Efficient SNP Discovery by Combining Microarray and  Lab-on-a-Chip Data for Animal Breeding and Selection

Huang, Chao‐Wei; Lin, Yang; Ding, Shih‐Torng; Lo, L. L.; Wang, Pei-Hwa; Lin, Eric S.; Liu, Fang-Wei; Lu, Yen‐Wen

doi:10.3390/microarrays4040570

“…We found evidence for direct links between CAD genes and fitness ( S4 and S5 Tables) including genes associated with reproductive ( PPAP2B , [ 53 ]) or twinning ( SMAD3 , [ 54 ]) capacity and number of offspring produced (e.g. KIAA1462 , [ 55 ], SLC22A5 , [ 56 ]). PHACTR1 , LPL , SMAD3 , ABO and SLC22A5 may contribute to reproductive timing (menarche, menopause) in women [ 57 – 59 ] and animals [ 60 ].…”

Section: Resultsmentioning

confidence: 99%

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

Byars

¹

,

Huang

²

,

Gray

³

et al. 2017

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Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.

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“…We found evidence for direct links between CAD genes and fitness (S4 and S5 Tables) including genes associated with reproductive (PPAP2B, [53]) or twinning (SMAD3, [54]) capacity and number of offspring produced (e.g. KIAA1462, [55], SLC22A5, [56]). PHACTR1, LPL, SMAD3, ABO and SLC22A5 may contribute to reproductive timing (menarche, menopause) in women [57][58][59] and animals [60].…”

Section: Enrichment Of Cad Loci For Lifetime Reproductive Outcomes Anmentioning

confidence: 97%

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

Byars

¹

,

Huang

²

,

Gray

³

et al. 2016

Preprint

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Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.

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“…They also describe the pitfalls and issues when dealing with quality control of SNP array data from livestock species, especially regarding standardization and integration. The last paper evaluates the use of Lab-on-a-Chip data combined with SNP microarrays in the context of animal breeding and selection [9]. They give examples of SNP loci related to economical traits of common livestock and also suggestions for screening using a combination of Whole Genome Sequencing (WGS) and SNP chips.…”

Section: Contributionsmentioning

confidence: 99%

SNP Arrays

Louhelainen

¹

2016

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The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays) focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

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Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

Cited by 18 publications

References 125 publications

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

SNP Arrays

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