Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows

Ortega, M. Sofía; Denicol, Anna C.; Cole, J.B.; Null, D.J.; Taylor, Jeremy F.; Schnabel, Robert D.; Hansen, Peter J.

doi:10.3168/jds.2016-12260

Cited by 36 publications

(27 citation statements)

References 41 publications

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“…After comparing the loci identified in the current study with the 22 previous GWAA, 46 genomic regions were validated (Table 5). These loci were identified both within the Holstein breed [19,33,35,[37][38][39] and among other breeds such as crossbreed Angus [34], Brahman [40], Brangus [40], Jersey [19] and a tropical composite breed [40]. Identifying genomic regions in independent populations and across breeds suggests that these regions are near the causal mutation and have a common function related to fertility in cattle.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, loci associated with HCR1 and TBRD were compared to 22 previous studies investigating both dairy and beef cattle fertility. These studies investigated a variety of fertility traits, including: days to first service, non-return rate and calving interval [19,33], pregnancy success at day 28 [34] or day 42 [35], calving to first service [36], conception rates in heifers and in cows [37][38][39], and postpartum anestrous interval [40]. Loci locations were provided based on UMD 3.1 (ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/) and ARS-UCD 1.2 (https://www.animalgenome.org/repository/cattle/ UMC_bovine_coordinates/).…”

Section: Genome-wide Association Analysismentioning

confidence: 99%

“…In recent years, several GWAA have been conducted to identify regions strongly associated with both heifer and cow fertility traits. However, to date, few loci have been identified by independent populations or across breeds [19,20]. Therefore, the objective of this study was to identify loci associated with HCR using GWAA in U.S. Holstein heifers and determine if any previously identified loci were validated through these HCR associations.…”

Section: Introductionmentioning

confidence: 99%

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Validation of 46 loci associated with female fertility traits in cattle

et al. 2019

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Background: Subfertility is one challenge facing the dairy industry as the average Holstein heifer conception rate (HCR), the proportion of heifers that conceive and maintain a pregnancy per breeding, is estimated at 55-60%. Of the loci associated with HCR, few have been validated in an independent cattle population, limiting their usefulness for selection or furthering our understanding of the mechanisms involved in successful pregnancy. Therefore, the objectives here were to identify loci associated with HCR: 1) to the first artificial insemination (AI) service (HCR1), 2) to repeated AI services required for a heifer to conceive (TBRD) and 3) to validate loci previously associated with fertility. Breeding and health records from 3359 Holstein heifers were obtained after heifers were bred by AI at observed estrus, with pregnancy determined at day 35 via palpation. Heifer DNA was genotyped using the Illumina BovineHD BeadChip, and genome-wide association analyses (GWAA) were performed with additive, dominant and recessive models using the Efficient Mixed Model Association eXpedited (EMMAX) method with a relationship matrix for two phenotypes. The HCR1 GWAA compared heifers that were pregnant after the first AI service (n = 497) to heifers that were open following the first AI service (n = 405), which included those that never conceived. The TBRD GWAA compared only those heifers which did conceive, across variable numbers of AI service (n = 712). Comparison of loci previously associated with fertility, HCR1 or TBRD were considered the same locus for validation when in linkage disequilibrium (D' > 0.7). Results: The HCR1 GWAA identified 116, 187 and 28 loci associated (P < 5 × 10 − 8) in additive, dominant and recessive models, respectively. The TBRD GWAA identified 235, 362, and 69 QTL associated (P < 5 × 10 − 8) with additive, dominant and recessive models, respectively. Loci previously associated with fertility were in linkage disequilibrium with 22 loci shared with HCR1 and TBRD, 5 HCR1 and 19 TBRD loci. Conclusions: Loci associated with HCR1 and TBRD that have been identified and validated can be used to improve HCR through genomic selection, and to better understand possible mechanisms associated with subfertility.

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Section: Resultsmentioning

confidence: 99%

Section: Genome-wide Association Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Validation of 46 loci associated with female fertility traits in cattle

et al. 2019

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“…The FCER1G gene on BTA3 has been associated with QTLs related to pregnancy rate at first service, services per conception, and days open ( Supplementary Table S2). This gene affects the immune response and presents an important effect on reproductive functions 60 .…”

Section: Shared Regions Surround Genes For Afc On Medium and High Ec mentioning

confidence: 99%

Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers

Mota

Lopes²,

Júnior

et al. 2020

Sci Rep

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Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production. This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers' adaptation to a wide range of environments. Genomewide association studies through the reaction norm model were carried out to identify genomic regions associated with AFC in Nellore heifers, raised under different environmental conditions (EC). The SNP effects for AFC were estimated in three EC levels (Low, Medium, and High, corresponding to average contemporary group effects on yearling body weight equal to 159.40, 228.6 and 297.6 kg, respectively), which unraveled shared and unique genomic regions for AFC in Low, Medium, and High EC levels, that varied according to the genetic correlation between AFC in different EC levels. The significant genomic regions harbored key genes that might play an important biological role in controlling hormone signaling and metabolism. Shared genomic regions among EC levels were identified on BTA 2 and 14, harboring candidate genes associated with energy metabolism (IGFBP2, IGFBP5, SHOX, SMARCAL1, LYN, RPS20, MOS, PLAG1, CHCD7, and SDR16C6). Gene set enrichment analyses identified important biological functions related to growth, hormone levels affecting female fertility, physiological processes involved in female pregnancy, gamete generation, ovulation cycle, and age at puberty. the genomic regions highlighted differences in the physiological processes linked to AFC in different EC levels and metabolic processes that support complex interactions between the gonadotropic axes and sexual precocity in nellore heifers. open Scientific RepoRtS | (2020) 10:6481 | https://doi.org/10.1038/s41598-020-63516-4 www.nature.com/scientificreports www.nature.com/scientificreports/ pathway and gene network analyses from these results can be performed to uncover mechanisms whereby the environment can potentially affect the sexual precocity in cattle. Such knowledge regarding genomic regions and biological pathways involved with GxE interactions in Nellore heifers' sexual precocity is important to identify molecular mechanisms underlying the phenotypic responses to different environments. Hence, this study was carried out to evaluate the changes in the SNP effect estimates, as well as the biological processes associated with age at first calving in three environmental conditions, combining RN models and GWAS. Materials and Methodsethics approval. The animal procedures in this study were approved by Animal Care of the São Paulo State University (UNESP), School of Agricultural and Veterinary Science Ethical Committee (protocol number 18.340/16). All the data sampling was performed in accordance with CEUA/ FCAV-UNESP guidelines and regulations.phenotypic and genotypic data. Age at first calving (AFC) records were obtained from 185,356Nellore heifers belonging to three commercial breeding programs (DeltaGen, Paint -CRV Lagoa and Cia de Melhoramento), which are p...

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“…These results were surprising. There was a lack of association between the mutation in HSPA1L and PGR for genetic or phenotypic measurements of fertility in Holsteins (Cochran et al, 2013a;Ortega et al, 2016bOrtega et al, , 2017a and the deletion mutation was associated with a reduced proportion of females pregnant during the breeding season for Brahman cows (Rosenkrans et al, 2010). Small sample size could explain some of these discrepancies.…”

Section: Discussionmentioning

confidence: 97%