scholarly journals Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats

2021 ◽  
Author(s):  
Heidi Anderson ◽  
Stephen Davison ◽  
Katie M. Lytle ◽  
Leena Honkanen ◽  
Jamie Freyer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Domestic Cat ◽  
Blood Type ◽  
Domestic Cats ◽  
Breeding Programs ◽  
Genomic Databases ◽  
Panel Testing ◽  
Genome Wide ◽  
Physical Traits

In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB. Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination to investigate the causality of a number of tested variants across different breed backgrounds. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds. This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.

scholarly journals Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1369 ◽  
Author(s):  
Lois Balmer ◽  
Caroline Ann O’Leary ◽  
Marilyn Menotti-Raymond ◽  
Victor David ◽  
Stephen O’Brien ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Candidate Genes ◽  
The United States ◽  
Domestic Cat ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Preventative Health ◽  
Genome Wide ◽  
A Genome

Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH. Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.

scholarly journals Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

2021 ◽  
Author(s):  
Jialin Liu ◽  
Huimin Xie ◽  
Ting Lin ◽  
Congxiao Tie ◽  
Huolin Luo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variants ◽  
Pedigree Information ◽  
Biological Processes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Soybean Cultivars ◽  
Genome Wide

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.

scholarly journals Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool

2020 ◽  
Author(s):  
Mariangela Arca ◽  
Brigitte Gouesnard ◽  
Tristan Mary-Huard ◽  
Marie-Christine Le Paslier ◽  
Cyril Bauland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Haplotype Diversity ◽  
Inbred Lines ◽  
Genomic Diversity ◽  
Breeding Programs ◽  
Genome Wide ◽  
Dna Pools ◽  
Maize Landraces ◽  
Modern Breeding

ABSTRACTMaize landraces preserved in genebanks have a large genetic diversity that is still poorly characterized and underexploited in modern breeding programs. Here, we genotyped DNA pools from 156 American and European landraces with a 50K SNP Illumina array to study the effect of both human selection and environmental adaptation on the genome-wide diversity of maize landraces. Genomic diversity of landraces varied strongly in different parts of the genome and with geographic origin. We detected selective footprints between landraces of different geographic origin in genes involved in the starch pathway (Su1, Waxy1), flowering time (Zcn8, Vgt3, ZmCCT9) and tolerance to abiotic and biotic stress (ZmASR, NAC and dkg genes). Landrace diversity was compared to that of (i) 327 inbred lines representing American and European diversity (“CK lines) and (ii) 103 new lines derived directly from landraces (“DH-SSD lines”). We observed limited diversity loss or selective sweep between landraces and CK lines, except in peri-centromeric regions. However, analysis of modified Roger’s distance between landraces and the CK lines showed that most landraces were not closely related to CK lines. Assignment of CK lines to landraces using supervised analysis showed that only a few landraces, such as Reid’s Yellow Dent, Lancaster Surecrop and Lacaune, strongly contributed to modern European and American breeding pools. Haplotype diversity of CK lines was more enriched by DH-SSD lines that derived from the landraces with no related lines and the lowest contribution to CK lines. Our approach opens an avenue for the identification of promising landraces for pre-breeding.SIGNIFICANCE STATEMENTSMaize landraces are a valuable source of genetic diversity for addressing the challenges of climate change and the requirements of low input agriculture as they have been long selected to be well adapted to local agro-climatic conditions and human uses. However, they are underutilized in modern breeding programs because they are poorly characterized, genetically heterogeneous and exhibit poor agronomic performance compared to elite hybrid material. In this study, we developed a high-throughput approach to identify landraces that could potentially enlarge the genetic diversity of modern breeding pools. We genotyped DNA pools from landraces using 50K array technology, which is widely used by breeders to characterize the genetic diversity of inbred lines. To identify landraces that could enrich the modern maize germplasm, we estimated their contribution to inbred lines using supervised analysis and a new measurement of genetic distance.

Conservation of feline semen: Part I: Cooling and freezing protocols

2003 ◽  
Vol 5 (4) ◽  
pp. 203-208 ◽  
Author(s):  
G.C Luvoni ◽  
E Kalchschmidt ◽  
S Leoni ◽  
C Ruggiero
Keyword(s):  
Assisted Reproduction ◽  
Artificial Insemination ◽  
Domestic Cat ◽  
Accurate Data ◽  
Domestic Cats ◽  
Breeding Programs ◽  
Long Term Storage ◽  
Wild Felids ◽  
Term Storage

There has been increased interest recently in the conservation of wild felids and preservation of valuable cat breeds. Assisted reproduction, by means of artificial insemination (AI), is an important tool for developing breeding programs for conservation. Optimal use of AI requires accurate data on semen conservation protocols and its long-term storage/survival. In this paper, semen cooling and freezing processes are described, with special emphasis on the results obtained in experiments performed in the domestic cat. Conception rates after AI in wild and domestic cats are also reported.

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 Genetic Diversity of Insulin Resistance and Metabolic Syndrome

2020 ◽  
Author(s):  
Sanghoo Lee ◽  
Jinwoo Ahn ◽  
Jimyeong Park ◽  
Hyeonkyun Na ◽  
Youngkee Lee ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Genetic Diversity ◽  
Metabolic Syndrome ◽  
Genetic Variants ◽  
Association Studies ◽  
Public Health Problem ◽  
Genome Wide Association Studies ◽  
Global Public Health ◽  
Genome Wide ◽  
Rare Genetic Variants

A key in the etiology of a cluster of metabolic syndrome such as hyperglycemia, dyslipidemia, and obesity is known for insulin resistance, which is becoming a major global public health problem. Extensive studies have revealed many genetic factors for both insulin resistance and the components of metabolic syndrome. Advanced modern genotyping methods including genome-wide association studies and next-generation sequencing have allowed for the identification of both common and rare genetic variants related to these chronic disease-associated traits. Multiple genotype–phenotype studies are also needed to identify new and accurate genetic biomarkers in these conditions. The purpose of this chapter is to present genetic variants related to the pathogenesis of metabolic syndrome and insulin resistance and is to review the relevance between insulin resistance and metabolic syndrome clusters in terms of genetic diversity.

A Caution in Association of ABO Blood Group with COVID-19

2020 ◽  
Keyword(s):  
Gene Cluster ◽  
Clinical Outcomes ◽  
Blood Group ◽  
Association Analysis ◽  
Blood Type ◽  
Genome Wide Association ◽  
Chromosome 3 ◽  
Abo Blood Group ◽  
Genome Wide Association Analysis ◽  
Genome Wide

A comment on Zhao J, Yang Y, Huang H, Li D, Gu D, Lu X, et al. Association of ABO blood group and Covid19 susceptability. medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.03.11.20031096. Zeng X, Fan H, Lu D, Huang F, Meng X, Li Z, et al. Association between ABO blood group and clinical outcomes of Covid19. medRxiv[PREPRINT].2020; https://doi.org/10.1101/2020.04.15.20063107. Zietz M, Tatonetti N. Testing the association between blood type and COVID-19 infection, intubation, and death medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.04.08.20058073. Ellinghaus D, Degenhardt F, Bujanda L, al. e. The ABO blood group and a chromosome 3 gene cluster associate with SRAS-CoV2 respitarory failure in an Italy-Spain genome-wide association analysis. medRxiv. 2020; https://doi.org/10.1101/2020.05.31.20114991.

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