scholarly journals Genomic assessment of white clover and perennial ryegrass genetic resources

2020 ◽  
Vol 82 ◽  
pp. 27-34
Author(s):  
Marty J. Faville ◽  
Andrew G. Griffiths ◽  
Abdul Baten ◽  
Mingshu Cao ◽  
Rachael Ashby ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Iberian Peninsula ◽  
Perennial Ryegrass ◽  
White Clover ◽  
Eastern Mediterranean ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Phenotypic Characterisation

Forage resources conserved in genebanks, such as the Margot Forde Germplasm Centre (MFGC; PalmerstonNorth), are reservoirs of genetic diversity important for the development of cultivars adapted to abiotic stresses and environmental constraints. Genomic tools, including genotyping-by-sequencing (GBS), can support identification of manageable subsets (core collections) that are genetically representative of these large germplasm collections, for phenotypic characterisation. We used GBS to generate SNP (single nucleotide polymorphism) profiles for 172 white clover (WC) and 357 perennial ryegrass (PRG) MFGC-sourced accessions and estimated genetic relationships amongst accessions. In WC, accessions aligned along an east-west transect from Kazakhstan to Spain, identifying major diversity in Caucasus/Central Asia and Iberian Peninsula. A key feature was the reduced diversity present in New Zealand (NZL) accessions. Similarly, for PRG, most NZL accessions coalesced as one group, distinct from large clusters associated with the Iberian Peninsula, Italy and eastern Mediterranean/Caucasian region. These results emphasise the relatively narrow genetic diversity in NZL WC and PRG, and the broad extent of largely unexploited global diversity. Capturing global genetic variation incore collections will support pre-breeding programmes to mobilise novel genetic variation into New  Zealand-adapted genetic backgrounds, enabling development of cultivars with non-traditional traits including enhancedclimate resilience and environmental performance.

Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey

2021 ◽  
Vol 34 ◽  
pp. 3
Author(s):  
Yılmaz Çiftci ◽  
Oğuzhan Eroğlu ◽  
Şirin Firidin ◽  
Hacı Savaş ◽  
Yusuf Bektaş
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Relationships ◽  
Significance Test ◽  
Management Plan ◽  
Lake Van ◽  
Essential Information ◽  
Low Level ◽  
Lake Van Basin ◽  
Sustainable Fishery

In this study, the genetic relationships of 804 tarek (Alburnus tarichi) samples from a total of 18 populations, including the potamodromus and resident individuals from Lake Van basin in eastern Turkey, were studied by using nine microsatellite loci. A total of 93 alleles was detected, and the average number of alleles per locus was 10.3 ± 3.39. The mean estimated observed and expected heterozygosity were 0.340 ± 0.016 and 0.362 ± 0.015, respectively, which indicated a low level of polymorphism. After Bonferroni correction (P < 0.0027), the multi-locus test applied to each population revealed that 12 out of 18 populations were in Hardy-Weinberg equilibrium (HWE) (P = 0.0120–0.9981). Analysis of molecular variance (AMOVA) showed more than 76% genetic variability within individuals and 19% among populations, which was significantly higher than zero (FST = 0.19), and furthermore, a low level of genetic variation was observed among individuals within populations (4.84%: FIS = 0.06). Bayesian clustering analysis indicated that the total genetic variation grouped into 3 clusters. Additionally, the significance test results revealed that 11 of the 18 populations are threatened with extinction due to recent bottleneck events.We conclude that the tarek populations from the Lake Van basin can be classified into distinct genetic groups, based on microsatellite information. In addition, our results provide essential information for the development of a management plan that conserves the tarek's genetic diversity and achieves a sustainable fishery.

scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Genetic diversity and morphological characteristics of native seashore paspalum in Indonesia

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Rahayu Rahayu ◽  
Fatimah Suwardjo ◽  
Ji Bae Eun ◽  
Geun Mo Yang ◽  
Soo Choi Joon
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Warm Season ◽  
Morphological Characters ◽  
Seashore Paspalum ◽  
Turf Quality ◽  
Marker Cluster

Abstract. Rahayu, Fatimah, Bae EJ, Mo YG, Choi JS. 2020. Genetic diversity and morphological characteristics of native seashore paspalum in Indonesia. Biodiversitas 21: 4981-4989. Seashore paspalum (Paspalum vaginatum) is a warm-season turfgrass indigenous to tropical and coastal areas worldwide. The objectives of this study were to measure the genetic diversity and genetic variation of Indonesian seashore paspalum germplasm. Three turf quality, six morphological characters, and ten SSR (microsatellite) markers were used to assess genetic relationships and genetic variation among 22 germplasm resources from Indonesia and one commercial variety (Salam) from United States of America. The results showed significant variation for five morphological characters among 23 tested seashore paspalum accessions. The cluster analysis of morphological characters of 23 seashore paspalum accessions using 0,6 cut off divided into three morphological types: tall high-density, intermediate, and dwarf low-density ecotype. The genetic variation revealed 22 alleles with average number of alleles per locus was 2 and polymorphism information content (PIC) values average was 0.33. The microsatellite marker cluster analysis showed that 23 seashore paspalum accessions were grouped into two major groups, with a genetic similarity coefficient was 0,72. The low level of genetic diversity occurred among Indonesia natural grass germplasm and the genetic distance was relatively low between Indonesian germplasm and Salam variety. The genetic diversity and morphological characteristics will be useful for further study and utilization of Indonesian seashore paspalum germplasm.

