Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows

Yin, Tong; Jaeger, Maria; Scheper, Carsten; Grodkowski, Grzegorz; Sakowski, Tomasz; Klopčič, Marija; Bapst, Beat; König, Sven

doi:10.1371/journal.pone.0221973

Cited by 4 publications

(3 citation statements)

References 79 publications

(122 reference statements)

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“…The rather small number of detected SNP for the moderately to highly heritable polygenic traits is in line with our small sample size and its diversity (multi-breed), and is most likely due to a lack of power to detect variants with smaller effects. However, with regard to the functional annotations of the identified genomic regions, our study confirms the potential of multi-breed GWAS in detecting fewer variants, but more precise functional loci or causative mutation across breeds [75,132]. In this context, the SNP associated with morphometric traits in the present study may represent novel common variants for linear body traits in African breeds, suggesting further investigations.…”

Section: Genomic Regions Associated With Morphometric and Adaptation supporting

confidence: 79%

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

et al. 2020

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Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

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“…Recent studies provided insight into the body size variation in cetaceans, indicating that this gene was related to tall stature and overgrowth [ 47 ], and a genome-wide scan for selection signatures revealed that this gene was related to cardiac structure and function in Atlantic killifish [ 48 ]. Another multi-breed GWASs on dual-purpose bovine behavior traits identified this gene as related to rumination [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Abdalla,

Hui,

Nazar

et al. 2023

Animals

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Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10−7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.

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“…de Mol et al, 2013). Accelerometers have also been shown to readily detect changes in behavior (feeding, ruminating, general activity) in cows at pasture (Yin et al, 2019). Adriaens et al (2020) showed that a resilience ranking based on the above practical definition of ability to re-calve can be predicted with sensor data derived from milk yield and/or accelerometers.…”

Section: Ability To Re-calvementioning

confidence: 99%

Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait

Friggens¹,

Adriaens²,

R.³

et al. 2022

Peer Community Journal

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Climate change, with its increasing frequency of environmental disturbances puts pressures on the livestock sector. To deal with these pressures, more complex traits such as resilience must be considered in our management strategies and in our breeding programs. Resilient animals respond well to environmental challenges, and have a decreased probability of needing assistance to overcome them. This paper discusses the need for operational measures of resilience that can be deployed at large scale across different farm types and livestock species. Such measures are needed to provide more precise phenotypes of resilience for use in farm management, but also for use in animal breeding. Any measure of response and recovery reflects both the animals resilience and the perceived size of the environmental disturbance, which can vary over time, depending on multiple animal and farm-related contexts. Therefore, and because universal definitions of resilience are too broad to be operational, we argue that resilience should be seen as a latent construct that cannot be directly measured and selected for. This leads to the following two points: (1) any postulated operational measure of resilience to a disturbance should be constructed from a sufficient number of indicators that each individually capture different facets of the resilience, such that when combined they better reflect the full resilience response; and (2) any postulated operational measure of resilience will have to be validated against reference measures that are the accumulated consequences of good resilience (e.g. productive lifespan or ability to re-calve). In a dairy cow case study, a practical resilience definition for dairy cattle was proposed and tested based on a scoring system containing several categories. In general terms and within a given parity, a cow receives plus points for each calving, and for a shorter calving interval, fewer inseminations and a higher milk production compared to her herd peers. She will receive minus points in case the number of inseminations increases, for each curative treatment day, and if her milk production is lower compared to her herd peers. By using readily available farm data, we were able to assess a practical lifetime resilience score, based on which cows can then be ranked within the herd. Cows that reach a next parity were shown to have a higher rank than cows that are culled before the next parity. To examine the usefulness of such a score, this resilience ranking was linked to two precision livestock technology-derived measures, related to milk yield deviations and accelerometer-derived deviations. Higher resilience ranking cows had fewer drops in milk yield and a more stable activity pattern during the lactation. This case study, taking the operational approach to quantifying and defining resilience, shows the promise of a data-driven approach for identifying resilience measures when applied within a biologically logical framework.

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Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows

Cited by 4 publications

References 79 publications

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait

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