Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wi... more Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wide study we analyzed the signal intensity of 648,315 Single Nucleotide Polymorphisms (SNPs) and identified 1338 genes differentiating cows with ovarian pathologies from healthy cows. The sample consisted of six cows presenting an ovarian pathology and six healthy cows. SNP signal intensities were measured with a genotyping process using the Axiom Genome-Wide BOS 1 SNPchip. Statistical tests for equality of variance and mean were applied to SNP intensities, and significance p-values were obtained. A Benjamini-Hochberg multiple testing correction reveled significant SNPs. Corresponding genes were identified using the Bovine Genome UMD 3.1 annotation. Principal Components Analysis (PCA) confirmed differentiation. An analysis of Copy Number Variations (CNVs), obtained from signal intensities, revealed no evidence of association between ovarian pathologies and CNVs. In addition, a haplotype frequency analysis showed no association with ovarian pathologies. Results show that SNP signal intensity, which captures not only information for base-pair genotypes elucidation, but the amount of fluorescence nucleotide synthetization produced in an enzymatic reaction, is a rich source of information that, by itself or in combination with base-pair genotypes, might be used to implement differentiation, prediction and diagnostic procedures, increasing the scope of applications for Genotyping Microarrays.
Date palm crop was introduced to Mexico by Spanish colonizers. The best climatic conditions for p... more Date palm crop was introduced to Mexico by Spanish colonizers. The best climatic conditions for plant development were found in the San Luis Rio Colorado, Sonora and Mexicali, Baja California valleys. By 2015 both areas achieved the 97% of the national production. High quality Medjool variety is almost the only grown in the region, and is very demanded in international markets. Mexico is the second largest producer in the American continent, and the third largest producer in the world.
Molecular markers have become a very important resource for genetic studies in crops. Due to thei... more Molecular markers have become a very important resource for genetic studies in crops. Due to their genome-wide abundance, it has increased its use for genetic studies in genomes of animals and plants. They have been used in the germplasm of the date palm to identify genetic diversity, sex determination and gene characterization. RAPD, RFLP, AFLP, ISSR and SSR are DNA based molecular markers that have been used to perform genetic diversity analyses. Advantages and disadvantages have been judged based on the level of polymorphism they capture, the quality of template DNA needed, the development cost, the reliability and the level of skill required. Simple sequence repeats (SSR) are DNA based molecular markers that have been used to perform genetic diversity analyses, sex determination and gene characterization in date palm. The SSR markers satisfy most requirements for accurate analysis of genetic diversity. The current study assess the performance of 255 SSR microsatellites that were used in recent studies, where patterns of genetic diversity were analyzed among 1066 date palms, from 411 cultivars in 12 countries. In addition, the different results of genetic diversity are presented, and the 19 SSR markers showing the best performance, were identified for future analysis of genetic diversity in the date palm.
Genomic structural variations represent an important source of genetic variation in mammal genome... more Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ,770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r 2) of short range (#100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r 2 within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.
Copy number variations (CNVs) are an important source of genomic structural variation, and can be... more Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. Microarray technologies have recently been used to study the bovine genome. The objective of the present study was to develop CNVs in Holstein cows from the Northwest of Mexico using the Affymetrix Axiom Genome-Wide BOS 1 Array, which assays 648,315 SNPs and provides a wide coverage for
Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the... more Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the use of genome-wide SNP genotyping arrays. One of the highest densities commercially available SNPchips for cattle is the Affymetrix axiom genome-wide Bos 1, which assays 648,315 informative SNPs across the whole bovine genome. Here, we describe the microarray data, quality controls and validation implemented in a study published in Genetics and Molecular Research Journal in 2015 [1]. The microarray raw data has been deposited into Gene Expression Omnibus under accession #GSE54813.
Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wi... more Hypoplasia and ovarian cysts are the most common ovarian pathologies in cattle. In this genome-wide study we analyzed the signal intensity of 648,315 Single Nucleotide Polymorphisms (SNPs) and identified 1338 genes differentiating cows with ovarian pathologies from healthy cows. The sample consisted of six cows presenting an ovarian pathology and six healthy cows. SNP signal intensities were measured with a genotyping process using the Axiom Genome-Wide BOS 1 SNPchip. Statistical tests for equality of variance and mean were applied to SNP intensities, and significance p-values were obtained. A Benjamini-Hochberg multiple testing correction reveled significant SNPs. Corresponding genes were identified using the Bovine Genome UMD 3.1 annotation. Principal Components Analysis (PCA) confirmed differentiation. An analysis of Copy Number Variations (CNVs), obtained from signal intensities, revealed no evidence of association between ovarian pathologies and CNVs. In addition, a haplotype frequency analysis showed no association with ovarian pathologies. Results show that SNP signal intensity, which captures not only information for base-pair genotypes elucidation, but the amount of fluorescence nucleotide synthetization produced in an enzymatic reaction, is a rich source of information that, by itself or in combination with base-pair genotypes, might be used to implement differentiation, prediction and diagnostic procedures, increasing the scope of applications for Genotyping Microarrays.
Date palm crop was introduced to Mexico by Spanish colonizers. The best climatic conditions for p... more Date palm crop was introduced to Mexico by Spanish colonizers. The best climatic conditions for plant development were found in the San Luis Rio Colorado, Sonora and Mexicali, Baja California valleys. By 2015 both areas achieved the 97% of the national production. High quality Medjool variety is almost the only grown in the region, and is very demanded in international markets. Mexico is the second largest producer in the American continent, and the third largest producer in the world.
Molecular markers have become a very important resource for genetic studies in crops. Due to thei... more Molecular markers have become a very important resource for genetic studies in crops. Due to their genome-wide abundance, it has increased its use for genetic studies in genomes of animals and plants. They have been used in the germplasm of the date palm to identify genetic diversity, sex determination and gene characterization. RAPD, RFLP, AFLP, ISSR and SSR are DNA based molecular markers that have been used to perform genetic diversity analyses. Advantages and disadvantages have been judged based on the level of polymorphism they capture, the quality of template DNA needed, the development cost, the reliability and the level of skill required. Simple sequence repeats (SSR) are DNA based molecular markers that have been used to perform genetic diversity analyses, sex determination and gene characterization in date palm. The SSR markers satisfy most requirements for accurate analysis of genetic diversity. The current study assess the performance of 255 SSR microsatellites that were used in recent studies, where patterns of genetic diversity were analyzed among 1066 date palms, from 411 cultivars in 12 countries. In addition, the different results of genetic diversity are presented, and the 19 SSR markers showing the best performance, were identified for future analysis of genetic diversity in the date palm.
Genomic structural variations represent an important source of genetic variation in mammal genome... more Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ,770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r 2) of short range (#100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r 2 within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.
Copy number variations (CNVs) are an important source of genomic structural variation, and can be... more Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. Microarray technologies have recently been used to study the bovine genome. The objective of the present study was to develop CNVs in Holstein cows from the Northwest of Mexico using the Affymetrix Axiom Genome-Wide BOS 1 Array, which assays 648,315 SNPs and provides a wide coverage for
Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the... more Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the use of genome-wide SNP genotyping arrays. One of the highest densities commercially available SNPchips for cattle is the Affymetrix axiom genome-wide Bos 1, which assays 648,315 informative SNPs across the whole bovine genome. Here, we describe the microarray data, quality controls and validation implemented in a study published in Genetics and Molecular Research Journal in 2015 [1]. The microarray raw data has been deposited into Gene Expression Omnibus under accession #GSE54813.
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