scholarly journals Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk

2015 ◽  
Author(s):  
Rudiger Brauning ◽  
Paul J Fisher ◽  
Alan F McCulloch ◽  
Russell J Smithies ◽  
James F Ward ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Genetic Improvement ◽  
Large Scale ◽  
Red Deer ◽  
Reference Genome ◽  
Sequence Data ◽  
Single Nucleotide Polymorphism Discovery ◽  
Snp Discovery ◽  
Linkage Groups ◽  
Comparative Assembly

Deer farming is a significant international industry. For genetic improvement, using genomic tools, an ordered array of DNA variants and associated flanking sequence across the genome is required. This work reports a comparative assembly of the deer genome and subsequent DNA variant identification. Next generation sequencing combined with an existing bovine reference genome enabled the deer genome to be assembled sufficiently for large-scale SNP discovery. In total, 28 Gbp of sequence data were generated from seven Cervus elaphus (European red deer and Canadian elk) individuals. After aligning sequence to the bovine reference genome build UMD 3.0 and binning reads into one Mbp groups; reads were assembled and analyzed for SNPs. Greater than 99% of the non-repetitive fraction of the bovine genome was covered by deer chromosomal scaffolds. We identified 1.8 million SNPs meeting Illumina InfiniumII SNP chip technical threshold. Markers on the published Red x Pere David deer linkage map were aligned to both UMD3.0 and the new deer chromosomal scaffolds. This enabled deer linkage groups to be assigned to deer chromosomal scaffolds, although the mapping locations remain based on bovine order. Genotyping of 270 SNPs on a Sequenom MS system showed that 88% of SNPs identified could be amplified. Also, inheritance patterns showed no evidence of departure from Hardy-Weinberg equilibrium. A comparative assembly of the deer genome, alignment with existing deer genetic linkage groups and SNP discovery has been successfully completed and validated facilitating application of genomic technologies for subsequent deer genetic improvement.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

2017 ◽  
Author(s):  
Kelly J Vining ◽  
Natalia Salinas ◽  
Jacob A Tennessen ◽  
Jason D Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3731 ◽  
Author(s):  
Kelly J. Vining ◽  
Natalia Salinas ◽  
Jacob A. Tennessen ◽  
Jason D. Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria× ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to theF. vesca‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of theFvbreference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral speciesF. vescafor each chromosome. Linkage groups that were most similar to a second ancestral species,F. iinumae, were only resolved forFvb4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolvedF.× ananassachromosomal regions derived from diploid ancestorF. vesca.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

2017 ◽  
Author(s):  
Kelly J Vining ◽  
Natalia Salinas ◽  
Jacob A Tennessen ◽  
Jason D Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.

scholarly journals Genetic and Physical Mapping of Genic Microsatellites in Barley (Hordeum vulgare L.)

2011 ◽  
Vol 41 (No. 4) ◽  
pp. 153-159
Author(s):  
R.K. Varshney ◽  
U. Hähnel ◽  
T. Thiel ◽  
N. Stein ◽  
L. Altschmied ◽  
...  
Keyword(s):  
Large Scale ◽  
Expressed Sequence Tag ◽  
Sequence Data ◽  
Bac Library ◽  
Linkage Groups ◽  
Hordeum Vulgare L ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Mapping Populations ◽  
Genic Microsatellites

Due to the availability of sequence data from large-scale EST (expressed sequence tag) projects, it has become feasible to develop microsatellite or simple sequence repeat (SSR) markers from genes. A set of 111 090 barley ESTs (corresponding to 55.9 Mb of sequence) was employed for the identification of microsatellites with the help of a PERL5 script called MISA. As a result, a total of 9 564 microsatellites were identified in 8 766 ESTs (SSR-ESTs). Cluster analysis revealed the presence of 2 823 non-redundant SSR-ESTs in this set. From these 754 primer pairs were designed and analysed in a set of seven genotypes including the parents of three mapping populations. Finally, 185 microsatellite (EST-SSRs) loci were placed onto the barley genetic map. These markers show a uniform distribution on all the linkage groups ranging from 21 markers (on 7H) to 35 markers (3H). The polymorphism information content (PIC) for the developed markers ranged from 0.24 to 0.78 with an average of 0.48. For the assignment of these markers to BAC clones, a PCR-based strategy was established to screen the “Morex”-BAC library. By using this strategy BAC addresses were obtained for a total of 127 mapped EST-SSRs, which may provide at least two markers located on a single BAC. This observation is indicative of an uneven distribution of genes and may lead to the identification of gene-rich regions in the barley genome.  

scholarly journals A new gene mapping resource: interspecies hybrids between Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus).

Genetics ◽  
1995 ◽  
Vol 139 (3) ◽  
pp. 1383-1391
Author(s):  
M L Tate ◽  
H C Mathias ◽  
P F Fennessy ◽  
K G Dodds ◽  
J M Penty ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Restriction Enzymes ◽  
Specific Protein ◽  
F1 Hybrids ◽  
Type I ◽  
Linkage Groups ◽  
Gene Map ◽  
Père David’S Deer ◽  
Species Specific

Abstract Three male F1 hybrids between Père David's deer and red deer were mated to red deer to produce 143 backcross calves. The pedigrees are a rare example of a fertile hybrid between evolutionarily divergent species. We examined the use of these families for genetic mapping of evolutionarily conserved (Type I) loci by testing for genetic linkage between five species-specific protein variants and 12 conserved DNA probes. Two probes were homologous, and the remainder syntenic, to the protein coding loci in cattle or humans. Using six restriction enzymes, each DNA probe detected one or more restriction fragments specific to Père David's deer. Linkage analyses among the species-specific variants placed the loci into four linkage groups within which linkage between adjacent loci and gene order was supported by a LOD > 3. The linkage groups were (HPX, HBB)-FSHB-ACP2, LDHA-CD5-IGF2, BMP3-(GC, ALB)-(KIT, PDGFRA) and LDLR-C3-FGF1. Southern and protein analysis of LDHA and ALB provided identical segregation data. These linkage groups were consistent with the cattle gene map and provide new information for comparing the gene maps of ruminants, humans and mice. The deer hybrids are an important new resource that can contribute to the comparative analysis of the mammalian genome.

