Functional and population genetic features of copy number variations in two dairy cattle populations
Lee, Young Lim ; Bosse, Mirte ; Mullaart, Erik ; Groenen, Martien A.M. ; Veerkamp, Roel F. ; Bouwman, Aniek C. - \ 2020
BMC Genomics 21 (2020)1. - ISSN 1471-2164
Bos taurus - Copy number variations - Linkage disequilibrium - Population genetics
Background: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. Results: We discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r 2 = ~ 0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r 2 = ~ 0.5 at 10 kb distance). Conclusions: Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.
Recognizing peripheral ecosystems in marine protected : A case study of golden jellyfish lakes in Raja Ampat, Indonesia
Maas, Diede L. ; Capriati, Agustin ; Ahmad, Awaludinnoer ; Erdmann, Mark V. ; Lamers, Machiel ; Leeuw, Christiaan A. de; Prins, Luca ; Purwanto, ; Putri, Amanda P. ; Tapilatu, Ricardo F. ; Becking, Leontine E. - \ 2020
Marine Pollution Bulletin 151 (2020). - ISSN 0025-326X
Anchialine ecosystems - Customary tenure - Mastigias papua - Morphometrics - Population genetics - Tourism
Peripheral marine ecosystems can harbor endemic diversity and attract tourism attention, yet are generally not included in conservation management plans due to their remoteness or inland positioning. A case study in Raja Ampat of seven landlocked marine lakes containing golden jellyfish (Mastigias spp.) was conducted to address the lack of fundamental insights into evolutionary, ecological and social contexts of these ecosystems. An interdisciplinary approach was taken towards identifying the jellyfish lakes as distinct management units in order to incorporate them into existing Marine Protected Areas. Mastigias papua populations showed strong genetic (ϕST: 0.30–0.86) and morphological (F = 28.62, p-value = 0.001) structure among lakes, with putative new subspecies. Risks arising from rapid increase in tourism to Raja Ampat (30-fold since 2007) warrant restrictions on jellyfish lake use. Recommendations are provided for adaptive management and science-based conservation policies for jellyfish lakes across Indonesia.
Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites
Pourkhaloee, Ali ; Khosh-Khui, Morteza ; Arens, Paul ; Salehi, Hassan ; Razi, Hooman ; Niazi, Ali ; Afsharifar, Alireza ; Tuyl, Jaap van - \ 2018
Horticulture Environment and Biotechnology 59 (2018)6. - ISSN 2211-3452 - p. 875 - 888.
Bulb crop - Conservation implications - EST–SSR markers - Population genetics
Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRUCTURE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.
Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia
Fulgione, Andrea ; Koornneef, Maarten ; Roux, Fabrice ; Hermisson, Joachim ; Hancock, Angela M. - \ 2018
Molecular Biology and Evolution 35 (2018)3. - ISSN 0737-4038 - p. 564 - 574.
Admixture - Arabidopsis thaliana - Demography - Island - Population genetics - Relict
The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersal model (of size 10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).
Evidence for selection pressure from resistant potato genotypes but not from fungicide application within a clonal Phytophthora infestans population
Stellingwerf, J.S. ; Phelan, S. ; Doohan, F.M. ; Ortiz, V. ; Griffin, D. ; Bourke, A. ; Hutten, R.C.B. ; Cooke, D.E.L. ; Kildea, S. ; Mullins, E. - \ 2018
Plant Pathology 67 (2018)7. - ISSN 0032-0862 - p. 1528 - 1538.
Host resistance - Phytophthora infestans - Population genetics - Potato - SSR genotyping
Insight into pathogen population dynamics provides a key input for effective disease management of the potato late blight pathogen Phytophthora infestans. Phytophthora infestans populations vary from genetically complex to more simple with a few clonal lineages. The presence or absence of certain strains of P. infestans may impact the efficacy of fungicides or host resistance. Current evidence indicates that genetically, the Irish populations of P. infestans are relatively simple with a few clonal lineages. In this study, P. infestans populations were genetically characterized based on samples collected at the national centre for potato breeding during the period 2012-16. The dominance of clonal lineages within this P. infestans population was confirmed and the potential selection pressure of fungicide treatment (2013-15) and host resistance (2016) on this clonal P. infestans population was then investigated. It was found that fungicide products did not notably affect the genetic structure of sampled populations relative to samples from untreated control plants. In contrast, samples taken from several resistant potato genotypes were found to be more often of the EU_13_A2 lineage than those taken from control King Edward plants or potato genotypes with low resistance ratings. Resistant potato varieties Sarpo Mira and Bionica, containing characterized R genes, were found to strongly select for EU_13_A2 strains.
Isolation and characterization of microsatellites in Sparganium emersum and cross-species amplification in the related species S. erectum
Pollux, B.J.A. ; Ouborg, N.J. - \ 2006
Molecular Ecology Notes 6 (2006)2. - ISSN 1471-8278 - p. 530 - 532.
Dispersal - Gene flow - Microsatellites - Null alleles - Population genetics
We developed seven novel polymorphic microsatellite loci for the aquatic macrophyte Sparganium emersum (Sparganiaceae). These were characterized on 62 individuals collected from nine different populations. In this set of individuals, seven to 20 alleles per locus were detected and observed heterozygosity ranged between 0.16 and 0.95. Cross-species amplification was tested in the related species Sparganium erectum, and was successful for five of the seven microsatellite loci.