Cloning and characterization of FAM13A1—a gene near a milk protein QTL on BTA6: evidence for population-wide linkage disequilibrium in Israeli Holsteins☆

Cohen, Miri; Reichenstein, Moshe; Wind, Annelie Everts-van der; Heon-Lee, Jun; Shani, Moshe; Lewin, Harris A.; Weller, J. I.; Maymon, Ron; Seroussi, Eyal

doi:10.1016/j.ygeno.2004.03.005

Cited by 57 publications

(58 citation statements)

References 38 publications

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“…This gene encodes an integral membrane protein involved in intracellular calcium homeostasis and other signal transduction pathways (Nauli et al 2003). Cohen et al (2004b) suggested that SPP1 has an essential role in mammary gland differentiation and branching of the mammary epithelial ductal system, and is therefore a prime candidate. Furthermore, anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion (Nemir et al 2000).…”

Section: Discussionmentioning

confidence: 99%

“…This model estimated the effects associated with the polymorphisms on the sire evaluations for the milk production traits, with each polymorphism-trait combination analyzed separately (Cohen et al 2004a). The number of bulls with valid genotypes and the frequency of the more common allele for each marker are also given.…”

Section: Allele Substitution Effects and Dominancementioning

confidence: 99%

“…The BAC templates were prepared by picking colonies grown overnight and boiling them in 200 µL of ddH 2 O for 10 min. Bioinformatics procedures, management of DNA sequences and EST assembly were done as previously described (Cohen et al 2004a). …”

Section: Physical Mapping and Bioinformaticsmentioning

confidence: 99%

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Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle

Cohen¹,

Seroussi²,

Larkin³

et al. 2005

Genome Res.

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353

341

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We previously localized a quantitative trait locus (QTL) on chromosome 6 affecting milk fat and protein concentration to a 4-cM confidence interval, centered on the microsatellite BM143. We characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL. Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. The single nucleotide change capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 transporter was the only polymorphism corresponding to the segregation status of all 3 heterozygous and 15 homozygous sires for the QTL in the Israeli and U.S. Holstein populations. The allele substitution fixed effects on the genetic evaluations of 335 Israeli sires were −341 kg milk, +0.16% fat, and +0.13% protein (F-value = 200). No other polymorphism gave significant effect for fat and protein concentration in models that also included Y581S. The allele substitution effects on the genetic evaluations of 670 cows, daughters of two heterozygous sires, were −226 kg milk, 0.09% fat, and 0.08% protein (F-value = 394), with partial dominance towards the 581S homozygotes. We therefore propose that Y581S in ABCG2 is the causative site for this QTL.

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Section: Discussionmentioning

confidence: 99%

Section: Allele Substitution Effects and Dominancementioning

confidence: 99%

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Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle

Cohen¹,

Seroussi²,

Larkin³

et al. 2005

Genome Res.

Self Cite

353

341

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“…Although no significant differences in the mean values of the analyzed traits between the individuals with different genotypes of the analyzed loci were found in the presented study, other authors showed an effect of polymorphic variants on milkperformance traits. In the study by Cohen et al (11), the negative effect of allele C on milk yield and the positive effects of this allele on the remaining examined traits were shown for FAM13A1 C/A; however, only the effect of this allele on milk protein content was significant. In the same study, it was shown for the FAM13A1 G/A SNP that allele A also negatively affects milk yield, whereas it positively influences milk fat and protein content.…”

Section: Discussionmentioning

confidence: 89%

“…Both amino acids are nonpolar. Therefore, this exchange does not result in considerable changes in the protein conformation (11). In the case of LAP3 and the T/C nucleotide exchange, the Ala synonymous amino acid substitution occurs.…”

Section: Discussionmentioning

confidence: 99%

Genetic polymorphisms of FAM13A1, OPN, LAP3, and HCAP-G genes in Jersey cattle

Umul

2013

Turk J Vet Anim Sci

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IntroductionStudies by numerous authors indicate that many bovine chromosomes (BTAs), including BTA3,6,9,14,20, and 23, in particular, bear clusters of quantitative trait loci (QTL) of different milk performance traits. In numerous reports the studies concentrated on BTA6 within 2 regions, in which clusters of genes associated with milk performance traits are located (1). These regions are the fragments in the middle part of BTA6, close to the BM143 marker, and the region close to the casein genes complex (2,3). Previous literature suggests that genes located near BM143 affect 5 milk performance traits, including milk yield (kg), milk protein and fat yield (kg), and milk protein and fat content (%) (1). The region encompassing these genes extends from the FAM13A (family with sequence similarity 13, member A1) to the PPARGC1A (peroxisome proliferator-activated receptor-γ coactivator-1α) genes and spans approximately 6.2 cM. In this range, there are genes whose effects on the performance traits of cattle have already been examined, such as OPN (osteopontin), and genes that may potentially influence these traits, such as FAM13A1, LAP3 (leucine aminopeptidase 3), and HCAP-G (condensin subunit 3) (4-6).Osteopontin (OPN) is a phosphorylated glycoprotein that plays a role in different processes in the organism, for example in cell adhesion, chemotaxis, cell signaling, and the regulation of growth and development of the fetus, as well as in the initiation and maintenance of pregnancy ( 7). The presence of OPN in milk and its high level of expression in mammary epithelial cells may cause proliferation and differentiation of the mammary gland (8). Despite fulfilling so many functions, OPN is treated by most authors as a positional candidate gene for milkperformance traits harboring the QTL region on BTA6 (9,10). Other studied genes do not play such an important role in the organism and, therefore, are considered first of all as positional candidate genes.It was suggested that the FAM13A1, LAP3, and HCAP-G genes may be associated with milk-performance traits such as milk yield and milk composition, mainly due to their location in the analyzed region and due to the fact that the expression levels of these genes were found to be different in the mammary gland (4,(11)(12)(13). Preliminary assessments of the association of these genes with milkperformance traits were reported (5,(11)(12)(13). For instance, the LAP3 gene may affect milk fat and protein yield, the FAM13A1 and LAP3 genes may affect the change in milk protein content, and the LAP3 gene has been associated with milk yield (5,(11)(12)(13).On the basis of the above-mentioned data, this research aimed at determining the allele and genotype frequencies of the single-nucleotide polymorphisms (SNPs) in the FAM13A1, OPN, LAP3, and HCAP-G genes in a herd of Jersey cows, as well as establishing possible associations between the genotypes and the milk-performance traits of the examined herd of cattle.

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Emerging genetics of COPD

2012

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Since the discovery of alpha-1 antitrypsin in the early 1960s, several new genes have been suggested to play a role in chronic obstructive pulmonary disease (COPD) pathogenesis. Yet, in spite of those advances, much about the genetic basis of COPD still remains to be discovered. Unbiased approaches, such as genome-wide association (GWA) studies, are critical to identify genes and pathways and to verify suggested genetic variants. Indeed, most of our current understanding about COPD candidate genes originates from GWA studies. Experiments in form of cross-study replications and advanced meta-analyses have propelled the field towards unravelling details about COPD's pathogenesis. Here, we review the discovery of genetic variants in association with COPD phenotypes by discussing the available approaches and current findings. Limitations of current studies are considered and future directions provided.

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Cloning and characterization of FAM13A1—a gene near a milk protein QTL on BTA6: evidence for population-wide linkage disequilibrium in Israeli Holsteins☆

Cited by 57 publications

References 38 publications

Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle

Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle

Genetic polymorphisms of FAM13A1, OPN, LAP3, and HCAP-G genes in Jersey cattle

Emerging genetics of COPD

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