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

Abstract Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

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

The Journal of Agriculture of the University of Puerto Rico ◽

10.46429/jaupr.v99i2.3026 ◽

1969 ◽

Vol 99 (2) ◽

pp. 105-116

Author(s):

Jonael Bosques ◽

Melvin Pagán-Morales ◽

Américo Casas ◽

Aixa Rivera ◽

Danilo Cianzio

Keyword(s):

Puerto Rico ◽

Single Nucleotide Polymorphisms ◽

Beef Cattle ◽

Puerto Rican ◽

Nucleotide Polymorphisms ◽

Phenotypic Data ◽

Single Nucleotide ◽

Equal Distribution ◽

Allelic Frequencies

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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