Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: application in cattle breeds

Language is a vital feature of any human culture, but whether language gene polymorphisms have meaningful correlations with some cultural characteristics during the long-run evolution of human languages largely remains obscure (uninvestigated). This study would be an endeavor example to find evidences for the answer of above question. In this study, the collected basic data include 13 language genes and their randomly selected 111 single nucleotide polymorphisms (SNPs), SNP profiles, 29 culture/education parameters, and estimated cultural context values for 26 representative countries. In order to undertake principal component analysis (PCA) for correlation search, SNP genotypes, cultural context and all other culture/education parameters have to be quantitatively represented into numerical values. Based on the above conditions, this study obtained its preliminary results, the main points of which contain: (1) The 111 SNPs contain several clusters of correlational groups with positive and negative correlations with each other; (2) Low cultural context level significantly influences the correlational patterns among 111 SNPs in the principal component analysis diagram; and (3) Among 29 culture/education parameters, several basic characteristics of a language (the numbers of alphabet, vowel, consonant and dialect) demonstrate least correlations with 111 SNPs of 13 language genes.

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Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

South African Journal of Animal Science ◽

10.4314/sajas.v46i3.10 ◽

1970 ◽

Vol 46 (3) ◽

pp. 302-312

Author(s):

A.A. Zwane ◽

A. Maiwashe ◽

M.L. Makgahlela ◽

A. Choudhury ◽

J.F. Taylor ◽

...

Keyword(s):

Principal Component Analysis ◽

Single Nucleotide Polymorphisms ◽

South African ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Indigenous Cattle ◽

Single Nucleotide ◽

Cattle Breeds ◽

Polymorphic Snps ◽

Genome Wide

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds.

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Two-stage approach for identifying single-nucleotide polymorphisms associated with rheumatoid arthritis using random forests and Bayesian networks

BMC Proceedings ◽

10.1186/1753-6561-1-s1-s56 ◽

2007 ◽

Vol 1 (S1) ◽

Cited By ~ 18

Author(s):

Yan Meng ◽

Qiong Yang ◽

Karen T Cuenco ◽

L Adrienne Cupples ◽

Anita L DeStefano ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Single Nucleotide Polymorphisms ◽

Bayesian Networks ◽

Random Forests ◽

Nucleotide Polymorphisms ◽

Two Stage ◽

Single Nucleotide

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Financial performance evaluation of Japanese manufacturing industries: A combined use of DEA discriminant analysis with principal component analysis

2007 IEEE International Engineering Management Conference ◽

10.1109/iemc.2007.5235076 ◽

2007 ◽

Author(s):

Mika Goto ◽

Akihiko Suzuki ◽

Yasuhiro Fuwa ◽

Tomohiro Sato ◽

Toshiyuki Sueyoshi

Keyword(s):

Principal Component Analysis ◽

Performance Evaluation ◽

Discriminant Analysis ◽

Financial Performance ◽

Principal Component ◽

Component Analysis ◽

Manufacturing Industries ◽

Combined Use

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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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Single Nucleotide Polymorphisms in the Bovine TLR2 Extracellular Domain Contribute to Breed and Species-Specific Innate Immune Functionality

Frontiers in Immunology ◽

10.3389/fimmu.2021.764390 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marie-Christine Bartens ◽

Amanda J. Gibson ◽

Graham J. Etherington ◽

Federica Di Palma ◽

Angela Holder ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Bos Indicus ◽

Full Length ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Single Nucleotide ◽

Brown Swiss ◽

Cattle Breeds ◽

Species Specific ◽

Mycobacterial Antigens

Recent evidence suggests that several cattle breeds may be more resistant to infection with the zoonotic pathogen Mycobacterium bovis. Our data presented here suggests that the response to mycobacterial antigens varies in macrophages generated from Brown Swiss (BS) and Holstein Friesian (HF) cattle, two breeds belonging to the Bos taurus family. Whole genome sequencing of the Brown Swiss genome identified several potential candidate genes, in particular Toll-like Receptor-2 (TLR2), a pattern recognition receptor (PRR) that has previously been described to be involved in mycobacterial recognition. Further investigation revealed single nucleotide polymorphisms (SNP) in TLR2 that were identified between DNA isolated from cells of BS and HF cows. Interestingly, one specific SNP, H326Q, showed a different genotype frequency in two cattle subspecies, Bos (B.) taurus and Bos indicus. Cloning of the TLR2 gene and subsequent gene-reporter and chemokine assays revealed that this SNP, present in BS and Bos indicus breeds, resulted in a significantly higher response to mycobacterial antigens as well as tri-acylated lipopeptide ligands in general. Comparing wild-type and H326Q containing TLR2 responses, wild-type bovine TLR2 response showed clear, diminished mycobacterial antigen responses compared to human TLR2, however bovine TLR2 responses containing H326Q were found to be partially recovered compared to human TLR2. The creation of human:bovine TLR2 chimeras increased the response to mycobacterial antigens compared to the full-length bovine TLR2, but significantly reduced the response compared to the full-length human TLR2. Thus, our data, not only present evidence that TLR2 is a major PRR in the mammalian species-specific response to mycobacterial antigens, but furthermore, that there are clear differences between the response seen in different cattle breeds, which may contribute to their enhanced or reduced susceptibility to mycobacterial infection.

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