Segregation of polymorphisms in μ-calpain and calpastatin in beef cattle in Puerto Rico

The distribution of single nucleotide polymorphisms (SNP) in two regions of Calpain (CAPN1-316 and CAPN1-4751) and a SNP in Calpastatin (CAST) was determined in beef cattle raised in Puerto Rico (n=271). Genotypic and allelic frequencies were determined for each SNP in Senepol (n=53), Charolais (n=49), Angus (n=27), Charbray (n=38), Brahman (n=16), Zebu (n=16) and crossbred bulls (n=72). For CAPN1-ZAB, the global genotypic frequencies (n=219) were 0.07/CC (n=15), 0.38/CG (n=83) and 0.55/GG (n=121) with allelic frequencies of 0.21/C and 0.74/G. The CC genotype was absent in Charbray, Charoláis, Angus, Zebu and Brahman bulls. In Charolais, Zebu, Brahman and Charbray the GG genotype was in greater proportion than CG, while the inverse was observed in the Senepol breed. In Angus and crossbred animals, the CG and GG genotype were found in equal distribution. The global genotypic frequencies for CAPN1-4751 (n=256) were 0.17/CC (n=44), 0.45/CT (n=114) and 0.38/TT (n=98). The allelic frequencies were 0.39/C and 0.61/T. Animals inheriting the CT genotype were more frequent in Charolais, Senepol, Angus and crossbred bulls, while the TT was more common in Charbray and Brahman. For CAST, the global genotypic frequencies (n=261) were 0.04/CC (n=10), 0.26/CT (n=68), and 0.70/TT (n=183), respectively. The global allelic frequencies were 0.17/C and 0.83/T. The CC genotype was not found in Charoláis, Angus and Brahman breeds. The TT animals were more frequent in all breeds, as well as in the crossbred population. The segregation of polymorphisms in CAPN1 and CAST could potentially be associated with differences in economically important traits for Puerto Rican beef cattle, but this possibility should be evaluated by genotyping a broad range of animals with detailed phenotypic data before incorporating these SNP into markerassisted selection programs.

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Associations of single nucleotide polymorphisms in the bovine prolactin gene with phenotypic traits in beef cattle

Agri Gene ◽

10.1016/j.aggene.2017.06.002 ◽

2017 ◽

Vol 5 ◽

pp. 7-11 ◽

Cited By ~ 2

Author(s):

Laura Meyer ◽

Jeremy Powell ◽

Bryan Kutz ◽

Michael Looper ◽

A. Hayden Brown ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Prolactin Gene

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Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

BMC Genetics ◽

10.1186/1471-2156-15-14 ◽

2014 ◽

Vol 15 (1) ◽

pp. 14 ◽

Cited By ~ 27

Author(s):

Mohammed K Abo-Ismail ◽

Gordon Vander Voort ◽

James J Squires ◽

Kendall C Swanson ◽

Ira B Mandell ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Feed Efficiency ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

And Performance

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IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50K

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v16n2.2015.pp.59-70 ◽

2016 ◽

Vol 16 (2) ◽

pp. 59

Author(s):

Puji Lestari ◽

Habib Rijzaani ◽

Dani Satyawan ◽

Anneke Anggraeni ◽

Dwinita Wikan Utami ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Dairy Cattle ◽

Genetic Relatedness ◽

Bovine Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Snp Chip ◽

Cattle Breeds ◽

Base Extension

<p>Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.</p>

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3321 European Ancestry as a Risk Factor for Atrial Fibrillation in Puerto Rican Hispanics

Journal of Clinical and Translational Science ◽

10.1017/cts.2019.28 ◽

2019 ◽

Vol 3 (s1) ◽

pp. 10-11

Author(s):

Ariel Gonzalez-Cordero ◽

Jorge Duconge-Soler ◽

Ángel López-Candales

Keyword(s):

Atrial Fibrillation ◽

Risk Factor ◽

Single Nucleotide Polymorphisms ◽

Puerto Rican ◽

Population Sample ◽

European Ancestry ◽

Genetic Admixture ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

OBJECTIVES/SPECIFIC AIMS: Consequently, we have decided to evaluate the presence of single nucleotide polymorphism (SNP) previously associated with AF on a European-descent population in an attempt to first identify the most common loci present in the PRH population and then search for specific PRH SNP associated with AF. METHODS/STUDY POPULATION: A secondary analysis of a Puerto Rican population sample (n = 120) from The Pharmacogenetics of Warfarin in Puerto Ricans Study will be performed. We will implement data from the 1000 genome project to establish a control group of healthy PRH population. Will evaluate the presence of 111 known single nucleotide polymorphisms associated with AF in Europeans and determine the frequency in PRH population sample, and validate predictability of such SNPs. Using admixture informatic markers (AIM) analysis will determine the percentage of admixture by Yoruba, Native American and Iberic-European. Statistical analysis will include the use of the Pearson Product-Moment Coefficient correlation analysis and multivariate linear regression. For admixture will use Maximum Likelihood Estimation and Markov Chain Monte Carlo models. RESULTS/ANTICIPATED RESULTS: A higher frequency of AF associated European single nucleotide polymorphisms, and an overall higher percentage of European admixture will be associated with atrial fibrillation in Puerto Rican Hispanic patients. DISCUSSION/SIGNIFICANCE OF IMPACT: Our contributions here are expected to be the elucidation of European ancestry as a risk factor for AF. These contributions will be significant because it can provide a robust scientific basis for larger GWAS studies in the Puerto Rican community and further narrow down the mechanism specific to this population. Research in this subject could lead to early identification of patients with high risk of developing atrial fibrillation and further decrease incidence and disease burden in the PRH population. Puerto Rican Hispanics have an exclusive genetic admixture that makes for an appealing research subject that could deliver unique results.

