scholarly journals Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data

2021 ◽  
Vol 17 (4) ◽  
Author(s):  
Joukje Buiteveld ◽  
Herma JJ Koehorst-van Putten ◽  
Linda Kodde ◽  
Ivo Laros ◽  
Giorgio Tumino ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Relationship ◽  
Snp Array ◽  
Seed Orchard ◽  
Effective Population ◽  
Malus Sylvestris ◽  
Genebank Management ◽  
Genetic Resources Management ◽  
Genebank Collection ◽  
Close Genetic Relationship

AbstractThe Netherlands’ field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, for the first time for genotyping in M. sylvestris. We could readily detect the clonal copies and unexpected duplicates. Thirty-two M. sylvestris accessions (29%) showed a close genetic relationship (parent-child, full-sib, or half-sib) to another accession, which reflects the small effective population size of the in situ populations. Traces of introgression from M. domestica were only found in 7 individuals. This indicates that pollination preferentially took place among the M. sylvestris trees. We conclude that the collection can be considered as mainly pure M. sylvestris accessions. The results imply that it should be managed as one unit when used for seed production. A bias in allele frequencies in the seeds may be prevented by not harvesting all accessions with a close genetic relationship to the others in the seed orchard. We discuss the value of using the SNP array to elaborate the M. sylvestris genetic resources more in depth, including for phasing the markers in a subset of the accessions, as a first step towards genetic resources management at the level of haplotypes.

Population and quantitative genomic properties of the USDA soybean germplasm collection

2018 ◽  
Vol 16 (6) ◽  
pp. 513-523 ◽  
Author(s):  
Alencar Xavier ◽  
Rima Thapa ◽  
William M. Muir ◽  
Katy Martin Rainey
Keyword(s):  
Genetic Resources ◽  
Agronomic Traits ◽  
Snp Array ◽  
Genetic Material ◽  
Germplasm Collection ◽  
Effective Population ◽  
Department Of Agriculture ◽  
Soybean Germplasm ◽  
National Plant Germplasm System

AbstractThis study is the first assessment of the entire soybean [Glycine max (L.) Merr] collection of the United State Department of Agriculture National Plant Germplasm System (USDA) reporting quantitative and population genomic parameters. It also provides a new insight into soybean germplasm structure. Germplasm studies enable plant breeders to incorporate novel genetic resources into breeding pipelines to improve valuable agronomic traits. We conducted comprehensive analyses on the 19,652 soybean accessions in the USDA-ARS germplasm collection, genotyped with the SoySNP50 K iSelect BeadChip SNP array, to elucidate the quantitative properties of existing subpopulations inferred through hierarchical clustering performed with Ward's D agglomeration method and Nei's standard genetic distance. We found the effective population size to be approximately 106 individuals based on the linkage disequilibrium of unlinked loci. The cladogram indicated the existence of eight major clusters. Each cluster displays particular properties with regard to major quantitative traits. Among those, cluster 3 represents the tropical and semi-tropical genetic material, cluster 5 displays large seeds and may represent food-grade germplasm, and cluster 7 represents the undomesticated material in the germplasm collection. The average FST among clusters was 0.22 and a total of 914 SNPs were exclusive to specific clusters. Our classification and characterization of the germplasm collection into major clusters provides valuable information about the genetic resources available to soybean breeders and researchers.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

Paternity analysis with microsatellites in a Danish Abies nordmanniana clonal seed orchard reveals dysfunctions

2006 ◽  
Vol 36 (4) ◽  
pp. 1054-1058 ◽  
Author(s):  
O K Hansen ◽  
E D Kjær
Keyword(s):  
Asymptotic Variance ◽  
Seed Orchard ◽  
Paternity Analysis ◽  
Effective Population ◽  
Population Number ◽  
Clonal Seed Orchard ◽  
Relative Contribution ◽  
Male Gametes ◽  
Abies Nordmanniana ◽  
The Status

A paternity analysis using five microsatellite markers was conducted in a Danish clonal seed orchard with 13 Abies nordmanniana (Stev.) Spach clones. The purpose was to investigate potential seed-orchard dysfunctions, with special emphasis on nonequal pollen contributions and selfing. Male paternity was found for 232 seedlings germinated from seeds collected on three ramets, each of eight clones, and the relative contribution of each clone to the gene pool of male gametes was calculated. Furthermore, 49 ramets were genotyped to check for erroneous grafting. The effect of an unbalanced male contribution was quantified by means of two measures: (1) the status number (NS), which reflects buildup of coancestry in the seed-orchard crop as a result of a low number of clones and an unequal male contribution, and (2) the asymptotic variance effective population number (Ne(v)). The contributions by pollen donors from the 13 clones were highly skewed. Three clones were fathers to more than 75% of the progenies, while making up only 24% of the ramets in the seed orchard. Four clones sired no progenies at all. The unequal contribution on the male side corresponded to NS = 4.2 and Ne(v) = 5.8. Some selfing was observed, which may give rise to concern if clonal seed orchards with few clones are established. The estimated maximum pollen contamination from outside the seed orchard was 4.3%. No grafting–labelling errors were identified.

