scholarly journals Grapevine Diversity and Genetic Relationships in Northeast Portugal Old Vineyards

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2755
Author(s):  
Diana Augusto ◽  
Javier Ibáñez ◽  
Ana Lúcia Pinto-Sintra ◽  
Virgílio Falco ◽  
Fernanda Leal ◽  
...  
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Genetic Relationships ◽  
Product Diversification ◽  
Wine Production ◽  
Genetic Groups ◽  
Nuclear Ssr ◽  
The Mean ◽  
Genetic Profiles ◽  
Protected Designations Of Origin

More than 100 grapevine varieties are registered as suitable for wine production in “Douro” and “Trás-os-Montes” Protected Designations of Origin regions; however, only a few are actually used for winemaking. The identification of varieties cultivated in past times can be an important step to take advantage of all the potential of these regions grape biodiversity. The conservation of the vanishing genetic resources boosts greater product diversification, and it can be considered strategic in the valorisation of these wine regions. Hence, one goal of the present study was to prospect and characterise, through molecular markers, 310 plants of 11 old vineyards that constitute a broad representation of the grape genetic patrimony of “Douro” and “Trás-os-Montes” wine regions; 280 samples, grouped into 52 distinct known varieties, were identified through comparison of their genetic profiles generated via 6 nuclear SSR and 43 informative SNP loci amplification; the remaining 30 samples, accounting for 13 different genotypes, did not match with any profile in the consulted databases and were considered as new genotypes. This study also aimed at evaluating the population structure among the 65 non-redundant genotypes identified, which were grouped into two ancestral genetic groups. The mean probability of identity values of 0.072 and 0.510 (for the 6 SSR and 226 SNP sets, respectively) were determined. Minor differences were observed between frequencies of chlorotypes A and D within the non-redundant genotypes studied. Twenty-seven pedigrees were confirmed and nine new trios were established. Ancestors of eight genotypes remain unknown.

scholarly journals Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2174
Author(s):  
Marcello Borin ◽  
Fabio Palumbo ◽  
Alessandro Vannozzi ◽  
Francesco Scariolo ◽  
Gio Batta Sacilotto ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Sexual Behaviors ◽  
Cannabis Sativa ◽  
Genetic Research ◽  
Breeding Value ◽  
Germplasm Management ◽  
Genetic Groups ◽  
Legal Implications ◽  
Population Structure Analysis ◽  
Nuclear Ssr

Cannabis sativa (2n = 2x = 20) is a popular species belonging to the Cannabaceae family. Despite its use for medical, recreational, and industrial purposes as well as its long history, the genetic research on this species is in its infancy due to the legal implications and the prohibition campaigns. The recent legalization of Cannabis in many countries along with the use of genomics boosted the approaches aimed at marker-assisted selection, germplasm management, genetic discrimination, and authentication of cultivars. Nonetheless, the exploitation of molecular markers for the development of commercial varieties through marker-assisted breeding schemes is still rare. The present study aimed to develop an informative panel of simple sequence repeat markers to be used for the genotyping of high breeding value C. sativa lines. Starting from 41 nuclear SSR designated by in silico analyses, we selected 20 highly polymorphic and discriminant loci that were tested in 104 individuals belonging to 11 distinct hemp varieties. The selected markers were successful in accessing homozygosity, genetic uniformity, and genetic variation within and among varieties. Population structure analysis identified eight genetic groups, clustering individuals based on sexual behaviors (dioecious and monoecious) and geographical origins. Overall, this study provides important tools for the genetic characterization, authentication, conservation of biodiversity, genetic improvement and traceability of this increasingly important plant species.

Population structure in the clonal, woody wetland plant Melaleuca ericifolia (Myrtaceae): an analysis using historical aerial photographs and molecular techniques

2012 ◽  
Vol 60 (1) ◽  
pp. 9 ◽  
Author(s):  
Randall W. Robinson ◽  
Elizabeth A. James ◽  
Paul I. Boon
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Molecular Techniques ◽  
Aerial Photographs ◽  
Wetland Plant ◽  
Lateral Expansion ◽  
Inter Simple Sequence Repeats ◽  
Eastern Australia ◽  
The Mean ◽  
Simple Sequence

