Genome changes due to artificial selection in U.S. Holstein cattle

Ma, Li; Sonstegard, Tad S.; Cole, John B.; Vantassell, Curtis P.; Wiggans, G.R.; Crooker, B.A.; Tan, Cheng; Prakapenka, Dzianis; Liu, George E.; Da, Yang

doi:10.1186/s12864-019-5459-x

Cited by 44 publications

(31 citation statements)

References 38 publications

(39 reference statements)

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“…The GHR-PRLR region had the largest concentration of significant effects on milk yield with peak QTL effects in C6-PTGER4 downstream of GHR . This large QTL region was within the 28-Mb region of 21–49 Mb with the strongest evidence of selection signature by the analysis of extended haplotype homozygosity (Ma et al, 2019).…”

Section: Resultsmentioning

confidence: 99%

“…The Chr05 region at 83.69–102.28 Mb was 18.59 Mb in size, the Chr06 region of 83.37–93.94 Mb region was about 10.57 Mb in size, and the Chr20 region at 23.86–42.21Mb was 18.35-Mb in size. This large Chr20 QTL region was within the 28-Mb region of 21–49 Mb with the strongest evidence of selection signature by the analysis of extended haplotype homozygosity (Ma et al, 2019). In addition to the four chromosomes described in Figure 2, the additive SNP effects reported in this study involved all 29 bovine autosomes (Table S5), and identified additional regions with significant effects, including the 50.04–58.26 Mb of Chr03, the 105.45–106.36 Mb of chr05 and the 24.96–29.97 Mb of chr23 for protein yield; the 15.36–15.62 Mb of chr03 and the 64.00–71.84 Mb of Chr14 for protein percentage; the 60.23–72.08 Mb of Chr01 for daughter pregnancy rate and cow conception rate; and AFF1 for heifer conception rate.…”

Section: Resultsmentioning

confidence: 99%

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A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle

et al. 2019

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Genome-wide association study (GWAS) is a powerful approach to identify genomic regions and genetic variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. We conducted a large-scale GWAS using 294,079 first-lactation Holstein cows and identified new additive and dominance effects on five production traits, three fertility traits, and somatic cell score. Four chromosomes had the most significant SNP effects on the five production traits, a Chr14 region containing DGAT1 mostly had positive effects on fat yield and negative effects on milk and protein yields, the 88.07–89.60 Mb region of Chr06 with SLC4A4, GC, NPFFR2 , and ADAMTS3 for milk and protein yields, the 30.03–36.67 Mb region of Chr20 with C6 and GHR for milk yield, and the 88.19–88.88 Mb region with ABCC9 as well as the 91.13–94.62 Mb region of Chr05 with PLEKHA5, MGST1, SLC15A5 , and EPS8 for fat yield. For fertility traits, the SNP in GC of Chr06, and the SNPs in the 65.02–69.43 Mb region of Chr01 with COX17, ILDR1 , and KALRN had the most significant effects for daughter pregnancy rate and cow conception rate, whereas SNPs in AFF1 of Chr06, the 47.54–52.79 Mb region of Chr07, TSPAN4 of Chr29, and NPAS1 of Chr18 had the most significant effects for heifer conception rate. For somatic cell score, GC of Chr06 and PRLR of Chr20 had the most significant effects. A small number of dominance effects were detected for the production traits with far lower statistical significance than the additive effects and for fertility traits with similar statistical significance as the additive effects. Analysis of allelic effects revealed the presence of uni-allelic, asymmetric, and symmetric SNP effects and found the previously reported DGAT1 antagonism was an extreme antagonistic pleiotropy between fat yield and milk and protein yields among all SNPs in this study.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle

et al. 2019

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“…Recently, by comparing sperm methylomes between human and Holstein cattle, we demonstrated that genomic variants of morphology-relevant traits were consistently and significantly enriched in the evolutionarily conserved hypomethylated regions in human and cattle [26]. Furthermore, the rapidly reduced immune and reproductive capacity of dairy cattle has been observed during the strong selection for milk production over the past decades [27]. Using these cattle resources, it is possible to extrapolate genomic changes associated with immune and reproduction in cattle to further advance human biomedical researches.…”

Section: Introductionmentioning

confidence: 99%

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

Liu

Zhang

et al. 2020

BMC Biol

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Background: Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle. Results: We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. By uniformly analyzing 723 RNA-seq and 40 whole genome bisulfite sequencing (WGBS) datasets in cattle, we validated that cross-mapped histone marks captured tissue-specific expression and methylation, reflecting tissue-relevant biology. Through integrating cross-mapped tissue-specific histone marks with large-scale GWAS and selection signature results, we for the first time detected relevant tissues and cell types for 45 economically important traits and artificial selection in cattle. For instance, immune tissues are significantly associated with health and reproduction traits, multiple tissues for milk production and body conformation traits (reflecting their highly polygenic architecture), and thyroid for the different selection between beef and dairy cattle. Similarly, we detected relevant tissues for 58 complex traits and diseases in humans and observed that immune and fertility traits in humans significantly correlated with those in cattle in terms of relevant tissues, which facilitated the identification of causal genes for such traits. For instance, PIK3CG, a gene highly specifically expressed in mononuclear cells, was significantly associated with both age-at-menopause in human and daughter-still-birth in cattle. ICAM, a T cellspecific gene, was significantly associated with both allergic diseases in human and metritis in cattle.

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“…Prior to breeding for dairy production, the Holstein cow was visibly more muscular ( Figure 3). The very genome of the Holstein cow in the United States has been changed as a result of breeding by the dairy industry through artificial selection for economically important traits, resulting in the economically desired increased milk production and a regrettable concomitant decrease in fertility and immunity (Ma et al, 2019). The cow transformed by humans through biopower into a milk producer is presented to children as simply a cow.…”

Section: Thinking With a Holstein Cow Figurinementioning

confidence: 99%

Making “Cuts” with a Holstein Cow in Early Childhood Education and Care: The Joys of Representation

Aslanian¹,

Moxnes²

2020

J Child. Stud.

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This article explores children’s play with representations of animals, specifically the Holstein cow, as noninnocent care practices in the context of early childhood education and care environments. We use Barad’s relational ontology and Chaudhuri’s concept of zooësis to activate a temporal diffractive analysis of memory stories about children’s play with cows in ECEC read through facts from past, present, and future livestock-rearing practices. We connect the joy of playing with representations of nonhuman animals to the responsibility associated with multispecies lives, and to care as the production of flourishing.

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Genome changes due to artificial selection in U.S. Holstein cattle

Cited by 44 publications

References 38 publications

A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle

A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

Making “Cuts” with a Holstein Cow in Early Childhood Education and Care: The Joys of Representation

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