scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2018 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Wild Relatives ◽  
Human Migration ◽  
Structural Variations ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

AbstractSince its domestication in the Fertile Crescent ~8,000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4,506 landraces and cultivars originating from 105 different countries genotyped with a high-density SNP array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the apparition of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.One Sentence SummaryA phylogeographical study reveals the complex history of wheat genetic diversity through time and space.

scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2019 ◽  
Vol 5 (5) ◽  
pp. eaav0536 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism Array ◽  
Human Migration ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

scholarly journals Potential of Wild Relatives of Wheat: Ideal Genetic Resources for Future Breeding Programs

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1656
Author(s):  
Alireza Pour-Aboughadareh ◽  
Farzad Kianersi ◽  
Peter Poczai ◽  
Hoda Moradkhani
Keyword(s):  
Genetic Diversity ◽  
Gene Pool ◽  
Wheat Breeding ◽  
Wild Relatives ◽  
Accurate Information ◽  
Wild Relative ◽  
Breeding Programs ◽  
Main Gene ◽  
Induce Resistance ◽  
Close Relatives

Among cereal crops, wheat has been identified as a major source for human food consumption. Wheat breeders require access to new genetic diversity resources to satisfy the demands of a growing human population for more food with a high quality that can be produced in variable environmental conditions. The close relatives of domesticated wheats represent an ideal gene pool for the use of breeders. The genera Aegilops and Triticum are known as the main gene pool of domesticated wheat, including numerous species with different and interesting genomic constitutions. According to the literature, each wild relative harbors useful alleles which can induce resistance to various environmental stresses. Furthermore, progress in genetic and biotechnology sciences has provided accurate information regarding the phylogenetic relationships among species, which consequently opened avenues to reconsider the potential of each wild relative and to provide a context for how we can employ them in future breeding programs. In the present review, we have sought to represent the level of genetic diversity among the wild relatives of wheat, as well as the breeding potential of each wild species that can be used in wheat-breeding programs.

scholarly journals Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Nikolaos Alachiotis ◽  
Amidou N’Diaye ◽  
Curtis Pozniak ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Spring Wheat ◽  
Snp Array ◽  
Categorical Variables ◽  
Selective Sweeps ◽  
Wheat Cultivars ◽  
Breeding Programs ◽  
The Impact

AbstractPrevious molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.

scholarly journals Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current

2013 ◽  
Vol 79 (23) ◽  
pp. 7491-7501 ◽  
Author(s):  
Jenan J. Kharbush ◽  
Juan A. Ugalde ◽  
Shane L. Hogle ◽  
Eric E. Allen ◽  
Lihini I. Aluwihare
Keyword(s):  
Genetic Diversity ◽  
Water Column ◽  
Genetic Relationships ◽  
Structural Diversity ◽  
Low Oxygen ◽  
Structural Variations ◽  
Data Set ◽  
Pentacyclic Triterpenoid ◽  
History Of ◽  
Membrane Components

ABSTRACTHopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greatersqhCgenetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential “hot spots” of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

scholarly journals Common Vetch, Valuable Germplasm for Resilient Agriculture: Genetic Characterization and Spanish Core Collection Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Lucía De la Rosa ◽  
María Isabel López-Román ◽  
Juan M. González ◽  
Encarnación Zambrana ◽  
Teresa Marcos-Prado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Core Collection ◽  
Animal Feed ◽  
Plant Genetic Resources ◽  
Wild Relatives ◽  
Agricultural System ◽  
Protein Profiles ◽  
Common Vetch ◽  
Breeding Programs