scholarly journals Application of genotyping-by-sequencing data on inferring the phylogeny of Curcuma (Zingiberaceae) from China

2019 ◽  
Author(s):  
Heng Liang ◽  
Yan Zhang ◽  
Jiabing Deng ◽  
Gang Gao ◽  
Chunbang Ding ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Reference Genome ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Morphological Differentiation ◽  
Genotyping By Sequencing ◽  
Tibet Plateau ◽  
Sequencing Data

Abstract Background: Genotyping-by-sequencing (GBS), as one of the next generation sequences, has been applied to large scale genotyping in plants, which is poor in morphological differentiation and low in genetic divergence among different species. Curcuma is a significantly medicinal and edible genus. Improvement efforts of phylogenetic relationships and disentangling species are still a challenge due to poor morphology and lack in a reference genome. Result: A high-throughput genomic sequence data which was obtained through GBS protocols was used to investigate the relationships among 8 species with 60 total samples of Curcuma. Through the use of the ipyrad software, 437,061 loci and 997,988 filtered SNPs without reliance upon a reference genome were produced. After quality control (QC) of the filtered SNPs, 1,295 high-quality SNPs were used to clarify the phylogenetic relationships among Curcuma species. Based on these data, a supermatrix approach was used to speculate the phylogeny, and the phylogenetic trees and the relationships were inferred . Conclusions: Varying degrees of support can be explained, as well as the diversification events for Chinese Curcuma. The diversification events showed that the third intense uplift of Qinghai–Tibet Plateau (QTP) and formation of the Hengduan Mountains may speed up Curcuma interspecific divergence in China. The PCA suggested the same topology of the phylogenetic tree. The genetic structure analysis revealed that extensive hybridization may exist in Chinese Curcuma. Additionally, the GBS will be a promising approach for the phylogenetic and systematic study in the future.

scholarly journals Sex-biased dispersal in a northern ungulate population

Rangifer ◽  
2011 ◽  
Vol 31 (1) ◽  
pp. 139 ◽  
Author(s):  
Hallvard Haanes ◽  
Knut H. Røed ◽  
Olav Rosef
Keyword(s):  
Genetic Structure ◽  
Cervus Elaphus ◽  
Large Scale ◽  
First Generation ◽  
Red Deer ◽  
Small Scale ◽  
Bayesian Analyses ◽  
Allele Distribution ◽  
Population Information ◽  
Dispersal Distances

In most mammals dispersal is male-biased and in many polygynous ungulates female philopatry and matrilineal grouping involve small-scale genetic structure. We have through sex-related differences in microsatellite allele distribution addressed sex-biased dispersal in a spatially expanding northern ungulate population. The Norwegian red deer population (Cervus elaphus atlanticus) has the last hundred years grown substantially and expanded spatially after a major decline from 300 to 100 years ago. Previous Bayesian analyses suggest a present division of genetic variation into five geographically separated subpopulations. Among these subpopulations the overall Fst values were 0.067 (SE=0.014) for males and 0.094 (SE=0.017) for females. Pairwise Fst values were significantly higher for females than males, demonstrating a stronger genetic structure among females, and that dispersal has been lower in females than males. Accordingly, a higher number of male than female first generation dispersers were identified among the five subpopulations using Bayesian assignment with prior population information, but significantly so only with relaxed stringency levels of assignment. The identified male-biased dispersal distances varied from 30 to 300 kilometers suggesting male biased dispersal on a large scale in red deer.

Future tools for association mapping in crop plantsThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 1017-1023 ◽  
Author(s):  
Chris Duran ◽  
Dominic Eales ◽  
Daniel Marshall ◽  
Michael Imelfort ◽  
Jiri Stiller ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Improvement ◽  
Sequence Data ◽  
Nucleotide Polymorphisms ◽  
Snp Discovery ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Oilseed Brassicas ◽  
Paired Read ◽  
Selection Of

Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences.

Vocalizations in red deer (Cervus elaphus), sika deer (Cervus nippon), and red × sika hybrids

1998 ◽  
Vol 244 (1) ◽  
pp. 123-134 ◽  
Author(s):  
A. M. Long ◽  
N.P. Moore ◽  
T. J. Hayden
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Sika Deer ◽  
Cervus Nippon

The deer of the island of Lampedusa (Pelagian Archipelago, Italy): literary references and osteological evidence

2002 ◽  
Vol 29 (1) ◽  
pp. 51-66 ◽  
Author(s):  
MARCO MASSETP ◽  
BRUNO ZAVA
Keyword(s):  
Nineteenth Century ◽  
Cervus Elaphus ◽  
Red Deer ◽  
Scientific Literature ◽  
Taxonomic Relationships

During the nineteenth century, scientific literature and official reports recorded the occurrence of a population of red deer, Cervus elaphus, on the island of Lampedusa (Pelagian Archipelago, Italy). Osteological specimens collected by the zoologist Enrico Hillier Giglioli towards the end of the century confirmed these references. Since cervids are not found among the fossil fauna of the island, the red deer must have been introduced by man although we do not yet know precisely when. The former existence of the species on Lampedusa is discussed by comparison of literary material and bone evidence. The population's probable origins and its taxonomic relationships with other Mediterranean red deer populations are also analysed.

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