Low-density Single Nucleotide Polymorphism Research Articles

Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 51,2

Traditional genetic selection in cattle for traits with low heritability, such as reproduction, has had very little success. With the addition of DNA technologies to the genetic selection toolbox for livestock, the opportunity may exist to improve reproductive efficiency more rapidly in cattle. The US Meat Animal Research Center Production Efficiency Population has 9,186 twinning and 29,571 ovulation rate records for multiple generations of animals, but a significant number of these animals do not have tissue samples available for DNA genotyping. The objectives of this study were to confirm QTL for twinning and ovulation rate previously found on BTA5 and to evaluate the ability of GenoProb to predict genotypic information in a pedigree containing 16,035 animals when using genotypes for 24 SNP from 3 data sets containing 48, 724, or 2,900 animals. Marker data for 21 microsatellites on BTA5 with 297 to 3,395 animals per marker were used in conjunction with each data set of genotyped animals. Genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fitted as fixed effects in a 2-trait mixed model analysis by using multiple-trait derivative-free REML. Each SNP was analyzed individually, followed by backward selection fitting all individually significant SNP simultaneously and then removing the least significant SNP until only significant SNP were left. Five significant SNP associations were detected for twinning rate and 3 were detected for ovulation rate. Two of these SNP, 1 for each trait, were significant for imprinting. Additional modeling of paternal and maternal allelic effects confirmed the initial results of imprinting done by contrasting heterozygotes. These results are supported by comparative mapping of mouse and human imprinted genes to this region of bovine chromosome 5.

A Rare Case of JAK2 V617F Positive Polycythemia Vera in a Child with Neurofibromatosis Type I.

Polycythemia vera (PV), is a myeloproliferative disease (MPD) originating in a hematopoietic stem cell resulting in clonal expansion of erythroid progenitors. It is associated with thromboses and malignant transformation. Recently the V617F alteration arising from a mutation in JAK2 has been identified in greater than 90% of cases of PV in adults. PV is rare in children and the frequency of the common JAK2 mutation is significantly lower than in adult patients, indicating that alternative genetic events are involved in the pathogenesis of this disease. We have identified a child diagnosed with PV at the age of 15 months, the youngest described in the literature to date. Initial laboratory values demonstrated a WBC of 33 x109/L, hemoglobin 181 g/L, and platelet count of 579 x109/L. Bone marrow cytogenetics were normal. Erythroid colony forming units demonstrated erythropoietin-independent growth. Peripheral blood, buccal swab and saliva analysis revealed the presence of the common JAK2 V617F mutation, but a B lymphocyte cell line and skin-fibroblast-culture from this patient were negative, indicating that the JAK2 mutation was somatic. Peripheral blood from her parents and older brother demonstrated normal blood counts and wild type JAK2 status. This child was also diagnosed with Neurofibromatosis type 1 (NF1) based on meeting NIH consensus diagnostic criteria diagnostic criteria, having the requisite number of appropriately sized café-au-lait macules and Lisch nodules. NF1 and PV have no previously known association, however NF1 is associated with another MPD, juvenile myelomonocytic leukemia (JMML). Patients with NF1 and JMML demonstrate loss of heterozygosity (LOH) at the NF1 locus while 60% of JMML patients without NF1 alternatively demonstrate somatic mutations in NRAS, KRAS2 or PTPN11. Taken together, these genetic lesions result in hyperactivation of the RAS/MAPK pathway. Low density single nucleotide polymorphism arrays performed on peripheral blood from this patient failed to demonstrate obvious LOH at the NF1 locus. NF1 gene sequencing failed to identify the cause of the NF1 phenotype. Mutations were not identified in the commonly mutated regions of NRAS, KRAS2 or PTPN11. This case reveals the presence of the most commonly acquired somatic JAK2 mutation in a young child with PV and indicates that buccal swabs and saliva are unreliable sources of unaffected tissue for assessing the presence of germline mutations in PV patients. Moreover, it suggests that some patients with clinical NF1 are at risk for developing other MPDs besides JMML. For this patient, a novel unidentified genetic abnormality resulting in the clinical phenotype of NF1 may serve as a predisposing genetic event accounting for the unusually young age of presentation. The investigation of rare children with PV has the potential to provide valuable insight into the molecular interactions underlying the pathogenesis of MPDs.

Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map1,2

As genetic markers, SNP are well suited for the development of genetic tests for production traits in livestock. They are stable through many generations and can provide direct assessment of individual animal's genetic merit if they are in linkage disequilibrium and phase with functional genetic variation. Bovine chromosome 5 has been shown to harbor genetic variation affecting production traits in multiple cattle populations; thus, this chromosome was targeted for SNP-based marker development and subsequent association analysis with carcass and growth phenotypes. Discovery of SNP was performed in a panel of 16 sires representing two sires from each of seven beef breeds and two Holstein sires by PCR amplification and sequencing using primers designed from genomic sequence obtained by low-coverage sequencing of bacterial artificial chromosome (BAC) clones. From 550 SNP, 296 (54%) were tentatively identified as having a minor allele frequency >10%. Forty-five SNP derived from 15 BAC were chosen based on minor allele frequency and were genotyped in 564 steers and their sires. Production and carcass data were collected on the steers as a part of the Germplasm Evaluation (GPE), Cycle VII Project at the U.S. Meat Animal Research Center (Clay Center, NE), which involves of the evaluation of sires from seven of the most popular U.S. breeds. Haplotypes based on seven SNP derived from a BAC containing the bovine genes HEM1 and PDE1B were associated with traits related to carcass fat. Steers homozygous for the major haplotype had 0.15 +/- 0.04 cm less subcutaneous fat, 0.57 +/- 0.18 kg less rib fat, 0.18 +/- 0.07 lower yield grade, 1.11 +/- 0.35% less predicted fat yield, and 0.79 +/- 0.3% greater predicted retail product yield than heterozygotes. The frequency of the major haplotype was 0.70 in the steers, and it ranged from 0.44 (Limousin) to 0.98 (Simmental and Gelbvieh) in a panel consisting of an average of 20 purebred sires from each of the seven breeds. A second set of haplotypes based on four SNP derived from a BAC containing the genes NOL1 and CHD4 was associated with Warner-Bratzler shear force. Steers homozygous for the major haplotype had 0.27 +/- 0.11 kg greater shear force than those heterozygous for the major haplotype and one of two minor haplotypes. The frequency of the major haplotype was 0.59 in the steers and ranged from 0.27 (Hereford) to approximately 0.95 (Angus and Red Angus) in the panel of purebred sires. These results demonstrate the feasibility of targeting QTL regions for SNP-based marker development and that a low level of coverage can identify markers associated with phenotypic traits.