Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design

Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify QTL related to e...

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Published in:Journal of dairy science Vol. 107; no. 6; pp. 3794 - 3801
Main Authors: Rocha, R.F.B., Garcia, A.O., dos Santos, M.G., Otto, P.I., da Silva, M.V.B., Martins, M.F., Machado, M.A., Panetto, J.C.C., Calus, M.P.L., Guimarães, S.E.F.
Format: Journal Article
Language:English
Published: United States Elsevier Inc 01-06-2024
Subjects:
Animals
bovine
Breeding
Cattle - genetics
family analysis
Female
Genome
Genome-Wide Association Study - veterinary
Genomics
Genotype
Male
Oocytes
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
reproductive traits
Zebu dairy cattle
bovine
family analysis
reproductive traits
Zebu dairy cattle
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Summary:The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify QTL related to economic traits. The aim of this study was to identify genomic regions inherited by Gir sire families and genes associated with number of viable oocytes (VO), total number of oocytes (TO), and number of embryos (EMBR) based on a daughter design approach. In total, 15 Gir sire families were selected. The number of daughters per family ranged from 26 to 395, which were genotyped with different SNP panels and imputed to the Illumina BovineHD BeadChip (777K) and had phenotypes for oocyte and embryo production. Daughters had phenotypic data for VO, TO, and EMBR. The search for QTL was performed through GWAS based on GBLUP. The QTL were found for each trait among and within families based on the top 10 genomic windows with the greatest genetic variance. For EMBR, genomic windows identified among families were located on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16, and BTA17, and they were most frequent on BTA7 within families. For VO, genomic windows were located on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23, and BTA27 among families, being most frequent on BTA8 within families. For TO, the top 10 genomic windows were identified on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26, and BTA27, being most frequent on BTA7 and BTA8 within families. Considering all results, the greatest number of genomic windows was found on BTA7, where the VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3 genes were identified in the common regions. In conclusion, 15 Gir sire families with 26 to 395 daughters per family with phenotypes for oocyte and embryo production helped to identify the inheritance of several genomic regions, especially on BTA7, where the EDIL3, HAPLN1, and VCAN candidate genes were associated with number of oocytes and embryos in Gir cattle families.
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content type line 23
ISSN:0022-0302
1525-3198
DOI:10.3168/jds.2023-24111