scholarly journals Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety

2021 ◽  
Vol 12 ◽  
Author(s):  
Hélia Sales ◽  
Zlatko Šatović ◽  
Mara Lisa Alves ◽  
Pedro Fevereiro ◽  
João Nunes ◽  
...  
Keyword(s):  
Minimum Spanning Tree ◽  
Genetic Relationships ◽  
Morphological Variability ◽  
Age Groups ◽  
Genetic Erosion ◽  
Olive Tree ◽  
Gene Pools ◽  
Central Mediterranean ◽  
Ancestral Origin ◽  
Olive Variety

Olea europaea ‘Galega vulgar’ variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. ‘Galega vulgar’ is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of ‘Galega vulgar’, 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the ‘Galega vulgar’ intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the ‘Galega vulgar’, with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of ‘Galega vulgar’. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of ‘Galega vulgar’).

scholarly journals Algerian Olive Germplasm and Its Relationships with the Central-Western Mediterranean Varieties Contributes to Clarify Cultivated Olive Diversification

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 678
Author(s):  
Kamel Atrouz ◽  
Ratiba Bousba ◽  
Francesco Paolo Marra ◽  
Annalisa Marchese ◽  
Francesca Luisa Conforti ◽  
...  
Keyword(s):  
Mediterranean Basin ◽  
Genetic Relationships ◽  
Olive Tree ◽  
Mediterranean Area ◽  
Western Mediterranean ◽  
Central Mediterranean ◽  
Western Mediterranean Basin ◽  
New Information ◽  
Mediterranean History ◽  
New Synonymy

Olive tree with its main final product, olive oil, is an important element of Mediterranean history, considered the emblematic fruit of a civilization. Despite its wide diffusion and economic and cultural importance, its evolutionary and phylogenetic history is still difficult to clarify. As part of the Mediterranean basin, Algeria was indicated as a secondary diversification center. However, genetic characterization studies from Maghreb area, are currently underrepresented. In this context, we characterized 119 endemic Algerian accessions by using 12 microsatellite markers with the main goal to evaluate the genetic diversity and population structure. In order to provide new insights about the history of olive diversification events in the Central-Western Mediterranean basin, we included and analyzed a sample of 103 Italian accessions from Sicily and, a set of molecular profiles of cultivars from the Central-Western Mediterranean area. The phylogenetic investigation let us to evaluate genetic relationships among Central-Mediterranean basin olive germplasm, highlight new synonymy cases to support the importance of vegetative propagation in the cultivated olive diffusion and consolidate the hypothesis of more recent admixture events occurrence. This work provided new information about Algerian germplasm biodiversity and contributed to clarify olive diversification process.

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 Genetic flow among olive populations within the Mediterranean basin

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5260 ◽  
Author(s):  
Valentina di Rienzo ◽  
Sara Sion ◽  
Francesca Taranto ◽  
Nunzio D’Agostino ◽  
Cinzia Montemurro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Mediterranean Basin ◽  
Eastern Mediterranean ◽  
Olive Tree ◽  
Gene Pools ◽  
The North ◽  
The Mediterranean ◽  
And Migration ◽  
The Mediterranean Basin

Background The olive tree is a typical crop of the Mediterranean basin where it shows a wide diversity, accounting for more than 2,600 cultivars. The ability to discriminate olive cultivars and determine their genetic variability is pivotal for an optimal exploitation of olive genetic resources. Methods We investigated the genetic diversity within 128 olive accessions belonging to four countries in the Mediterranean Basin (Italy, Algeria, Syria, and Malta), with the purpose of better understanding the origin and spread of the olive genotypes across Mediterranean Basin countries. Eleven highly polymorphic simple sequence repeat (SSR) markers were used and proved to be very informative, producing a total of 179 alleles. Results Cluster analysis distinguished three main groups according to their geographical origin, with the current sample of Maltese accessions included in the Italian group. Phylogenetic analysis further differentiated Italian and Maltese olive accessions, clarifying the intermediate position of Maltese accessions along the x/y-axes of principal coordinate analysis (PCoA). Model-based and neighbor clustering, PCoA, and migration analysis suggested the existence of two different gene pools (Algerian and Syrian) and that the genetic exchange occurred between the Syrian, Italian and Maltese populations. Discussion The close relationship between Syrian and Italian and Maltese olives was consistent with the historical domestication and migration of olive tree from the North Levant to eastern Mediterranean basin. This study lays the foundations for a better understanding of olive genetic diversity in the Mediterranean basin and represents a step toward an optimal conservation and exploitation of olive genetic resources.

