Pedigree reconstruction and population structure using SNP markers in Gir cattle

• Published in: Journal of applied genetics Vol. 64; no. 2; pp. 329 - 340
• Main Authors: Garcia, Arielly Oliveira, Otto, Pamela Itajara, Glatzl Junior, Luiz Afonso, Rocha, Renata de Fátima Bretanha, dos Santos, Mateus Guimarães, de Oliveira, Daniele Alves, da Silva, Marcos Vinicius Gualberto Barbosa, Panetto, João Cláudio do Carmo, Machado, Marco Antônio, Verneque, Rui da Silva, Guimarães, Simone Eliza Facioni
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.05.2023; Springer; Springer Nature B.V
• Subjects: Analysis; Animal Genetics and Genomics; Animal Genetics • Original Paper; Animals; Biomedical and Life Sciences; Biotechnology industry; Cattle; Coefficients; Female; Genetic variability; Genomic analysis; Genomics; Genotype; Genotypes; Homozygosity; Homozygote; Human Genetics; Inbreeding; Life Sciences; Likelihood ratio; Linkage disequilibrium; Male; Microbial Genetics and Genomics; Pedigree; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; Population number; Population structure; Reconstruction; Single-nucleotide polymorphism; Brazil; Canada; Austria; United States; Runs of homozygosity; Inbreeding; Parentage; Linkage disequilibrium; Relationship
• ISSN: 1234-1983; 2190-3883
• DOI: 10.1007/s13353-023-00747-x

Our objective was to establish a SNPs panel for pedigree reconstruction using microarrays of different densities and evaluate the genomic relationship coefficient of the inferred pedigree, in addition to analyzing the population structure based on genomic analyses in Gir cattle. For parentage analysis and genomic relationship, 16,205 genotyped Gir animals (14,458 females and 1747 males) and 1810 common markers to the four SNP microarrays were used. For population structure analyses, including linkage disequilibrium, effective population size, and runs of homozygosity (ROH), genotypes from 21,656 animals were imputed. Likelihood ratio (LR) approach was used to reconstruct the pedigree, deepening the pedigree and showing it is well established in terms of recent information. Coefficients for each relationship category of the inferred pedigree were adequate. Linkage disequilibrium showed rapid decay. We detected a decrease in the effective population size over the last 50 generations, with the average generation interval around 9.08 years. Higher ROH-based inbreeding coefficient in a class of short ROH segments, with moderate to high values, was also detected, suggesting bottlenecks in the Gir genome. Breeding strategies to minimize inbreeding and avoid massive use of few proven sires with high genetic value are suggested to maintain genetic variability in future generations. In addition, we recommend reducing the generation interval to maximize genetic progress and increase effective population size.