scholarly journals Genotyping-by-sequencing based cytoplasmic markers underpin population structural variation of perennial ryegrass

2019 ◽  
Author(s):  
Mingshu Cao ◽  
Marty Faville ◽  
Jeanne Jacobs ◽  
Marcelo Carena
Keyword(s):  
Structural Variation ◽  
Selective Breeding ◽  
Genotyping By Sequencing ◽  
Plant Performance ◽  
Mitochondrial Genomes ◽  
Nuclear Markers ◽  
Plant Populations ◽  
Cytoplasmic Genome ◽  
Genome Wide ◽  
Mitochondrial Origin

AbstractChloroplast and mitochondrial genomes provide unique information in studying plant populations because cytoplasmic genes exhibit a different mode of inheritance and a different rate of gene mutation compared to nuclear genes. Despite this, cytoplasmic genomic contributions to plant population performance are largely unexplored because few methods are available to characterize and evaluate cytoplasmic genome-wide variations. Here we have developed cytoplasmic markers based on genotyping-by-sequencing (GBS), which enable us to characterize thousands of samples, to survey gene variants across cytoplasmic genomes, and to monitor within-population variations of chloroplast or mitochondrial origin. Using these cytoplasmic genome-wide markers we have found that within-population differentiations are evident in ryegrass (Lolium perenne), beyond the explanation of nuclear markers. Moreover, chloroplast and mitochondrial variations exhibit different patterns, with mitochondrial markers more readily reflecting the maternal origins. Application of GBS-based cytoplasmic markers should facilitate quantifying the contribution of cytoplasmic inheritance to plant performance through selective breeding or under natural selection pressure.

scholarly journals AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs

2018 ◽  
Author(s):  
Gregor Gorjanc ◽  
John M. Hickey
Keyword(s):  
Genetic Diversity ◽  
Genetic Gain ◽  
Selection Criteria ◽  
Selective Breeding ◽  
Conservation Management ◽  
Specific Information ◽  
Plant Populations ◽  
Breeding Programs ◽  
Genome Wide ◽  
Gender Specific

ABSTRACTSummaryAlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimisation can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimisation objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.AvailabilityExecutable versions of AlphaMate for Windows, Mac, and Linux platforms are available at http://www.alpha-genes.roslin.ed.ac.uk/[email protected]

scholarly journals An FGA Frameshift Variant Associated with Afibrinogenemia in Dachshunds

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1065
Author(s):  
Reinhard Mischke ◽  
Julia Metzger ◽  
Ottmar Distl
Keyword(s):  
Protein Sequence ◽  
Sanger Sequencing ◽  
Selective Breeding ◽  
Genome Wide Association Study ◽  
Frameshift Mutation ◽  
Homozygosity Mapping ◽  
Genomic Region ◽  
Severe Bleeding ◽  
Genome Wide ◽  
A Genome

Congenital fibrinogen disorders are very rare in dogs. Cases of afibrinogenemia have been reported in Bernese Mountain, Bichon Frise, Cocker Spaniel, Collie, Lhasa Apso, Viszla, and St. Bernard dogs. In the present study, we examined four miniature wire-haired Dachshunds with afibrinogenemia and ascertained their pedigree. Homozygosity mapping and a genome-wide association study identified a candidate genomic region at 50,188,932–64,187,680 bp on CFA15 harboring FGB (fibrinogen beta chain), FGA (fibrinogen alpha chain), and FGG (fibrinogen gamma-B chain). Sanger sequencing of all three fibrinogen genes in two cases and validation of the FGA-associated mutation (FGA:g.6296delT, NC_006597.3:g.52240694delA, rs1152388481) in pedigree members showed a perfect co-segregation with afibrinogenemia-affected phenotypes, obligate carriers, and healthy animals. In addition, the rs1152388481 variant was validated in 393 Dachshunds and samples from 33 other dog breeds. The rs1152388481 variant is predicted to modify the protein sequence of both FGA transcripts (FGA201:p.Ile486Met and FGA-202:p.Ile555Met) leading to proteins truncated by 306 amino acids. The present data provide evidence for a novel FGA truncating frameshift mutation that is very likely to explain the cases of severe bleeding due to afibrinogenemia in a Dachshund family. This mutation has already been spread in Dachshunds through carriers before cases were ascertained. Genetic testing allows selective breeding to prevent afibrinogenemia-affected puppies in the future.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals Global genome diversity of the Leishmania donovani complex

2019 ◽  
Author(s):  
Susanne U. Franssen ◽  
Caroline Durrant ◽  
Olivia Stark ◽  
Bettina Moser ◽  
Tim Downing ◽  
...  
Keyword(s):  
Structural Variation ◽  
Leishmania Donovani ◽  
Geographical Origin ◽  
Genomic Variation ◽  
Protozoan Parasites ◽  
Suspected Drug ◽  
Genetic Groups ◽  
Genome Wide ◽  
Future Work ◽  
Globally Distributed

AbstractProtozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.

scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

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