Close genetic relationship between central Thai and Mon people in Thailand revealed by autosomal microsatellites

2020 ◽  
Author(s):  
Suparat Srithawong ◽  
Kanha Muisuk ◽  
Metawee Srikummool ◽  
Jatupol Kampuansai ◽  
Pittayawat Pittayaporn ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Close Genetic Relationship ◽  
Autosomal Microsatellites

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

GENETIC RESOURCES MANAGEMENT WITH NETWORKS: THE EXAMPLE OF THE NETWORK

2007 ◽  
pp. 99-104 ◽  
Author(s):  
M. Briard ◽  
V. Le Clerc ◽  
D. Peltier ◽  
A. Suel ◽  
J. Granger ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Resources Management ◽  
Genetic Resources Management

scholarly journals Tracing the genetic history of the ‘Cañaris’ from Ecuador and Peru using uniparental DNA markers

BMC Genomics ◽  
2020 ◽  
Vol 21 (S7) ◽  
Author(s):  
José R. Sandoval ◽  
Daniela R. Lacerda ◽  
Marilza M. S. Jota ◽  
Paulo Robles-Ruiz ◽  
Pierina Danos ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Genetic Relationship ◽  
Tandem Repeats ◽  
Geographic Proximity ◽  
Lake Titicaca ◽  
Control Region Sequences ◽  
History Of ◽  
Historical Question ◽  
Close Genetic Relationship

Abstract Background According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lambayeque (Peru). Other families were probably taken from the Central Andes to a place close to Kañaris, named Inkawasi. Evidence of this migration comes from the presence near the Kañaris–Inkawasi communities of a village, a former Inka camp, which persists until the present day. This scenario could explain these toponyms, but it is still controversial. To clarify this historical question, the study presented here focused on the inference of the genetic relationship between ‘Cañaris’ populations, particularly of Cañar and Ferreñafe, compared to other highland populations. We analysed native patrilineal Y chromosome haplotypes composed of 15 short tandem repeats, a set of SNPs, and maternal mitochondrial DNA haplotypes of control region sequences. Results After the genetic comparisons of local populations—three from Ecuador and seven from Peru—, Y chromosome analyses (n = 376) indicated that individuals from the Cañar region do not share Y haplotypes with the Kañaris, or even with those of the Inkawasi. However, some Y haplotypes of Ecuadorian ‘Cañaris’ were associated with haplotypes of the Peruvian populations of Cajamarca, Chivay (Arequipa), Cusco and Lake Titicaca, an observation that is congruent with colonial records. Within the Kañaris and Inkawasi communities there are at least five clans in which several individuals share haplotypes, indicating that they have recent common ancestors. Despite their relative isolation, most individuals of both communities are related to those of the Cajamarca and Chachapoyas in Peru, consistent with the spoken Quechua and their geographic proximity. With respect to mitochondrial DNA haplotypes (n = 379), with the exception of a shared haplotype of the D1 lineage between the Cañar and Kañaris, there are no genetic affinities. Conclusion Although there is no close genetic relationship between the Peruvian Kañaris (including Inkawasi) and Ecuadorian Cañar populations, our results showed some congruence with historical records.

scholarly journals Safeguarding and using global banana diversity: a holistic approach

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Ines Van den houwe ◽  
Rachel Chase ◽  
Julie Sardos ◽  
Max Ruas ◽  
Els Kempenaers ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Holistic Approach ◽  
Global Strategy ◽  
Ex Situ ◽  
Phenotypic Traits ◽  
Research Activities ◽  
Genebank Management

AbstractThe CGIAR genebank International Musa Germplasm Transit Centre (ITC) currently holds 1617 banana accessions from 38 countries as an in vitro collection, backed-up by a cryopreserved collection to safeguard global Musa diversity in perpetuity. The ITC also serves as a vital safety backup and transit centre for national banana genebanks and ensures that germplasm is clean of pests and diseases and freely available under the International Treaty on Plant Genetic Resources for Food and Agriculture. In more than 35 years of activity, the ITC has distributed over 18,000 banana accession samples to researchers and farmers in 113 countries. Ex situ conservation of vegetatively-propagated crops such as banana poses very particular challenges. Maintaining the ITC genebank is labor intense and costly. Efficiencies are sought through research and development of techniques on detecting viruses, the genetic integrity of accessions, and on innovative means of safeguarding banana diversity, such as conserving populations of wild species by seed banking. Although the conservation of global banana diversity is the main objective of the ITC, significant value comes from its holistic approach to better understand and promote its germplasm through numerous research activities and resources. Techniques for morphological and molecular characterization serve to identify and describe the collection, while also determining what gaps should be filled by collecting missions with national partners. The evaluation of desirable agronomic traits inherent in Musa spp. are investigated by a high-throughput phenotyping platform, which helps breeding programs to select cultivars resistant or tolerant to biotic and abiotic stresses. Genomic and bioinformatic studies of several banana wild relatives greatly enhance our understanding of Musa genetic diversity, links to important phenotypic traits and bring new methods for management of the collection. Collectively, these research activities produce enormous amounts of data that require curation and dissemination to the public. The two information systems at the ITC, Musa Genebank Management System and the Musa Germplasm Information System, serve to manage the genebank activities and to make public germplasm-related data for over 30 banana collections worldwide, respectively. By implementing the 10-year workplan set out in the Global Strategy for the Conservation and Use of Musa Genetic Resources, the network MusaNet supports Musa researchers and stakeholders, including the ITC, and most importantly, links to the world’s banana-producing countries via three regional banana networks.

Sign in / Sign up

Export Citation Format

Share Document