Analyses of historical aerial photographs from 1957 to 2003 were combined with two molecular techniques to examine population structure of the swamp paperbark (Melaleuca ericifolia Sm., Myrtaceae) in Dowd Morass, a large, brackish-water wetland of the Gippsland Lakes, Australia. Molecular markers (microsatellites and inter-simple sequence repeats) demonstrated that the large, dome-shaped stands of M. ericifolia evident in the field were individual genets and that adjacent genets did not intermingle. The development of 18 individual stands visible in aerial photographs from 1964 to 2003, but absent from 1957 images, allowed us to calculate that stands expanded at (individual) mean rates of 25–77 m2 year–1 over the period 1964–2003. Rates of lateral expansion, however, varied significantly between 1964 and 2003; the mean rates were highest in 1978–1982 and 1982–1991 (75 ± 7 and 73 ± 9 m2 year–1, respectively) and significantly lower in 1991–2003 (45 ± 3 m2 year–1). A slowing of lateral expansion rate may indicate stand senescence, although competition and space limitations as clones abut each other may also be relevant processes. Clonality has several important implications for the conservation and rehabilitation of Melaleuca-dominated wetlands in south-eastern Australia, including the ability of plants to maintain themselves under adverse hydrological and salinity regimes.

scholarly journals Prié blanc and Legiruela: a unique grape cultivar grown in distant European regions

OENO One ◽  
2010 ◽  
Vol 44 (1) ◽  
pp. 1
Author(s):  
Anna Schneider ◽  
Daniela Torello Marinoni ◽  
María Teresa De Andrés ◽  
Stefano Raimondi ◽  
Félix Cabello ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Ssr Loci ◽  
Ancient Times ◽  
Nuclear Ssr ◽  
Genetic Profiles ◽  
Grape Varieties ◽  
Unique Genotype ◽  
Simple Sequence ◽  
Chloroplast Ssr ◽  
Grape Cultivars

<p style="text-align: justify;"><strong>Aims</strong>: The aim of this study was to identify synonyms among grape cultivars growing in two distant regions, Spain and Italy, based on comparative analysis of genetic markers. The identification of synonyms and genetically-related cultivars should contribute to our understanding of their history and the preservation of biodiversity.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Using a set of 9 nuclear simple sequence repeats (SSR) markers, we compared the genetic profiles of major and currently neglected grape cultivars from two laboratories in Spain and Italy. A set of approximately 700 genotypes were analyzed and several putative synonyms were discovered. Among these, a clear synonymy was identified (confirmed by ampelographic observations) between two minor varieties: the Spanish Legiruela and the Italian Prié blanc, known in the past as Agostenga. Using an additional set of 25 nuclear SSR loci, two white cultivars, Albillo Real (or Albillo de Madrid) and Luglienga bianca, from Spain and Italy, respectively, showed a genetic relationship with Prié blanc/Legiruela. To further characterize this parent/progeny kinship, chloroplast SSR analyses were performed. Several hypotheses on the origin and movements of these traditional ancient grapes are discussed.</p><p style="text-align: justify;"><strong>Conclusion</strong>: The Italian Prié blanc and the Spanish Legiruela cultivars correspond to a unique genotype. The occurrence in Spain under the name of Legiruela, a cultivar long-recognized in Italie, and the presence in both countries of very old grape varieties genetically related to this genotype, indicate that Prié blanc/Legiruela has moved from its original to actual growing area several centuries ago.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: By identifying synonyms, accurately establishing the « true to type » of traditional grapes (used for commercial trade or maintained in collections), and studying their genetic relationships, the present work affects marketing and commercial exploitations related to grape cultivars. It also contributes to the knowledge of cultivar history and movements in ancient times.</p>

scholarly journals PSV-16 Infrared thermography technology as a promising tool for assessing temperament of water buffaloes

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 220-221
Author(s):  
Caroline L Francisco ◽  
André M Castilhos ◽  
Daiane C Marques da Silva ◽  
Fabiola Martinez da Silva ◽  
Aline S Aranha ◽  
...  
Keyword(s):  
Infrared Thermography ◽  
Fixed Effects ◽  
Thermal Imager ◽  
Initial Body Weight ◽  
Water Buffaloes ◽  
Promising Tool ◽  
Genetic Groups ◽  
Body Regions ◽  
The Mean ◽  
Positive Correlations

