523. Sequence-based GWAS meta-analyses for beef production traits

Sanchez, Marie-Pierre; Tribout, Thierry; Kadri, Naveen Kumar; Chitneedi, P. K.; Maak, Steffen; Hozé, Chris; Boussaha, Mekki; Croiseau, Pascal; Philippe, Romain; Spengeler, Mirjam; Kühn, Christa; Wang, Y; Pausch, Hubert; Boichard, Didier

doi:10.3920/978-90-8686-940-4_523

Cited by 3 publications

(2 citation statements)

References 9 publications

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“…RAB2A gene harbors the most signi cant genomic region for body con rmation, the study further reported the genes to have the highest proportion of the total additive genetic variance (3.89%) of body con rmation [28]. [29] reported SLIT2 to be associated with growth and carcass traits Simmental vs Angus, or with a function that may be related to meat production, which was different to our fundings. Tetraspanin 9 (TSPAN9) revealed an association with lactation persistency for Simmental vs Angus, which was consistent with a study by [30] who reported the gene to have an association with lactation persistency in Canadian Holstein.…”

Section: Discussioncontrasting

confidence: 61%

Genome-wide Scans Reveal Selection Signatures and Cross- Population Variation in South African and European Beef Cattle Breeds

Modiba,

Magoro,

Nephawe

et al. 2024

Preprint

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Background In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. This natural selection can leave distinct genetic footprints of signatures, such as changes in allele frequencies, the presence of specific mutations, or patterns of genetic variation. Selection signatures provide information about the evolutionary forces that have shaped a population over time. Methods In this study, a total of 96 samples from four different cattle breeds, namely Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25) were subjected to quality control, following quality control, a total of 105,675 SNPs from 73 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis was conducted using XP-EHH, Rsb, and Fst methods to assess the genetic differences between breeds. Results For the iHS analyses of individual breeds, two genomic regions identified signatures of selection for Bonsmara, six for Simmental, four for Nguni, and one for Angus. Ten regions were identified as being under selection, with BTA 12 shared between Nguni and Bonsmara. Cross-population comparisons using XP-EHH, Rsb, and FST methods revealed specific genomic regions differentially selected between breeds. Gene annotation analyses revealed candidate genes associated with several Quantitative Trait Loci (QTL). For instance, in Simmental cattle, the gene FAM110B was associated with carcass weight and body confirmation score. Bonsmara cattle had fewer candidate genes, including CDK8 and FLT1, while Angus revealed no candidate genes on BTA 18. Nguni cattle revealed the following candidate genes CRB1, PLAG2GA, and VASH2, with CDK8 shared between Bonsmara and Nguni on BTA 12. Cross population comparisons further revealed candidate genes associated with specific traits. For Bonsmara vs Nguni, genes including PLCXD3, FAM149B1, and GRIK2 were identified, whereas, for Simmental vs Angus, SLIT2 and TSPAN9 genes were identified. Furthermore, the study highlighted gene functions, revealing associations with meat quality traits, reproduction, health, diseases, fertility, and body conformation score. Gene interaction analysis using the STRING database identified a network of 63 candidate genes, revealing the structure of genetic interactions. Some genes had multiple functions, indicating multiple roles in various biological processes. Conclusion This extensive genomic study can assist in highlighting the importance of the genetic background of breed-specific traits, and in this way contributes to selective breeding and trait improvement in cattle populations.

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Section: Discussioncontrasting

confidence: 61%

Genome-wide Scans Reveal Selection Signatures and Cross- Population Variation in South African and European Beef Cattle Breeds

Modiba,

Magoro,

Nephawe

et al. 2024

Preprint

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“…The identification of essential genes, haplotypes, and their regulatory mechanisms as markers for quantitative traits has the potential to enhance strategies for selecting beef cattle both currently and in the future [22]. There has been a significant focus on conducting genome-wide association studies (GWAS) to investigate economic traits in cattle, including fertility traits [23][24][25][26][27][28], production traits [29][30][31], somatic cell score [32][33][34][35], and disease resistance [36][37][38][39] in recent years. Numerous significant single nucleotide polymorphisms (SNPs) and biologically relevant genes were identified.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

Haque,

Lee,

et al. 2024

BMC Genomics

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Background Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement. Results A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows. Conclusions The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.

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Unveiling Genetic Potential for Equine Meat Production: A Bioinformatics Approach

Šimon,

Kaić,

Potočnik

2024

Animals

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In view of the predicted significant increase in global meat production, alternative sources such as horsemeat are becoming increasingly important due to their lower environmental impact and high nutritional value. This study aimed to identify SNP markers on the GeneSeek® Genomic Profiler™ Equine (Neogen, Lansing, MI, USA) that are important for horsemeat production traits. First, orthologous genes related to meat yield in cattle and common genes between horses and cattle within QTLs for body size and weight were identified. Markers for these genes were then evaluated based on predicted variant consequences, GERP scores, and positions within constrained elements and orthologous regulatory regions in pigs. A total of 268 markers in 57 genes related to meat production were analyzed. This resulted in 27 prioritized SNP markers in 22 genes, including notable markers in LCORL, LASP1, IGF1R, and MSTN. These results will benefit smallholder farmers by providing genetic insights for selective breeding that could improve meat yield. This study also supports future large-scale genetic analyses such as GWAS and Genomic Best Linear Unbiased Prediction (GBLUP). The results of this study may be helpful in improving the accuracy of genomic breeding values. However, limitations include reliance on bioinformatics without experimental validation. Future research can validate these markers and consider a wider range of traits to ensure accuracy in equine breeding.

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523. Sequence-based GWAS meta-analyses for beef production traits

Cited by 3 publications

References 9 publications

Genome-wide Scans Reveal Selection Signatures and Cross- Population Variation in South African and European Beef Cattle Breeds

Genome-wide Scans Reveal Selection Signatures and Cross- Population Variation in South African and European Beef Cattle Breeds

Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

Unveiling Genetic Potential for Equine Meat Production: A Bioinformatics Approach

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