Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle

• Published in: Theriogenology 2024-04, Vol.218, p.214-222
• Main Authors: Dias, Mayra Silva, Pedrosa, Victor Breno, Rocha da Cruz, Valdecy Aparecida, Silva, Marcio Ribeiro, Batista Pinto, Luis Fernando
• Format: Article
• Language: English
• Subjects: Cattle; Genes; Heritability; Reproduction; SNPs; Zebu
• ISSN: 0093-691X; 1879-3231
• DOI: 10.1016/j.theriogenology.2024.01.034

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270–730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle. •This is the first GWAS analysis for the calving interval in a Zebu cattle breed.•GWAS analysis found 20 SNPs associated with calving interval.•36 protein-coding genes were found near the SNPs associated with calving interval.•Various significant SNPs are in regions where 70 QTLs were previously reported.•Various significant SNPs are in signature selection reported for cattle.