Abstract This study evaluated the use of the infrared thermography (IT) as a tool to identify the temperament of 75 non-castrated water buffaloes (390±32 days of age; 310±61.27 kg of initial body weight) of 3 genetic groups (GG:Jafarabadi, Mediterranean, and Murrah; n = 25 for each GG). The animals were classified for temperament through the temperament score (TSc) obtained by the mean of the sum of the scores of the time of entry into the squeeze chute (1 to 5: 1=greater time spent for entry; 5=less time spent for entry) and the exit velocity score (1 to 5: 1=lower speed; 5=higher speed) calculated after the period of adaptation to the feedlot (d0). The animals were categorized into adequate (ADQ; TSc≤3) or excitable (EXC; TSc &gt;3) temperaments. The rectal temperature was measured and IT images were obtained (Testo 882 Thermal Imager, Testo, Inc, Germany) from regions of the chest, eye, snout, cheek, foreleg (left side), ribs, hind legs, rear area (left side), and scrotum on d0. Data were analyzed using MIXED procedure in SAS, considering the GG, temperament, and the resulting interaction as fixed effects. Correlation was analyzed using the CORR procedure of SAS. There were no effects of interactions (P ≥ 0.14). ADQ animals showed lower rectal (P = 0.02) and ribs (P = 0.05) temperatures than EXC animals (Table1). Tendencies for temperament effect were detected for chest (P = 0.06) and rear area (P = 0.07). There was no effect of temperament for other variables (P = 0.19). Positive correlations were verified between the TSc and rectal (r=0.36; P &lt; 0.01), chest (r=0.35; P &lt; 0.01), and rear area (r=0.33; P &lt; 0.01) temperatures. Tendency for a positive correlation was detected between TSc and scrotum (r=0.23; P = 0.07). In conclusion, the temperament causes changes in the temperature of some body regions suggesting the IT technology may be a promising tool for assessing the temperament of water buffaloes. Supported by FAPESP (#2018/25939-1; #2014/05473-7).

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Genetic relationships and population structure in three Italian Merino-derived sheep breeds

2011 ◽  
Vol 96 (2-3) ◽  
pp. 111-119 ◽  
Author(s):  
Emiliano Lasagna ◽  
Matteo Bianchi ◽  
Simone Ceccobelli ◽  
Vincenzo Landi ◽  
Amparo Martínez Martínez ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Relationships ◽  
Sheep Breeds

scholarly journals Population structure of Chinese southwest wheat germplasms resistant to stripe rust and powdery mildew using the DArT-seq technique

2018 ◽  
Vol 48 (4) ◽  
Author(s):  
Tianqing Chen ◽  
Piyada Alisha Tantasawat ◽  
Wei Wang ◽  
Xu Gao ◽  
Liyi Zhang
Keyword(s):  
Population Structure ◽  
Disease Resistance ◽  
Polymorphic Information Content ◽  
Wheat Breeding ◽  
Wheat Varieties ◽  
Group I ◽  
Population Structure Analysis ◽  
Specific Allele ◽  
The Mean ◽  
Different Origins

ABSTRACT: Understanding genetic variability in existing wheat accessions is critical for collection, conservation and use of wheat germplasms. In this study, 138 Chinese southwest wheat accessions were investigated by genotyping using two resistance gene makers (Pm21 and Yr26) and DArT-seq technique. Finally, about 50% cultivars (lines) amplified the specific allele for the Yr26 gene (Gwm11) and 40.6% for the Pm21 gene (SCAR1265). By DArT-seq analysis, 30,485 markers (6486 SNPs and 23999 DArTs) were obtained with mean polymorphic information content (PIC) value 0.33 and 0.28 for DArT and SNP marker, respectively. The mean Dice genetic similarity coefficient (GS) was 0.72. Two consistent groups of wheat varieties were identified using principal coordinate analysis (PCoA) at the level of both the chromosome 6AS and the whole-genome, respectively. Group I was composed of non-6VS/6AL translocation lines of different origins, while Group II was composed of 6VS/6AL translocation (T6VS/6AL) lines, most of which carried the Yr26 and Pm21 genes and originated from Guizhou. Besides, a model-based population structure analysis revealed extensive admixture and further divided these wheat accessions into six subgroups (SG1, SG2, SG3, SG4, SG5 and SG6), based on their origin, pedigree or disease resistance. This information is useful for wheat breeding in southwestern China and association mapping for disease resistance using these wheat germplasms in future.

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

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