Mixing gene pools to prevent inbreeding issues in translocated populations of clonal species

2021 ◽  
Author(s):  
Fabienne Van Rossum ◽  
Sarah Le Pajolec
Keyword(s):  
Gene Pools ◽  
Clonal Species

Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo

Parasitology ◽  
1999 ◽  
Vol 118 (6) ◽  
pp. 541-551 ◽  
Author(s):  
N. E. COLLINS ◽  
B. A. ALLSOPP
Keyword(s):  
Genetic Recombination ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Gene Pools ◽  
Theileria Parva ◽  
Causative Agents ◽  
Internal Transcribed Spacer Sequences

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5·8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93·5% of T. p. parva isolates examined were detected by probe TPP1 and 81·8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

Collection and characterization of banana gene pools (Musa spp.) in Manipur (N.E. India) using PCR–RFLP and RAPD and ISSR markers

2021 ◽  
Author(s):  
Warepam Amuchou Singh ◽  
Nandeibam Samarjit Singh ◽  
Elangbam Julia Devi ◽  
Pratap Jyoti Handique ◽  
Huidrom Sunitibala Devi
Keyword(s):  
Issr Markers ◽  
Gene Pools ◽  
Musa Spp ◽  
Pcr Rflp ◽  
Rapd And Issr

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals The Unexplored Socio-Cultural Benefits of Coffee Plants: Implications for the Sustainable Management of Ethiopia’s Coffee Forests

2021 ◽  
Vol 13 (7) ◽  
pp. 3912
Author(s):  
Bikila Jabessa Bulitta ◽  
Lalisa A. Duguma
Keyword(s):  
Value Chain ◽  
Natural Habitat ◽  
Ethnographic Study ◽  
Gene Pools ◽  
Group Discussions ◽  
Cultural Services ◽  
Study Approach ◽  
Jimma Zone ◽  
Food And Drink

Coffee is among the most popular commodity crops around the globe and supports the livelihoods of millions of households along its value chain. Historically, the broader understanding of the roles of coffee has been limited to its commercial value, which largely is derived from coffee, the drink. This study, using in-depth interviews and focus group discussions, explores some of the unrevealed socio-cultural services of coffee of which many people are not aware. The study was conducted in Gomma district, Jimma Zone, Oromia National Regional state, Ethiopia, where arabica coffee was first discovered in its natural habitat. Relying on a case study approach, our study uses ethnographic study methods whereby results are presented from the communities’ perspectives and the subsequent discussions with the communities on how the community perspectives could help to better manage coffee ecosystems. Coffee’s utilities and symbolic functions are numerous—food and drink, commodity crop, religious object, communication medium, heritage and inheritance. Most of the socio-cultural services are not widely known, and hence are not part of the benefits accounting of coffee systems. Understanding and including such socio-cultural benefits into the wider benefits of coffee systems could help in promoting improved management of the Ethiopian coffee forests that are the natural gene pools of this highly valuable crop.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

scholarly journals DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 317
Author(s):  
Darius Danusevičius ◽  
Jurata Buchovska ◽  
Vladas Žulkus ◽  
Linas Daugnora ◽  
Algirdas Girininkas
Keyword(s):  
Baltic Sea ◽  
Scots Pine ◽  
Sea Water ◽  
Pcr Amplification ◽  
Balkan Peninsula ◽  
Gene Pools ◽  
Genetic Associations ◽  
The Baltic Sea ◽  
Assignment Probability ◽  
The Baltic

We aimed to extract DNA and amplify PCR fragments at the mitochondrial DNA Nad7.1 locus and 11 nuclear microsatellite loci in nine circa 11,000-year-old individuals of Scots pine found at the bottom of the Baltic sea and test the genetic associations with the present-day gene pool of Scots pine in Lithuania. We followed a strict anticontamination protocol in the lab and, simultaneously with the aDNA specimens, tested DNA-free controls. The DNA was extracted by an ATMAB protocol from the ancient wood specimens sampled underwater from Scots pine stumps located circa 20–30 m deep and circa 12 km ashore in western Lithuania. As the references, we used 30 present-day Lithuanian populations of Scots pine with 25–50 individuals each. The aDNA yield was 11–41 ng/μL. The PCR amplification for the mtDNA Nad7.1 locus and the nDNA loci yielded reliable aDNA fragments for three and seven out of nine ancient pines, respectively. The electrophoresis profiles of all the PCR tested DNA-free controls contained the sizing standard only, indicating low likelihood for contamination. At the mtDNA Nad7.1 locus, all three ancient Scots pine individuals had the type A (300 bp) allele, indicating postglacial migration from the refugia in Balkan peninsula. The GENECLASS Bayesian assignment tests revealed relatively stringer and consistent genetic associations between the ancient Scots pine trees and the present-day southern Lithuanian populations (assignment probability 0.37–0.55) and several wetlands in Lithuania. Our study shows that salty sea water efficiently preserves ancient DNA in wood at the quality levels suitable for genetic testing of trees dated back as far as 11,000 years before present.

