scholarly journals Identification of Single Nucleotide Polymorphism in Y-chromosome Specific DDX3Y Gene in Murrah Buffalo Bulls

2022 ◽  
Author(s):  
P. Ramajayan ◽  
S.N. Sivaselvam ◽  
S.M.K. Karthickeyan ◽  
A. Gopinathan ◽  
S. Poobitha
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Phylogenetic Tree ◽  
Y Chromosome ◽  
Bos Taurus ◽  
Production Performance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Murrah Buffalo ◽  
Frozen Semen ◽  
Single Nucleotide Variations

Background: Molecular markers based approaches are essential to select fertile bulls for frozen semen production at an early age. The present investigation was undertaken to perform the molecular characterization and identify single nucleotide polymorphisms (SNP) in Y-chromosome specific DDX3Y gene in Murrah buffalo bulls. Methods: The genomic DNA isolated from the blood samples of 70 Murrah buffalo bulls, covering bulls with normal seminal traits and poor production performance (poor semen quality, freezability, libido), were subjected to PCR amplification. The sequences of DDX3Y gene were analyzed for single nucleotide polymorphism using the seqman module of DNASTAR LASERGENE software. The single nucleotide variations in the sequences with reference to the Bos taurus sequence were determined using Clustal W. The phylogenetic tree and genetic distance were constructed using the MegAlign module. Result: The analysis of sequences revealed that the exons and their adjacent intronic regions of the DDX3Y gene are monomorphic in nature without any variations indicating that the sequences are highly conserved in the studied population of Murrah buffalo bulls. However, a considerable number of single nucleotide variations were observed in the sequences of Murrah buffalo compared with Bos taurus sequences. Furthermore, the phylogenetic tree analysis revealed less divergence and close genetic association between the sequences of Murrah buffalo and other species in the bovinae family than the caprinea species. Further studies on DDX3Y gene in a more extensive and diverse population of Murrah buffalo bulls distributed in different regions could aid to discover substantial SNPs.

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

scholarly journals Frecuencias alélicas para variantes SNP en el gen Nramp1 en bovinos infectados con Brucella abortus o clasificados por resistencia al patógeno

2009 ◽  
Vol 10 (1) ◽  
pp. 43
Author(s):  
Fernando Cerquera M. ◽  
Rodrigo Martínez S. ◽  
Rubén Toro O. ◽  
Jaime Tobón C. ◽  
Jaime Gallego G. ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Brucella Abortus ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Natural Resistance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Allelic Frequencies ◽  
Bos Taurus Indicus

<p>La resistencia natural a la brucelosis en bovinos ha sido asociada a factores genéticos, principalmente a algunos polimorfismos de nucleótido simple ubicados dentro del gen Nramp1. La presente investigación evalúa el efecto de variantes tipo polimorfismos de nucleótido simple presentes en regiones codificantes y en la región 3’UTR del gen Nramp1, en la clasificación de los animales como resistentes o susceptibles; además se determinan los genotipos predominantes en animales naturalmente infectados y comprobados como positivos por la presencia de anticuerpos anti <em>Brucella abortus</em>. Se establecieron las frecuencias genotípicas y alélicas para cinco polimorfismos de nucleótido simple identificados dentro del gen Nramp1 en animales de las razas blanco orejinegro (<em>Bos taurus taurus</em>) y cebú (<em>Bos taurus indicus</em>) y en muestras serológicamente positivas provenientes de animales cruzados (<em>Bos taurus </em>x <em>Bos indicus</em>). La determinación de genotipos se realizó mediante la metodología polimorfismo conformacional de cadena sencilla. Se realizó un ensayo de desafío infeccioso in vitro, para estimar la capacidad de los macrófagos bovinos para controlar la sobrevivencia bacterial, lo que permitió definir los individuos como resistentes o susceptibles. Los resultados sugieren una asociación significativa del SNP4 (<em>p </em>= 0,0506) con la variación para el fenotipo de susceptibilidad, pues se encontró el genotipo homocigoto (BB) en alta frecuencia en animales catalogados como resistentes y el genotipo heterocigoto (AB) en alta frecuencia en animales catalogados como susceptibles y en animales con títulos de anticuerpos anti <em>Brucella abortus</em>.  </p><p> </p><p><strong>Allelic frequencies for SNP variants in the gene Nramp1 in bovine infected with </strong><strong><em>Brucella abortus </em></strong><strong>or classified by resistance to the pathogen</strong>  </p><p>The natural resistance to brucellosis in cattle has been associated to genetic factors mainly to some single nucleotide polymorphism (SNP), located within Nramp1 gen. The current research has studied the effect of nucleotide variants to be found in coding regions and other one located in 3 non translated region of Nramp1 gene, on the animal classification as resistant or susceptible, moreover was identified the main genotypes to be found on the infected animals, confirmed as positives by antibody antibrucella titles. Was established the genotypic and allelic frequencies for five single nucleotide polymorphism in animals from blanco orejinegro (<em>Bos taurus taurus</em>) and zebu breeds (<em>Bos taurus indicus</em>) and serum samples belonging to positive crossbred animals (<em>Bos taurus x Bos indicus</em>). The genotype was defined by the methodology known as “single strand conformational polymorphism”. To estimate the macrophage capacity to control the bacterial survival, an in vitro assay was performed, which allowed define the phenotype as resistant or susceptible. The results suggest a significant association for SNP4 (p = 0.0506) with the phenotypic variation for resistant or susceptibility, because was found the genotype (BB) at higher frequency in susceptible animals and naturally infected animals, than those resistant animals. </p>