scholarly journals Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

2019 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, the Ethiopian population from lake Tana showed to be more divergent than expected suggesting that it might be a different species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities. O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction of genetic diversity, which can be a consequence of bottleneck caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stoking activities. Conclusions The anthropogenic activities particularly in the East African O. niloticus translocations, promoted admixture and contact with the native congenerics which may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

scholarly journals Allozyme analysis of geographical and seasonal variation of Illex coindetii (Cephalopoda: Ommastrephidae) from central Mediterranean and Iberian Atlantic

2005 ◽  
Vol 85 (1) ◽  
pp. 177-184 ◽  
Author(s):  
P. Martínez ◽  
P. Belcari ◽  
A. Sanjuan ◽  
A. Guerra
Keyword(s):  
Minimum Spanning Tree ◽  
Geographical Area ◽  
Genetic Distances ◽  
Group Method ◽  
Central Mediterranean ◽  
Homogeneous Population ◽  
Pair Group ◽  
Morphological Studies ◽  
Temporal Variance ◽  
Population Pattern

Previous morphological studies of Illex coindetii from the Mediterranean have shown both juvenile and mature individuals all year round suggesting an homogeneous population pattern, however, seasonal spawning variation seems to exist varying with geographical area. Present work analysed 240 individuals from the northern Tyrrhenian and Atlantic Iberian waters at the four year-round seasons using 33 presumptive enzyme-coding loci to compare geographical and temporal variances. Genetic variability was low (Ho=0·02–0·04). Moderate variation at some loci was found due to both temporal and geographical factors (12% of total genetic variance) and to temporal variance (FST=0·004–0·015). Unweighted pair-group method using arithmetric averages (UPGMA) and Multidimensional scaling–minimum spanning tree (MDS–MST) analyses after Cavalli-Sforza & Edwards (1967) chord genetic distances showed the summer Italian and the spring Atlantic samples as the most divergent among the whole.

scholarly journals S-genotyping Supports the Genetic Relationships between Turkish and Hungarian Apricot Germplasm

2010 ◽  
Vol 135 (5) ◽  
pp. 410-417 ◽  
Author(s):  
Júlia Halász ◽  
Andrzej Pedryc ◽  
Sezai Ercisli ◽  
Kadir Ugurtan Yilmaz ◽  
Attila Hegedűs
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Prunus Armeniaca ◽  
Molecular Evidence ◽  
Gene Pools ◽  
Historical Events ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Central Turkey

The S-genotypes of a set of Turkish and Hungarian apricot (Prunus armeniaca L.) cultivars were determined by polymerase chain reaction (PCR) amplification of their S-RNase intron regions. In addition, the S-genotyping method was extended to the SFB gene to detect the non-functional SC-haplotype and hence reliably identify self-compatible apricot cultivars. We determined the complete S-genotype of 51 cultivars and the partial S-genotype of four cultivars. A total of 32 different S-genotypes were assigned to the 51 cultivars, and many of them (28) were classified into newly established cross-incompatibility groups III through XIV. Another 12 cultivars demonstrated unique incompatible genotypes and seven self-compatible cultivars were identified in the examined accessions. The fact that Turkish and Hungarian apricot cultivars carry 12 and five S-alleles, respectively, and all five alleles detected in Hungarian cultivars were also present in Turkish apricots furnished molecular evidence supporting the long-suspected historical connection between Hungarian and Turkish apricots. The connection between these two gene pools appeared to be relatively recent and associated with historical events dating back 300 years. Our results confirm that Turkish germplasm contributed considerably to the development of several desirable Hungarian apricot cultivars. Results suggest that the mutation rendering the SC-haplotype non-functional might have occurred somewhere east of central Turkey.

