scholarly journals RAPD and Cytological Analyses of Picea Spp. from Different Provenances: Genomic Relationships among Taxa

Hereditas ◽  
2004 ◽  
Vol 130 (2) ◽  
pp. 137-144 ◽  
Author(s):  
K. K. Nkongolo
Keyword(s):  
Genomic Relationships

scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

scholarly journals DArTseq-based analysis of genomic relationships among species of tribe Triticeae

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Offiong U. Edet ◽  
Yasir S. A. Gorafi ◽  
Shuhei Nasuda ◽  
Hisashi Tsujimoto
Keyword(s):  
Genomic Relationships ◽  
Tribe Triticeae

scholarly journals Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries)

2020 ◽  
Vol 98 (10) ◽  
Author(s):  
Elizabeth M Ross ◽  
Ben J Hayes ◽  
David Tucker ◽  
Jude Bond ◽  
Stuart E Denman ◽  
...  
Keyword(s):  
Methane Production ◽  
Prediction Accuracy ◽  
Live Weight ◽  
Ovis Aries ◽  
Prediction Algorithm ◽  
Genomic Relationship ◽  
Time Points ◽  
Genomic Relationships ◽  
Genomic Predictions ◽  
Time Point

Abstract Methane production from rumen methanogenesis contributes approximately 71% of greenhouse gas emissions from the agricultural sector. This study has performed genomic predictions for methane production from 99 sheep across 3 yr using a residual methane phenotype that is log methane yield corrected for live weight, rumen volume, and feed intake. Using genomic relationships, the prediction accuracies (as determined by the correlation between predicted and observed residual methane production) ranged from 0.058 to 0.220 depending on the time point being predicted. The best linear unbiased prediction algorithm was then applied to relationships between animals that were built on the rumen metabolome and microbiome. Prediction accuracies for the metabolome-based relationships for the two available time points were 0.254 and 0.132; the prediction accuracy for the first microbiome time point was 0.142. The second microbiome time point could not successfully predict residual methane production. When the metabolomic relationships were added to the genomic relationships, the accuracy of predictions increased to 0.274 (from 0.201 when only the genomic relationship was used) and 0.158 (from 0.081 when only the genomic relationship was used) for the two time points, respectively. When the microbiome relationships from the first time point were added to the genomic relationships, the maximum prediction accuracy increased to 0.247 (from 0.216 when only the genomic relationship was used), which was achieved by giving the genomic relationships 10 times more weighting than the microbiome relationships. These accuracies were higher than the genomic, metabolomic, and microbiome relationship matrixes achieved alone when identical sets of animals were used.

scholarly journals Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH

2007 ◽  
Vol 94 (12) ◽  
pp. 1963-1971 ◽  
Author(s):  
G. Seijo ◽  
G. I. Lavia ◽  
A. Fernandez ◽  
A. Krapovickas ◽  
D. A. Ducasse ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Genomic Relationships ◽  
Cultivated Peanut ◽  
Close Relatives

scholarly journals Evaluation of the pathogenic potential, antimicrobial susceptibility, and genomic relations of Yersinia enterocolitica strains from food and human origin

2015 ◽  
Vol 61 (11) ◽  
pp. 851-860 ◽  
Author(s):  
Cecilia S.M. Lucero-Estrada ◽  
José Miguel Soria ◽  
Gabriela Isabel Favier ◽  
María Esther Escudero
Keyword(s):  
Yersinia Enterocolitica ◽  
Antimicrobial Susceptibility ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Pathogenic Potential ◽  
Human Samples ◽  
Virulence Markers ◽  
San Luis ◽  
Food Borne ◽  
Genomic Relationships

Yersinia enterocolitica is a food-borne pathogen that causes gastroenteritis with occasional postinfection sequels. This study was aimed to determinate the pathogenic potential, antimicrobial susceptibility, and genomic relationships of Y. enterocolitica strains of different bioserotypes (B/O) isolated from foods and human samples in San Luis, Argentina. Strains obtained by culture were bioserotyped and characterized by phenotypic and genotypic virulence markers, antimicrobial susceptibility, and pulsed-field gel electrophoresis (PFGE). Yersinia enterocolitica was detected in 9.2% of 380 samples, with a distribution of 10.6% (30/284) for food products and 5.2% (5/96) for human samples. Regarding the pathogenic potential, B1A strains of different serotypes were virF– ail–, of which 72.0% (13/18) were ystB+ with virulence-related phenotypic characteristics. Among B2/O:9 isolates, 75.0% (9/12) exhibited the genotype virF+ ail+ ystB– along with phenotypic traits associated with virulence; the same genotype was observed in 80.0% (4/5) of B3/O:3 and B3/O:5 strains. By PFGE, it was possible to separate Y. enterocolitica biotypes into 4 clonal groups (A to D) with 23 genomic types, generating a discriminatory index of 0.96. All isolates were susceptible to antimicrobials used for clinical treatment. This study highlights the presence of pathogenic bioserotypes and the high genomic diversity of the Y. enterocolitica strains isolated in our region.

Genomic relationships between Dasypyrum villosum (L.) Candargy and D. hordeaceum (Cosson et Durieu) Candargy

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 83-92 ◽  
Author(s):  
A. Blanco ◽  
R. Simeone ◽  
P. Resta ◽  
C. De Pace ◽  
V. Delre ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Dasypyrum Villosum ◽  
Repeated Dna ◽  
Esterase Isozyme ◽  
Dot Blot ◽  
Genomic Relationships ◽  
Repeated Dna Sequence

The origin and genomic constitution of the tetraploid perennial species Dasypyrum hordeaceum (2n = 4x = 28) and its phylogenetic relationships with the annual diploid Dasypyrum villosum (2n = 2x = 14) have been investigated by comparing the two genomes using different methods. There is no apparent homology between the conventional or Giemsa C-banded karyotypes of the two Dasypyrum species, nor can the karyotype of D. hordeaceum be split up into two similar sets. Polymorphism within several chromosome pairs was observed in both karyotypes. Cytophotometric determinations of the Feulgen–DNA absorptions showed that the genome size of D. hordeaceum was twice as large as that of D. villosum. Both the cross D. villosum × D. hordeaceum (crossability rate 12.1%) and the reciprocal cross (crossability rate 50.7%) produced plump seeds. Only those from the former cross germinated, producing sterile plants with a phenotype that was intermediate between those of the parents. In these hybrids (2n = 21), an average of 13.77 chromosomes per cell paired at meiotic metaphase I. Trivalents were only rarely observed. Through dot-blot hybridizations, a highly repeated DNA sequence of D. villosum was found not to be represented in the genome of D. hordeaceum. By contrast, very similar restriction patterns were observed when a low-repeated DNA sequence or different single-copy sequences of D. villosum or two sequences in the plastidial DNA of rice were hybridized to Southern blots of the genomic DNAs of the two Dasypyrum species digested with different restriction endonucleases. By analyzing glutamic-oxaloacetic-transaminase, superoxide dismutase, alcohol dehydrogenase, and esterase isozyme systems, it was shown that both Dasypyrum species shared the same phenotypes, which differed from those found in hexaploid wheat. In situ hybridizations using DNA sequences encoding gliadins showed that these genes were located close to the centromere of three pairs of D. villosum chromosomes and that they had the same locations in six pairs of D. hordeaceum chromosomes. We conclude that the autoploid origin of D. hordeaceum from D. villosum, which cannot be defended on the basis of chromosomal traits, is suggested by the other findings obtained by comparing the two genomes. Key words : Dasypyrum hordeaceum, Dasypyrum villosum, phylogenetic relationships.

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