Patterns of homozygosity in insular and continental goat breeds

Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and F values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management. The online version of this article (10.1186/s12711-018-0425-7) contains supplementary material, which is available to authorized users

Organ explant culture of neonatal rat ventricles: a new model to study gene and cell therapy.

Testing cardiac gene and cell therapies in vitro requires a tissue substrate that survives for several days in culture while maintaining its physiological properties. The purpose of this study was to test whether culture of intact cardiac tissue of neonatal rat ventricles (organ explant culture) may be used as a model to study gene and cell therapy. We compared (immuno) histology and electrophysiology of organ explant cultures to both freshly isolated neonatal rat ventricular tissue and monolayers. (Immuno) histologic studies showed that organ explant cultures retained their fiber orientation, and that expression patterns of α-actinin, connexin-43, and α-smooth muscle actin did not change during culture. Intracellular voltage recordings showed that spontaneous beating was rare in organ explant cultures (20%) and freshly isolated tissue (17%), but common (82%) in monolayers. Accordingly, resting membrane potential was -83.9±4.4 mV in organ explant cultures, -80.5±3.5 mV in freshly isolated tissue, and -60.9±4.3 mV in monolayers. Conduction velocity, measured by optical mapping, was 18.2±1.0 cm/s in organ explant cultures, 18.0±1.2 cm/s in freshly isolated tissue, and 24.3±0.7 cm/s in monolayers. We found no differences in action potential duration (APD) between organ explant cultures and freshly isolated tissue, while APD of monolayers was prolonged (APD at 70% repolarization 88.8±7.8, 79.1±2.9, and 134.0±4.5 ms, respectively). Organ explant cultures and freshly isolated tissue could be paced up to frequencies within the normal range for neonatal rat (CL 150 ms), while monolayers could not. Successful lentiviral (LV) transduction was shown via Egfp gene transfer. Co-culture of organ explant cultures with spontaneously beating cardiomyocytes increased the occurrence of spontaneous beating activity of organ explant cultures to 86%. We conclude that organ explant cultures of neonatal rat ventricle are structurally and electrophysiologically similar to freshly isolated tissue and a suitable new model to study the effects of gene and cell therapy

Patterns of homozygosity in insular and continental goat breeds

Background: Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. Results: Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and FROH values (P value Conclusions: These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management.This article is published as Cardoso, Taina F., Marcel Amills, Francesca Bertolini, Max Rothschild, Gabriele Marras, Geert Boink, Jordi Jordana et al. "Patterns of homozygosity in insular and continental goat breeds." Genetics Selection Evolution 50 (2018): 56. doi: 10.1186/s12711-018-0425-7.</p

Patterns of homozygosity in insular and continental goat breeds

BACKGROUND: Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. RESULTS: Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and FROH values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. CONCLUSIONS: These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management

Summary data from optical mapping.

<p>Values are n (%) or mean ± standard error of the mean. CL, cycle length; CV, conduction velocity; d(%APA)/dt<i>_max</i>_,, maximal upstroke velocity. *−* or †−† statistically different from each other, p<0.05.</p

Summary data from intracellular recordings.

<p>Values are n (%) or mean ± standard error of the mean. RMP, resting membrane potential; MDP, maximal diastolic potential. *−* or †−† statistically different from each other, p<0.05.</p

Organ explant cultures can be used to study the effects of gene and cell therapy.

<p><b>A,</b> EGFP expression in organ explant cultures transduced with LV-<i>Egfp</i>. <b>B,</b> Percentage of preparations showing spontaneous beating, comparing organ explant cultures alone with organ explants co-cultured with spontaneously beating neonatal rat ventricular cardiomyocytes. <b>C,</b> Isochronal activation map of organ explant culture with spontaneously beating neonatal rat ventricular cardiomyocytes, constructed from the moment of maximal action potential upstroke velocity. Spontaneous beating originates from the monolayer, with capture of organ explant culture. Numbers are activation times in ms.*−* statistically different from each other, p<0.05.</p

Optical mapping results comparing monolayers cultured in monolayer medium or organ explant medium.

<p><b>A,</b> Percentage of monolayers showing spontaneous beating activity. <b>B,</b> Cycle length of spontaneously beating monolayers (ms; mean ± SEM). <b>C,</b> Conduction velocity (cm/s; mean ± SEM). <b>D,</b> Action potential duration at 20%, 50%, 70% and 90% repolarization (ms; mean ± SEM). <b>E,</b> Percentage of monolayers showing propagated action potentials when stimulated at 500, 400, 300, 200, 150, and 100 ms cycle length.</p

Typical examples from intracellular recordings.

<p>Typical examples of action potentials as measured with intracellular recordings when stimulated at 500 ms cycle length.</p

Organ explant cultures are (immuno) histologically similar to freshly isolated tissue.

<p>From left to right: organ explant cultures, freshly isolated tissue, and monolayers. <b>A,</b> Hematoxylin-eosin staining. <b>B,</b> Immunohistochemistry for α-actinin (green). <b>C,</b> Immunohistochemistry for connexin-43 (green). <b>D,</b> Immunohistochemistry for α-smooth muscle actin (green). Nuclei are stained with sytox orange (red).</p