Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

Strillacci, M.G.; Frigo, E.; Schiavini, F.; Samoré, A.B.; Canavesi, F.; Vevey, Mario; Cozzi, M.C.; Soller, M.; Lipkin, E.; Bagnato, A.

doi:10.1186/s12863-014-0106-7

Cited by 42 publications

(35 citation statements)

References 32 publications

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“…Other identified genes in our current study are involved in somatic cell score and meat quality traits, such as GRIN2B (Wu et al. 2014) and PLXNA4 (Strillacci et al. 2014).…”

Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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“…Other identified genes in our current study are involved in somatic cell score and meat quality traits, such as GRIN2B (Wu et al. 2014) and PLXNA4 (Strillacci et al. 2014).…”

Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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“…This study also identified ACSL1 associated with the milk fatty acid traits (Li et al 2014) and supported by other studies (Widmann et al 2011;Gao et al 2013;Weber et al 2013). Other identified genes in our current study are involved in somatic cell score and meat quality traits, such as GRIN2B (Wu et al 2014) and PLXNA4 (Strillacci et al 2014). …”

Section: Strs Overlap With Regions Under Selection Predicted Based Onmentioning

confidence: 68%

0309 Systematic profiling of short tandem repeats in the cattle genome

Liu

Haasl

et al. 2016

Journal of Animal Science

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Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2-6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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“…Strillacci et al . () reported a list of the chromosome regions (including IGF1R region) defined by at least three SNPs that are strongly associated with mastitis resistance and somatic cell score. There are also manuscripts in which there was no effect of IGF1R gene on milk traits (Jiang et al .…”

Section: Discussionmentioning

confidence: 99%

“…IGF1R was also shown to control innate immunity in mammals and served as a potential tool in mastitis prevention (Sugimoto & Sugimoto 2012). Strillacci et al (2014) reported a list of the chromosome regions (including IGF1R region) defined by at least three SNPs that are strongly associated with mastitis resistance and somatic cell score. There are also manuscripts in which there was no effect of IGF1R gene on milk traits (Jiang et al 2010;Meredith et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Polymorphism in exon 2 encoding the putative ligand binding pocket of the bovine insulin‐like growth factor 1 receptor affects milk traits in four different cattle breeds

Szewczuk

2016

J Animal Breeding Genetics

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As a member of the somatotropic axis, insulin-like growth factor I receptor (IGF1R) seems to be a promising candidate gene. Two silent polymorphisms, identified by MspI and TaqI restriction enzymes, were selected within exon 2, encoding the majority of the putative ligand binding pocket. A total of 1169 cows of four pure breeds (Polish Holstein Friesian, Montbeliarde, Jersey and Holstein Friesian) were genotyped. The T (IGF1R/e2/MspI) and G (IGF1R/e2/TaqI) alleles were found to be prevalent. Three combinations of genotypes (TT/GG, TT/AG and CT/GG) were associated with the highest productivity (milk, protein and fat yields) among all breeds under study, as opposed to individuals carrying the worst CC/AA combination. In view of the specific structure of the ligand binding pocket and the significance of insulin-like growth factor I signalling promoting the development and differentiation in a variety of tissues (not only limited to mammary gland), the existence of missense mutation is unlikely. Potential mutations are likely limited to mRNA transcription and further post-transcriptional modifications. Further investigations should follow searching for the most useful IGF1R haplotypes, associated with higher milk production traits, exerting at the same time positive or neutral impact on health and welfare of individuals.

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Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

Cited by 42 publications

References 32 publications

Systematic profiling of short tandem repeats in the cattle genome

Systematic profiling of short tandem repeats in the cattle genome

0309 Systematic profiling of short tandem repeats in the cattle genome

Polymorphism in exon 2 encoding the putative ligand binding pocket of the bovine insulin‐like growth factor 1 receptor affects milk traits in four different cattle breeds

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