scholarly journals Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

2010 ◽  
Vol 90 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Z I Talukder ◽  
E Anderson ◽  
P N Miklas ◽  
M W Blair ◽  
J Osorno ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Allelic Variation ◽  
Gene Pools ◽  
Gene Sequences ◽  
Mineral Contents ◽  
Discriminatory Ability ◽  
Fe Content ◽  
Mapping Populations ◽  
Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

scholarly journals Molecular Markers Dispute the Existence of the Afro-Andean Group of the Bean Angular Leaf Spot Pathogen, Phaeoisariopsis griseola

2002 ◽  
Vol 92 (6) ◽  
pp. 580-589 ◽  
Author(s):  
George S. Mahuku ◽  
María Antonia Henríquez ◽  
Jaime Munõz ◽  
Robin A. Buruchara
Keyword(s):  
Genetic Differentiation ◽  
Leaf Spot ◽  
Multiple Correspondence Analysis ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
Angular Leaf Spot ◽  
Gene Pools ◽  
Phaeoisariopsis Griseola ◽  
Intergenic Spacer Region

Coevolution of the angular leaf spot pathogen, Phaeoisariopsis griseola, with its common bean host has been demonstrated, and P. griseola isolates have been divided into Andean and Mesoamerican groups that correspond to defined bean gene pools. Recent characterization of P. griseola isolates from Africa has identified a group of isolates classified as Andean using random amplified polymorphic DNA (RAPD), but which are able to infect some Mesoamerican differential varieties. These isolates, designated Afro-Andean, have been identified only in Africa. Random amplified microsatellites, RAPD, and restriction digestion of amplified ribosomal intergenic spacer region were used to elucidate the relationships among the Afro-Andean, Andean, and Mesoamerican groups of P. griseola. Cluster and multiple correspondence analysis of molecular data separated isolates into Andean and Meso-american groups, and the Afro-Andean isolates clustered with Andean isolates. Analysis of molecular variance ascribed 2.8% of the total genetic variation to differences between Afro-Andean and Andean isolates from Africa. Gene diversity analysis revealed no genetic differentiation (GST = 0.004) between Afro-Andean and Andean isolates from Africa. However, significant levels of genetic differentiation (GST = 0.39) were observed between Afro-Andean or Andean isolates from Africa and Andean isolates from Latin America, revealing significant geographical differentiation within the Andean lineage. Results from this study showed that Afro-Andean isolates do not constitute a new P. griseola group and do not represent long-term evolution of the pathogen genome, but rather are likely the consequents of point mutations in genes for virulence. This finding has significant implications in the deployment of resistant bean genotypes.

Optical imaging of orientation and ocular dominance maps in area 17 of cats with convergent strabismus

2002 ◽  
Vol 19 (1) ◽  
pp. 39-49 ◽  
Author(s):  
RALF ENGELMANN ◽  
JOHN M. CROOK ◽  
SIEGRID LÖWEL
Keyword(s):  
Optical Imaging ◽  
Developmental Plasticity ◽  
Functional Organization ◽  
Ocular Dominance ◽  
Gene Pools ◽  
Area 17 ◽  
Intrinsic Signals ◽  
Functional Layout ◽  
Adult Cats ◽  
And Control

Strabismus (or squint) is both a well-established model for developmental plasticity of the brain and a frequent clinical symptom. While the layout and topographic relationship of functional domains in area 17 of divergently squinting cats has been analyzed extensively in recent years (e.g. Löwel et al., 1998), functional maps in convergently squinting animals have so far not been visualized with comparable detail. We have therefore investigated the functional organization of area 17 in adult cats with a surgically induced convergent squint angle. In these animals, visual acuity was determined by both behavioral tests and recordings of visual evoked potentials, and animals with comparable acuities in both eyes were selected for further experiments. The functional layout of area 17 was visualized using optical imaging of intrinsic signals. Monocular iso-orientation domains had a patchy appearance and their layout was different for left and right eye stimulation, so that segregated ocular dominance domains could be visualized. Iso-orientation domains exhibited a pinwheel-like organization, as previously described for normal and divergently squinting cats. Mean pinwheel density was the same in the experimental and control animals (3.4 pinwheel centers per mm2 cortical surface), but significantly (P < 0.00001) higher than that reported previously for normal and divergently squinting cats (2.7/mm2). A comparison of orientation with ocular dominance maps revealed that iso-orientation domains were continuous across the borders of ocular dominance domains and tended to intersect these borders at steep angles. However, in contrast to previous reports in normally raised cats, orientation pinwheel centers showed no consistent topographical relationship to the peaks of ocular dominance domains. Taken together, these observations indicate an overall similarity between the functional layout of orientation and ocular dominance maps in area 17 of convergently and divergently squinting cats. The higher pinwheel densities compared with previous reports suggest that animals from different gene pools might generally differ in this parameter and therefore also in the space constants of their cortical orientation maps.

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