FISH and GISH analysis of the genomic relationships amongPanax species

2009 ◽  
Vol 31 (1) ◽  
pp. 99-105 ◽  
Author(s):  
Hae-Woon Choi ◽  
Dal-Hoe Koo ◽  
Kyong-Hwan Bang ◽  
Kee-Yoeup Paek ◽  
Nak-Sul Seong ◽  
...  
Keyword(s):  
Genomic Relationships ◽  
Gish Analysis

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.

Cytogenetic analyses of intergeneric hybrids between barley and nine species of Elymus

Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 897-904 ◽  
Author(s):  
N.-S. Kim ◽  
G. Fedak ◽  
F. Han ◽  
W. Cao
Keyword(s):  
Wild Species ◽  
Meiotic Chromosome ◽  
Abiotic Stress Tolerance ◽  
Chromosome Analysis ◽  
Intergeneric Hybrids ◽  
Biotic And Abiotic Stress ◽  
Crop Species ◽  
Barley Cultivars ◽  
Bivalent Formation ◽  
Gish Analysis

Wild species in the Triticeae tribe are very valuable resources for agronomic improvement in cereal crop species. Intergeneric hybrids were produced between several barley cultivars and perennial species in the genera Elymus , Thinopyrum , and Pseudoroegneria . Caryopsis formation and subsequent plantlet regeneration from embryo culture were variable depending on the hybrid combinations. Chromosome numbers and hybrid identity were confirmed by GISH analysis on the somatic cells of the hybrids. While the hybrids showed very robust vegetative growth and exceeded the parental spikes in size, their floral morphologies resembled that of the wild species. Meiotic chromosome analysis revealed that the bivalent formation frequency per cell ranged from 0.06 in Hordeum vulgare ‘Betzes’ × Elymus curvatus to 3.0 in Elymus humidus  × H. vulgare ‘Manley’. By GISH analysis on the meiocytes of the hybrid E. humidus × ‘Manley’, the frequency of autosyndetic bivalents exceeded the allosyndetic bivalent formation, which gave an insight into the genome constitution of E. humidus as an autoallohexploid species. Regardless of the low allosyndetic chromosome pairing between barley and E. humidus, this combination may be useful for further input, since E. humidus is known to carry many valuable genes for biotic and abiotic stress tolerance.

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

Construction of chromosomal recombination maps of three genomes of lilies (Lilium) based on GISH analysis

Genome ◽  
2009 ◽  
Vol 52 (3) ◽  
pp. 238-251 ◽  
Author(s):  
Nadeem Khan ◽  
Rodrigo Barba-Gonzalez ◽  
M. S. Ramanna ◽  
Richard G.F. Visser ◽  
Jaap M. Van Tuyl
Keyword(s):  
Molecular Markers ◽  
Interspecific Hybrids ◽  
The Other ◽  
A Genome ◽  
Chromosomal Recombination ◽  
Gish Analysis ◽  
The Way

Chromosomal recombination maps were constructed for three genomes of lily ( Lilium ) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum × Asiatic (LA) and Oriental × Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called “recombination sites”. Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments.

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 GISH analysis revealed new aspect of genomic constitution of Thinopyrum intermedium

2012 ◽  
Vol 41 (Special Issue) ◽  
pp. 92-95 ◽  
Author(s):  
M. Kishii ◽  
R.R.-C. Wang ◽  
H. Tsujimoto
Keyword(s):  
Full Text ◽  
Thinopyrum Intermedium ◽  
Genomic Constitution ◽  
Gish Analysis

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