scholarly journals Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

2018 ◽  
Author(s):  
Marco A. Escalante ◽  
Charles Perrier ◽  
Francisco J. García-De León ◽  
Arturo Ruiz-Luna ◽  
Enrique Ortega-Abboud ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Local Adaptation ◽  
Population Genomics ◽  
Landscape Heterogeneity ◽  
Genotyping By Sequencing ◽  
Anthropogenic Factors ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Potential

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

scholarly journals Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

2017 ◽  
Vol 47 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Magdalena Szeliga ◽  
Joanna Ciura ◽  
Mirosław Tyrka
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Veratrum Album ◽  
Metabolic Properties

Abstract Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

scholarly journals Liveweight changes in lambs grazing six perennial ryegrass cultivars

1999 ◽  
pp. 31-35
Author(s):  
C.T. Westwood ◽  
M.G. Norriss
Keyword(s):  
New Zealand ◽  
Perennial Ryegrass ◽  
White Clover ◽  
Dry Matter ◽  
Moisture Stress ◽  
Botanical Composition ◽  
Independent Research ◽  
Ewe Lambs ◽  
Research Organisation ◽  
Clover Content

Liveweight changes were measured for lambs grazing six high endophyte perennial ryegrasses, in a grazing experiment run by an independent research organisation in Canterbury, New Zealand. Ryegrass cultivars were sown under code in a binary mix with white clover in February 1997. Plots were strategically irrigated to avoid moisture stress, and stocked at approximately 27 Coopworth ewe lambs per ha in May 1997. Common pasture residual mass was maintained across cultivars by strategic addition of extra lambs, with extra grazing days recorded for each replicate. Lamb liveweight gains and botanical composition of replicates were assessed quarterly. Lamb liveweight gains differed significantly between treatments in Years 1 and 2 of this ongoing 3 year study. Lambs grazing 'Quartet' tetraploid perennial ryegrass gained, on average, 37.4 kg and 36.1 kg liveweight during Years 1 and 2 respectively, and together with 'Aries HD' (35.0 and 35.9 kg) produced significantly greater liveweight gain compared with 'Grasslands Nui' (22.0 and 23.7 kg) and 'Bronsyn' (22.5 and 24.1 kg), LSD0.05 = 6.0 and 7.4. Lambs grazing 'Embassy' gained 31.6 kg and 28.7 kg, and 'Vedette' 29.8 kg and 28.0 kg. Extra grazing days expressed as a percentage of base grazing days were between 3.8 and 6.7% across cultivars for Year 1 and between 2.0 and 6.5% across cultivars for Year 2. This study demonstrated significant differences in animal productivity between perennial ryegrass cultivars that produce comparable yields of dry matter. Differences may reflect variation in forage quality, endophyte toxins, clover content in the sward or other unidentified cultivar characteristics. Keywords: digestibility, endophyte, lamb, liveweight, perennial ryegrass, tetraploid

scholarly journals Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol

Insects ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 441 ◽  
Author(s):  
Thomas W. R. Harrop ◽  
Marissa F. Le Lec ◽  
Ruy Jauregui ◽  
Shannon E. Taylor ◽  
Sarah N. Inwood ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Biological Control ◽  
Genetic Variation ◽  
New Zealand ◽  
Insect Pests ◽  
Rapid Evolution ◽  
Parasitoid Wasp ◽  
Control Agent ◽  
Agricultural Landscapes ◽  
Effective Population

Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent’s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil have high levels of heterozygosity and low population structure, consistent with a large effective population size and frequent gene flow. This implies that Argentine stem weevils were able to evolve more rapidly than their biocontrol agent, which reproduces asexually. These findings show that monitoring genetic diversity in biocontrol agents and their targets is critical for long-term success of biological control.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

More feed for New Zealand dairy systems

2001 ◽  
pp. 283-288 ◽  
Author(s):  
D.A. Clark ◽  
C. Matthew ◽  
J.R. Crush
Keyword(s):  
New Zealand ◽  
Plant Breeding ◽  
Perennial Ryegrass ◽  
White Clover ◽  
Crude Protein ◽  
Plant Stress ◽  
Net Photosynthesis ◽  
Potential Yield ◽  
C3 Plant ◽  
Upper Limit

An upper limit to productivity of perennial ryegrass-white clover pastures in New Zealand at about 15 t DM/ha per year has been identified as a constraint to future increases in productivity. With potential yields of 26.6 t DM/ha per year from temperate grasses and 45 t DM/ha per year from maize at mid-latitudes, the challenge for New Zealand dairy farming systems is to achieve greater than 15 t DM/ha per year without imposing additional production or environmental costs. Given these constraints a major switch to crops is not feasible because those that produce more than pasture, e.g., maize, have insufficient crude protein to support lactation. Theoretically, a farm area allocation to 78% perennial ryegrass-white clover and 22% maize-winter oats could provide 23.3 t DM/ha per year at a crude protein content of 16%. This is greater than the 20 t DM/ha per year upper limit of irrigated perennial ryegrass-white clover. Incremental yield improvements of grasses and clovers by traditional plant breeding are low (1.5% per year), and difficult to capture. Future plant breeding gains are more likely to come from increased plant stress tolerance. Improved pasture monitoring to allow timely removal of constraints, will enable potential yields to be achieved. Biotechnology offers the possibility of improving the potential yield of net photosynthesis by 20% either through the transfer of genes from a C4 plant (e.g., maize) or a C3 plant (e.g., perennial ryegrass), or use of the major photosynthetic enzymes, rubisco, from a thermophilic alga. Biotechnology is also providing new knowledge about the control of plant development and response to stresses. The application of this knowledge may allow dairy farmers to achieve another 5 t DM/ha per year from perennial ryegrass-white clover pastures. Keywords: biotechnology, dairy, perennial ryegrass, photosynthesis, white clover, yield limitation

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