Animals
Bos indicus
Cattle - genetics
Genomics
Haplotypes
Nerve Tissue Proteins - genetics
Polymorphism, Single Nucleotide
Receptors, Immunologic - genetics
Selective signatures
Whole Genome Sequencing
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Summary:Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2022.110304