Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

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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

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (similar to 16.10x) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, similar to 121.2 million single nucleotide polymorphisms, similar to 61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3 '-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep

Greining á tegundafjölbreytni sveppa sem sýkja bygg í íslenskum ökrum

For the past 50 years the importance of barley in Icelandic agriculture has increased, not least as a result of environmental change and new cultivars. Following this the impact of pathogens is expected to increase as well as the importance of knowing which pathogens affect barley in Iceland. Presented here is the first analysis of the diversity of barley fungal pathogens in Iceland. Samples collected from around the country were analysed using molecular methods. At least twelve species of fungi were identified, including R. secalis, a known pathogen in Iceland, as well as fungi not previously recorded on barley in Iceland, including Microdochium nivale, Fusarium avenaceum, and Epicoccum nigrum. Three species, Pyrenophora teres f. teres, Didymella exitialis, and Itersonilia perplexans, are new to the Icelandic funga. The results show that diversity of barley fungal pathogens in Iceland is greater than previously thought and this will have implications for future breeding projects.Síðastliðin 50 ár hefur mikilvægi byggræktar aukist í íslenskum landbúnaði, ekki síst vegna veðurfarsbreytinga og nýrra byggyrkja. Í kjölfar þessarar aukningar er viðbúið að skaðvaldar valdi meira tjóni í ræktun. Því er brýnt að afla þekkingar á hvaða skaðvaldar geta haft áhrif á bygg við íslenskar aðstæður. Rannsóknin sem kynnt er hér er sú fyrst þar sem tegundafjölbreytni sveppasýkla á byggi er greind á Íslandi. Sýnum var safnað umhverfis landið og þau greind með sameindaerfðafræðilegum aðferðum. Að minnsta kosti tólf tegundir sveppa voru greindar, þar með talið Rhyncosporium secalis, þekktur sjúkdómsvaldur í íslenskum byggökrum, en auk þess fundust sveppir sem ekki hafa fundist áður á byggi á Íslandi, svo sem Microdochium nivale, Fusarium avenaceum og Epicoccum nigrum. Þrjár tegundir, Pyrenophora teres f. teres, Didymella exitialis og Itersonilia perplexans eru nýjar í fungu Íslands. Niðurstöðurnar sýna að tegundafjölbreytni sveppa sem sýkja bygg við íslenskar aðstæður er meiri en áður var talið og eru því mikilvægt innlegg til framtíðar ræktunarverkefna

Virulence of Rhynchosporium commune isolates collected in Iceland

Various fungal species continue to be one of the most difficult challenges faced by farmers, and hence societies in whole, when it comes to securing plentiful and wholesome food for a rapidly growing human population. Understanding the biology of pathogenic fungi in detail, both at the population and molecular levels, combined with continued emphasis on resistance breeding of important crops, offers the most obvious sustainable solution to this pressing problem. Here we present results of virulence testing and microsatellite analysis on a collection of Icelandic Rynchosporium commune isolates to test whether the previously demonstrated genetic diversity observed translated into functional diversity in the virulence of these isolates. Our results show considerable diversity in the virulence of the Icelandic R. commune samples with each isolate having a unique virulence spectrum on the 15 near-isogenic barley lines used for screening. Our findings have practical implications, showing that even with short continuous barley cultivation and isolation by geographical distance, breeding for Icelandic, and likely other remote or isolated locations, still needs to consider the importance of disease resistance in breeding decisions and variation in local pathotypes. Moreover, our analysis is the first step to focused breeding for disease resistance for Icelandic conditions, an important step in the ongoing Icelandic barley breeding project

Virulence of Icelandic Pyrenophora teres f. teres populations and resistance of Icelandic spring barley lines

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An overview of barley breeding and variety trials in Iceland in 1987-2014

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