Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

Schmid, Markus; Bennewitz, Jörn

doi:10.5194/aab-60-335-2017

Cited by 39 publications

(47 citation statements)

References 51 publications

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“…Selection of lines to be used in breeding programs can be optimized by understanding the genetic architecture of the trait, allowing breeders to better determine which elite lines to use in crosses (Massman et al, 2011; Xiao et al, 2017). A GWAS provides information such as the number of genes involved in controlling a trait and the effects of the SNP (Schmid and Bennewitz, 2017). A GWAS can also be used to inform genomic selection (GS) models, where highly significant SNPs revealed by the GWAS can be used as fixed effects in the GS model (Begum et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

2019

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Fusarium head blight (FHB) is an important disease of wheat (Triticum aestivum L.) that has caused billions of dollars in losses in recent decades. Although a massive breeding effort has been undertaken on multiple continents, there are no wheat cultivars with immunity to the disease. Resistance is conditioned by multiple loci and is further complicated by the role of the environment in expression of the disease phenotype. The objectives of our study were (i) to evaluate the phenotypic response to FHB in a large, diverse soft red winter wheat mapping panel; and (ii) to identify promising quantitative trait loci (QTL) associated with FHB resistance based on a genome‐wide association study (GWAS). We evaluated the mapping panel in 2014–2015 and 2015–2016 in an irrigated, inoculated scab nursery near Lexington, KY. Traits evaluated were heading date, plant height, FHB rating, severity, incidence, index, Fusarium‐damaged kernels (FDK), and deoxynivalenol (DON). There were significant (p < 0.05) differences among genotypes for all traits measured. The GWAS (based on 2‐yr entry means) identified 16 significant (p < 0.001) single nucleotide polymorphisms (SNPs) associated with disease traits on multiple chromosomes. Single nucleotide polymorphism association ranged from −2.14 to 4.01% of the mean of a given trait. We detected SNPs associated with FDK and DON on chromosomes 4A, 5B and 6B, and these SNPs decreased DON levels by 1.5, 2.1 and 3.2 mg kg−1, respectively. Our study demonstrated that even small‐effect QTL can potentially decrease disease levels and thus be useful in breeding programs.

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Section: Discussionmentioning

confidence: 99%

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

2019

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“…Until now, a variety of association studies have been conducted to decipher the genetic architecture of quantitative traits such as ESS, which led to the identification of a valuable repertoire of genes controlling a range of traits (see the reviews [11][12][13]). Finding loci associated with a trait through genome wide association studies (GWAS) is commonly based on single-SNP based models that test each SNP for its association with the phenotype, ignoring its dependency on the neighboring SNPs.…”

Section: Introductionmentioning

confidence: 99%

Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests

Ramzan

Klees

Schmitt

et al. 2020

Genes

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In today’s chicken egg industry, maintaining the strength of eggshells in longer laying cycles is pivotal for improving the persistency of egg laying. Eggshell development and mineralization underlie a complex regulatory interplay of various proteins and signaling cascades involving multiple organ systems. Understanding the regulatory mechanisms influencing this dynamic trait over time is imperative, yet scarce. To investigate the temporal changes in the signaling cascades, we considered eggshell strength at two different time points during the egg production cycle and studied the genotype–phenotype associations by employing the Random Forests algorithm on chicken genotypic data. For the analysis of corresponding genes, we adopted a well established systems biology approach to delineate gene regulatory pathways and master regulators underlying this important trait. Our results indicate that, while some of the master regulators (Slc22a1 and Sox11) and pathways are common at different laying stages of chicken, others (e.g., Scn11a, St8sia2, or the TGF- β pathway) represent age-specific functions. Overall, our results provide: (i) significant insights into age-specific and common molecular mechanisms underlying the regulation of eggshell strength; and (ii) new breeding targets to improve the eggshell quality during the later stages of the chicken production cycle.

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“…Compared with humans, long-range LD blocks are more common in dairy cattle, especially in HF cows. This is due to the intensive use of relatively few sires for breeding the next generation, which results in a relatively small effective population size (Schmid and Bennewitz, 2017).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study of normal and atypical progesterone profiles in Holstein-Friesian dairy cows

Nyman

Duchemin

Koning

et al. 2019

Journal of Dairy Science

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Female fertility has a major role in dairy production and affects the profitability of dairy cattle. The genetic progress obtained by traditional selection can be slow because of the low heritability of classical fertility traits. Endocrine fertility traits based on progesterone concentration in milk have higher heritability and more directly reflect the cow's own reproductive physiology. The aim of our study was to identify genomic regions for 7 endocrine fertility traits in dairy cows by performing a genome-wide association study with 54,000 SNP. The next step was to fine-map targeted genomic regions with significant SNP using imputed sequences to identify potential candidate genes associated with the normal and atypical progesterone profiles. The association between a SNP and a phenotype was assessed by a single SNP analysis, using a linear mixed model that included a random polygenic effect. Phenotypes and genotypes were available for 1,126 primiparous and multiparous Holstein-Friesian cows from research herds in Ireland, the Netherlands, Sweden, and the United Kingdom. In total, 44 significant SNP associated with 7 endocrine fertility traits were identified on Bos taurus autosome (BTA) 1-4, 6, 8-9, 11-12, 14-17, 19, 21-24, and 29. Three chromosomes, BTA8, BTA17, and BTA23, were imputed from 54,000 SNP genotypes to the whole-genome sequence level with Beagle version 4.1. The fine-mapping identified several significant associations with delayed cyclicity, cessation of cyclicity, commencement of luteal activity, and inter-ovulatory interval. These associations may contribute to an index of markers for genetic improvement of fertility. Several potential candidate genes reported to affect reproduction were also identified in the targeted genomic regions. However, due to high linkage disequilibrium, it was not possible to identify putative causal genes or polymorphisms for any of the regions.

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Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

Cited by 39 publications

References 51 publications

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests

Genome-wide association study of normal and atypical progesterone profiles in Holstein-Friesian dairy cows

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