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Effect of single nucleotide polymorphisms ofCAPN1andCASTgenes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses withBos taurus

Animal Genetics ◽

10.1111/j.1365-2052.2009.01859.x ◽

2009 ◽

Vol 40 (4) ◽

pp. 456-462 ◽

Cited By ~ 39

Author(s):

R. A. Curi ◽

L. A. L. Chardulo ◽

M. C. Mason ◽

M. D. B. Arrigoni ◽

A. C. Silveira ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Bos Indicus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Su1074 – Association Between Single Nucleotide Polymorphisms in Il-1β, Il-6 and Il-10 and Early-Onset Colorectal Cancer in Puerto Rican Hispanics

Gastroenterology ◽

10.1016/s0016-5085(19)38127-2 ◽

2019 ◽

Vol 156 (6) ◽

pp. S-501-S-502

Author(s):

Jorge J. Cruz-Cruz ◽

Maria Gonzalez-Pons ◽

Noe E. Crespo ◽

Lorena Gonzalez-Sepulveda ◽

Lenis N. Rovira Torres ◽

...

Keyword(s):

Colorectal Cancer ◽

Single Nucleotide Polymorphisms ◽

Puerto Rican ◽

Early Onset ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Early Onset Colorectal Cancer

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Influence of single nucleotide polymorphisms in some candidate genes related to the performance traits in Italian beef cattle breeds

Livestock Science ◽

10.1016/j.livsci.2019.103834 ◽

2019 ◽

Vol 230 ◽

pp. 103834 ◽

Cited By ~ 1

Author(s):

Francesca Maria Sarti ◽

Simone Ceccobelli ◽

Emiliano Lasagna ◽

Piera Di Lorenzo ◽

Fiorella Sbarra ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Candidate Genes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cattle Breeds ◽

Performance Traits ◽

Beef Cattle Breeds

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Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle

BMC Genetics ◽

10.1186/1471-2156-14-94 ◽

2013 ◽

Vol 14 (1) ◽

pp. 94 ◽

Cited By ~ 34

Author(s):

Nick VL Serão ◽

Dianelys González-Peña ◽

Jonathan E Beever ◽

Dan B Faulkner ◽

Bruce R Southey ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Feed Efficiency ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Association of Multiple Sclerosis Phenotypes with Single Nucleotide Polymorphisms of IL7R, LAG3, and CD40 Genes in a Jordanian Population: A Genotype-Phenotype Study

Biomolecules ◽

10.3390/biom10030356 ◽

2020 ◽

Vol 10 (3) ◽

pp. 356 ◽

Cited By ~ 2

Author(s):

Laith AL-Eitan ◽

Malak Al Qudah ◽

Majdi Al Qawasmeh

Keyword(s):

Multiple Sclerosis ◽

Vitamin D ◽

Single Nucleotide Polymorphisms ◽

P Value ◽

Fisher Exact Test ◽

Nucleotide Polymorphisms ◽

Phenotypic Data ◽

Single Nucleotide ◽

Jordanian Population ◽

Il7r Gene

It is thought that genetic variations play a vital role in the Multiple Sclerosis (MS) etiology. However, the role of genetic factors that influence the clinical features of MS remains unclear. We investigated the correlation between 21 single nucleotide polymorphisms within three genes (IL7R, LAG3, and CD40) and MS clinical characteristics in the Jordanian population. Blood samples and clinical phenotypic data were collected from 218 Arab Jordanian MS patients, vitamin D was measured, genomic DNA was extracted, and genotyping of the candidate genes’ polymorphisms were analyzed using the Sequenom MassARRAY® system. The association of these single nucleotide polymorphisms (SNPs) with MS was performed using a Chi-square, Fisher exact test, and one-way ANOVA. We found a significant association between vitamin D deficiency and three SNPs of the IL7R gene, namely rs987107 (P-value = 0.047), rs3194051 (P-value = 0.03), and rs1494571 (P-value = 0.036), in addition to two SNPs of CD40, namely rs1883832 and rs6074022 (P-value = 0.049 for both). rs3194051 of the IL7R gene (P-value = 0.003) and rs1922452 of the LAG3 gene (P-value = 0.028) were strongly associated with comorbidity. The number of relapses before drug onset was found to be correlated with IL7R SNPs rs969128 (P-value = 0.04) and rs1494555 (P-value = 0.027), whereas the expanded disability status scale (EDSS) was associated with rs1494555 polymorphism of IL7R gene (P-value = 0.026). Current findings indicate important correlations between certain SNPs and the risk of various phenotypes of multiple sclerosis in the Jordanian community. Therefore, this will not only contribute to the understanding of MS, but will also assist with the development of personalized treatment procedures.

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