Mitochondrial DNA genetic diversity in six Italian donkey breeds (<i>Equus asinus</i>)

<p>Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.</p

Extent of LD in domestic cats.

<p>a) Decay of <i>r²</i> value of autosomal chromosomes combined as a function of distance (Kb). Colored decay lines represent selected populations that depict upper, middle, and lower estimates of the LD measures. Gray decay lines represent the remaining populations. Filled circles indicate the point of 50% decay of <i>r²</i> maximum value. b) Distance in kilobases at which <i>r²</i> decays to 50% of the maximum value, which is the distance at <i>r²</i> ≈ 0.25. The distances correspond to the filled circles in (a).</p

Fraction of GWAS-informative SNP pairs at different distance classes in domestic cat breeds.

<p>Colored lines represent selected populations that depict upper, middle, and lower examples whereas the gray lines represent the remaining populations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053537#pone.0053537.s012" target="_blank">Table S6</a>).</p

Population based SNP analysis of the domestic cat.

<p>Number of monomorphic SNPs (left) and SNPs with a minor allele frequency 0< MAF <0.05 (right). Legend corresponds to the ten chromosomal regions.</p

Population and statistic summary of cat breeds for LD study.

*<p>Percent inflation in the estimate of the extent of LD when using MAF ≥0.1.</p>**<p>Fraction of pairs of SNPs at distance class (40–60 Kb) with <i>r²</i> value ≥0.8.</p>***<p>Random bred is combing both eastern and western random bred samples.</p

Domestic cat haplotype structure and diversity of two autosomal regions.

<p>a) Haplotype analysis of chromosome A1 region, which exhibits long extent of LD. b) Haplotype analysis of chromosome C2 region, which exhibits short extent of LD. Breeds/populations are represented on the y-axis and the position of haplotype blocks are shown on the x axis. Haplotype blocks are represented by horizontal rectangles. The frequency of individual haplotypes within a block is proportional to the height of the color. Major haplotype is represented by black color, intermediate haplotypes with frequency >0.1 are represented by blue, light blue, red, green and yellow, respectively. Pink color represents the sum of the frequencies of all haploypes with a frequency <0.1. Empty regions between blocks indicate lack any informative markers (MAF ≥0.05) and can be considered monomorphic across all individuals within a population.</p

Data_Sheet_1_Classification of feline hypertrophic cardiomyopathy-associated gene variants according to the American College of Medical Genetics and Genomics guidelines.docx

IntroductionThe correct labeling of a genetic variant as pathogenic is important as breeding decisions based on incorrect DNA tests can lead to the unwarranted exclusion of animals, potentially compromising the long-term health of a population. In human medicine, the American college of Medical Genetics (ACMG) guidelines provide a framework for variant classification. This study aims to apply these guidelines to six genetic variants associated with hypertrophic cardiomyopathy (HCM) in certain cat breeds and to propose a modified criterion for variant classification.MethodsGenetic samples were sourced from five cat breeds: Maine Coon, Sphynx, Ragdoll, Devon Rex, and British Short- and Longhair. Allele frequencies were determined, and in the subset with phenotypes available, odds ratios to determine the association with HCM were calculated. In silico evaluation followed with joint evidence and data from other publications assisting in the classification of each variant.ResultsTwo variants, MYBPC3:c.91G > C [A31P] and MYBPC3:c.2453C > T [R818W], were designated as pathogenic. One variant, MYH7:c.5647G > A [E1883K], was found likely pathogenic, while the remaining three were labeled as variants of unknown significance.DiscussionRoutine genetic testing is advised solely for the MYBPC3:c.91G > C [A31P] in the Maine Coon and MYBPC3:c.2453C > T [R818W] in the Ragdoll breed. The human ACMG guidelines serve as a suitable foundational tool to ascertain which variants to include; however, refining them for application in veterinary medicine might be beneficial.</p

MOESM5 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 5: Figure S2. Relationship between the number of ROH and the length of the genome (Mb) covered by ROH per individual

MOESM6 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb)

MOESM11 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 11: Table S4. Results of the f3 test