scholarly journals Random Forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle

2013 ◽  
Vol 96 (10) ◽  
pp. 6716-6729 ◽  
Author(s):  
C. Yao ◽  
D.M. Spurlock ◽  
L.E. Armentano ◽  
C.D. Page ◽  
M.J. VandeHaar ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dairy Cattle ◽  
Random Forests ◽  
Feed Intake ◽  
Residual Feed Intake ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle1

2013 ◽  
Vol 91 (8) ◽  
pp. 3502-3513 ◽  
Author(s):  
B. K. Karisa ◽  
J. Thomson ◽  
Z. Wang ◽  
P. Stothard ◽  
S. S. Moore ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Candidate Genes ◽  
Feed Intake ◽  
Residual Feed Intake ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals FABP4is a leading candidate gene associated with residual feed intake in growing Holstein calves

2016 ◽  
Vol 48 (5) ◽  
pp. 367-376 ◽  
Author(s):  
Miri Cohen-Zinder ◽  
Aviv Asher ◽  
Ehud Lipkin ◽  
Roi Feingersch ◽  
Rotem Agmon ◽  
...  
Keyword(s):  
Feed Intake ◽  
Scale Validation ◽  
Residual Feed Intake ◽  
Significant Snps ◽  
Nucleotide Polymorphisms ◽  
Special Equipment ◽  
Single Nucleotide ◽  
Fatty Acid Binding ◽  
Holstein Breed ◽  
Holstein Calves

Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1–3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 ( FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.

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

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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