scholarly journals Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0249825
Author(s):  
Qun Ji ◽  
Honglian Zhu ◽  
Xinfang Huang ◽  
Kai Zhou ◽  
Zhengwei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Phylogenetic Tree ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Linear Leaf ◽  
Water Dropwort

The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.

scholarly journals Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

2009 ◽  
Vol 10 (8) ◽  
pp. R82 ◽  
Author(s):  
Sebastian H Eck ◽  
Anna Benet-Pagès ◽  
Krzysztof Flisikowski ◽  
Thomas Meitinger ◽  
Ruedi Fries ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bos Taurus ◽  
Single Nucleotide Polymorphism Discovery ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphism Discovery

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

2020 ◽  
Vol 60 (15) ◽  
pp. 1769
Author(s):  
J. B. S. Ferraz ◽  
X. -L. Wu ◽  
H. Li ◽  
J. Xu ◽  
R. Ferretti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Selection ◽  
Bos Taurus ◽  
Imputation Accuracy ◽  
Bos Indicus ◽  
Zebu Cattle ◽  
Low Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Chip

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

scholarly journals Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

2018 ◽  
Vol 135 (6) ◽  
pp. 432-441 ◽  
Author(s):  
Nilesh Nayee ◽  
Goutam Sahana ◽  
Swapnil Gajjar ◽  
Ananthasayanam Sudhakar ◽  
Kamlesh Trivedi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Genomic Studies

scholarly journals Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

Insects ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 230
Author(s):  
Zhiming Chen ◽  
Guihua Wang ◽  
Min Li ◽  
Zhengqiang Peng ◽  
Habib Ali ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Structure Analysis ◽  
Restriction Site ◽  
Southern China ◽  
Leaf Beetle ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Invasion Pathway

To determine population genomic structure through high-throughput sequencing techniques has revolutionized research on non-model organisms. The coconut leaf beetle, Brontispa longissima (Gestro), is a widely distributed pest in Southern China. Here, we used restriction site-associated DNA (RAD) genotyping to assess the invasion pathway by detecting and estimating the degree of genetic differentiation among 51 B. longissima accessions collected from Southern China. A total of 10,127 SNPs were obtained, the screened single nucleotide polymorphism (SNP) information was used to construct the phylogenetic tree, FST analysis, principal component analysis, and population structure analysis. Genetic structure analysis was used to infer the population structure; the result showed that all accessions were divided into Hainan population and non-Hainan population. The Hainan population remained stable, only the Sansha population differentiated, and the non-Hainan populations have gradually differentiated into smaller sub-populations. We concluded that there are two sources of invasion of B. longissima into mainland China: Taiwan and Hainan. With the increase of the invasion time, the Hainan population was relatively stable, and the Taiwan population was differentiated into three sub-populations. Based on the unrooted phylogenetic tree, we infer that Taiwan and Hainan are the two invasive base points. The Taiwan population invaded Fujian, Guangdong, and Guangxi, while the Hainan population invaded Yunnan and Sansha. Our results provide strong evidence for the utility of RAD sequencing (RAD-seq) in population genetics studies, and our generated SNP resource could provide a valuable tool for population genomics studies of B. longissima in the future.

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