scholarly journals Qtl-Genes in Breeds and Hybrids of Ukrainian Sheep

2020 ◽  
Vol 74 (3) ◽  
pp. 215-221
Author(s):  
Vasyl’ Iovenko ◽  
Yurii Vdjvichenko ◽  
Igor Gorbatenko ◽  
Kostantyn Skrepets ◽  
Ilona Hladii ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Live Weight ◽  
Gene Pools ◽  
Growth Hormone Gene ◽  
Homozygous Genotype ◽  
Meat Productivity ◽  
High Level ◽  
Genotype A

AbstractFor the first time, the genetic structure of sheep breeds (Ascanian Fine-Fleeced, Ascanian Meat-and-Wool, AND Ascanian Karakul) and the hybrid Ascanian Fine-Fleeced × Texel was studied for structural gene variants: growth hormone, calpastatin, myostatin, and Booroola bone morphogenetic protein. In all studied groups, sheep were characterised by polymorphism of two loci, growth hormone and calpastatin. Two genotypes (A/A, A/B) represent genes of growth hormone structure, and three (M/M, M/N, N/N) represent genes of calpastatin structure. Other genes are in a monomorphic state. Analysis of the genetic relationships between the studied gene pools showed that there was a definite relationship between productivity of sheep herds and their molecular genetic parameters. Thus, the frequencies of individual genotypes and alleles change in the direction from Fine-Fleeced animals to sheep bred for meat productivity. For example, the heterozygous genotype A/B proportion of growth hormone gene increases in this direction from 0% to 38.2%, and allele A from 0.083 to 0.191. The live weight of Fine-Fleeced lambs with geno-type A/B at birth was 4.5 kg, and with homozygous genotype A/A — 4.9 kg (p < 0.001). This difference is genetically related to the meat productivity of sheep. A similar relationship was established for young Ascanian Karakul sheep. According to the distribution of polymorphic loci variants, the gene pools of Ascanian Meat-and-Wool breed and cross-bred animals are most similar closest among themselves, which is explained by the same direction of their productivity. At the same time, all populations are in genetic equilibrium according to Hardy-Weinberg equations, which indicates a high level of their consolidation. Sheep, which have the A/A homozygote of the gene growth hormone, have increased body weight.

scholarly journals Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

2019 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, the Ethiopian population from lake Tana showed to be more divergent than expected suggesting that it might be a different species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities. O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction of genetic diversity, which can be a consequence of bottleneck caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stoking activities. Conclusions The anthropogenic activities particularly in the East African O. niloticus translocations, promoted admixture and contact with the native congenerics which may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

Genetic diversity of Canadian elite summer rape (Brassica napus L.) cultivars from the pre- to post-canola quality era

2010 ◽  
Vol 90 (1) ◽  
pp. 23-33 ◽  
Author(s):  
Y -B. Fu ◽  
R K Gugel
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Low Erucic Acid ◽  
Simple Sequence ◽  
Canola Quality

The development of canola quality Brassica napus oilseed cultivars was a major achievement of Canadian public oilseed breeding programs. Simple sequence repeat (SSR) markers were applied to assess the genetic diversity of 300 plants representing one landrace introduced from Argentina in 1943, seven Canadian elite cultivars developed and released by Agriculture and Agri-Food Canada since 1954, and two European cultivars that were the source of the low erucic acid and low glucosinolate traits that define canola quality. Application of 22 SSR primer pairs from eight linkage groups detected 88 polymorphic alleles from 33 likely loci. The allelic frequencies in 300 samples ranged from 0.003 to 0.993 and averaged 0.388. The estimates of mean heterozygosity for these cultivars ranged from 0.055 to 0.203 and averaged 0.139. The most SSR variation was detected in the cultivars Argentine, Golden and Oro. A trend of decline in SSR variation was observed over the years of breeding effort. The proportion of total SSR variation residing among the cultivars was 51.4%; between high vs. low erucic acid cultivars 15% and between high vs. low glucosinolate cultivars 21.2%. Pairwise genetic differentiations among these cultivars ranged from 0.140 to 0.819 and averaged 0.500. Cluster analysis revealed that the genetic relationships of these cultivars were consistent with their known pedigrees. These findings are useful for broadening the genetic base of improved B. napus gene pools, selecting genetically diverse genotypes for hybrid combinations, and conserving summer rape germplasm.Key words: Simple sequence repeat, summer rape, Brassica napus, genetic diversity, genetic relationship, genetic structure

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