Lehmien ylläpitotarpeen ja muuntokelpoisen energian käytön tehokkuuden perinnöllinen vaihtelu maidontuotannossa

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Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

<div><p>In many parts of the world the damaging potato late blight pathogen, <i>Phytophthora infestans</i>, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 <i>P</i>. <i>infestans</i> isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of <i>P</i>. <i>infestans</i>.</p></div

Spatial consistency in drivers of population dynamics of a declining migratory bird

1. Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of- the-art analytical tools are typically tailored to specific datasets. 2. We capitalized on a recent data harmonization initiative (SPI-Birds) and linked it to a generalized modelling framework to identify the demographic and environmental drivers of large-scale population decline in migratory pied flycatchers (Ficedula hypoleuca) breeding across Britain. 3. We implemented a generalized integrated population model (IPM) to estimate age-specific vital rates, including their dependency on environmental conditions, and total and breeding population size of pied flycatchers using long-term (34–64 years) monitoring data from seven locations representative of the British breeding range. We then quantified the relative contributions of different vital rates and population structure to changes in short-and long-term population growth rate using transient life table response experiments (LTREs). 4. Substantial covariation in population sizes across breeding locations suggested that change was the result of large-scale drivers. This was supported by LTRE analyses, which attributed past changes in short-term population growth rates and long-term population trends primarily to variation in annual survival and dispersal dynamics, which largely act during migration and/or nonbreeding season. Contributions of variation in local reproductive parameters were small in comparison, despite sensitivity to local temperature and rainfall within the breeding period. 5. We show that both short-and long-term population changes of British breeding pied flycatchers are likely linked to factors acting during migration and in nonbreeding areas, where future research should be prioritized. We illustrate the potential of multi-population analyses for informing management at (inter)national scales and highlight the importance of data standardization, generalized and accessible analytical tools, and reproducible workflows to achieve them. annual survival, comparative analysis, environmental effects, full annual cycle, integrated population model, LTRE, multi-population, pied flycatcherpublishedVersio

Forensic use of the genomic relationship matrix to validate and discover livestock pedigrees

Correct pedigree is essential to produce accurate genetic evaluations of livestock populations. Pedigree validation has traditionally been undertaken using microsatellites and more recently, based on checks on opposing homozygotes using single nucleotide polymorphisms (SNPs). In this study, the genomic relationship matrix was examined to see whether it was a useful tool to forensically validate pedigree and discover unknown pedigree. Using 5,993 genotyped Limousin animals which were imputed to a core set of 38,907 SNPs, the genomic relationships between animals were assessed to validate the reported pedigree. Using already pedigree-verified animals, the genomic relationships between animals of different relationships were shown to be on average 0.58, 0.59, 0.32, 0.32, 0.19, and 0.14 between animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents, respectively. Threshold values were defined based on the minimum genomic relationship reported between already pedigree-verified animals; 0.46, 0.41, 0.17, 0.17, 0.07, and 0.05, respectively for animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents. Using the wider population and the above genomic relationship threshold values, potential pedigree conflicts were identified within each relationship type. Pedigree error rates of between 0.9% (animal and great great grandparent) and 4.0% (full siblings) were identified. A forensic genomic pedigree validation and discovery system was developed to enable pedigree to be verified for individual genotyped animals. This system verifies not just the parents, but also a wide number of other genotyped relatives and can therefore identify more potential errors in the pedigree than current conventional methods. A novel aspect to this algorithm is that it can also be used to discover closely related animals on the basis of their genomic relationships although they are not recorded as such in the pedigree. This functionality enables missing pedigree information to be discovered and corrected in the pedigree of livestock populations. The methods in this paper demonstrate that the genomic relationship matrix can be a useful tool in the validation and discovery of pedigree in livestock populations. However, the method does rely on being able to define threshold values appropriate to the specific livestock population, which will require sufficient number of animals to be genotyped and pedigree validated before it can be used

Genomic Regions Underlying Susceptibility to Bovine Tuberculosis in Holstein-Friesian Cattle

BACKGROUND: The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics. METHODS: The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control. RESULTS: The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB. CONCLUSION: Genomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle susceptibility to bTB and enhance genetic improvement programmes aiming at controlling and eradicating the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0493-7) contains supplementary material, which is available to authorized users

Pembelajaran Materi Bangun Datar Melalui Cerita Menggunakan Pendekatan Pendidikan Matematika Realistik Indonesia (PMRI) Di Sekolah Dasar

Tujuan dari penelitian ini untuk memperoleh gambaran pembelajaran materi bangun datar menggunakan pendekatan PMRI di Sekolah Dasar (SD). Subjek penelitian adalah siswa kelas II SDN117 Palembang yang terdiri dari 36 siswa. Penelitian ini menggunakan studi deskriptif. Teknik pengumpulan data adalah observasi untuk mengetahui aktivitas siswa selama proses pembelajaran berlangsung, serta dokumen untuk mengetahui hasil kerja siswa pada Lembar Aktivitas Siswa (LAS) saat proses pembelajaran untuk mengetahui kemampuan siswa. Dari analisis data dapat disimpulkan bahwa hasil observasi menunjukkan semua siswa aktif mengikuti pembelajaran dengan baik. Dari hasil kerja siswa pada LAS dan latihan menunjukkan bahwa semua siswa mampu menyelesaikan pembelajaran materi bangun datar dengan rata-rata 86,3% termasuk dalam kategori sangat baik.The aim of this research is to describe the intructional process of polygon the use of PMRI approach in primary school. Participant of this research are 36 students grade two of state prymary school number 117 Palembang. This research is descriptive study. Data were collected using observation and document. The results show all of students are active during the learning process. Also about 86,3% of students able to follow learning with very good level