Common vetch (Vicia sativa L.) is a legume used for animal feed because of its high protein content and great capacity for nitrogen fixation, making this crop relevant in sustainable agriculture. The Spanish vetch collection, conserved at the Spanish Plant Genetic Resources Center (CRF), is one of the largest collections of this species worldwide, including landraces, wild relatives mainly collected in Spain, and commercial cultivars, but also accessions of international origin. The analysis of the genetic diversity of this material, whose genome has not been sequenced yet, and the assembly of a representative collection could play a pivotal role in conserving and exploiting these genetic resources in breeding programs mainly in those focused on consequences and demands of climate change. In this work, a set of 14 simple sequence repeat (SSR) reference alleles for genetic diversity analysis of the CRF vetch collection has been developed, used for genotyping more than 545 common vetch accessions from all over the world and validated. All the tested markers were polymorphic for the analyzed accessions. Overall, at least 86 different loci were identified with 2–11 alleles per locus with an average of 6.1 alleles per locus. Also, the analyses of the generated SSR database support that most of these SSR markers are transferable across closely related species of Vicia genus. Analysis of molecular variance revealed that wild relatives have a higher genetic diversity than landraces. However, cultivars have similar diversity than landraces, indicating that genetic variability has been barely lost due to the breeding of this legume. Low differences of genetic variations between Spanish and non-Spanish accessions have been observed, suggesting a high degree of diversity within Spanish genotypes, which provide 95% of the total genetic variation, so we have focused our efforts on characterizing genotypes of Spanish origin that were further studied using storage protein profiles. Based on SSR, seed protein profiles, and agromorphological and passport data, a vetch core collection (VCC) containing 47 V. sativa accessions of Spanish origin has been established. In this collection, the characterization has been expanded using ISSR markers, and it has been reevaluated with new agromorphological data, including drought tolerance characters. This VCC presents a minimum loss of genetic diversity concerning the total collection and constitutes an invaluable material that can be used in future breeding programs for direct use in a resilient agricultural system.

scholarly journals Genetic Diversity of Local Accessions of Dimocarpus longan Revealed By ISSR Markers

2016 ◽  
Vol 17 (1) ◽  
pp. 25 ◽  
Author(s):  
Baiq Dina Mariana ◽  
A. Sugiyatno ◽  
A. Supriyanto
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Issr Markers ◽  
Breeding Programs ◽  
Dimocarpus Longan ◽  
History Of ◽  
Research Institute

<p>Keragaman Genetik Aksesi Lenggkeng Lokal Dimocarpus longan Berdasarkan Penanda ISSR. Lengkeng telah berkembang di Indonesia, namun studi tentang tanaman ini belum banyak dilakukan. Studi untuk mengetahui keragaman genetik lengkeng lokal telah dilakukan di Balai Penelitian Tanaman Jeruk dan Buah Subtropika (Balitjestro) pada bulan Maret- April 2008. Penanda ISSR digunakan untuk mengidentifikasi keragaman genetik antar delapan genotipe lengkeng lokal yang telah dikoleksi oleh Balitjestro. Dendogram yang dibuat berdasarkan UPGMA menggunakan metode SAHN menunjukkan nilai kemiripan sebesar 0,34-0,86. Nilai kemiripan tertinggi diperoleh dari KL I dan KL II (0,86) dan nilai kemiripan terendah diperoleh dari KL I dan KL V/KL VI (0,34). Penanda ISSR dapat digunakan untuk mengidentifikasi lengkeng dan dapat memberikan informasi yang berguna untuk program pemuliaan lengkeng di kemudian hari.</p><p> </p><p><strong>Abstrak</strong></p><p>There is no clear history of longan development in Indonesia even though it has developed well in Indonesia for many years. The study aimed at revealing genetic of diversity of local longan was done in Indonesian Citrus and Subtropical Research Institute (ICSFRI) from March to April 2008. ISSR markers were employed to identify the genetic variation among eight morphologically more or less alike accessions of longan ssp. Matrix data was counted and dendogram of samples was constructed using UPGMA and SAHN method. The cluster showed similarity value 0.34-0.86. The highest similarity value was observed between KL I and KL II (0.86) while the lowest one was obtained between KL I and KL V/KL VI (0.34). ISSR markers were able to identify the genetic diversity of longan and were helpful to provide information on genetic diversities especially for future breeding programs.</p>

scholarly journals The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles

2020 ◽  
Vol 11 ◽  
Author(s):  
Elisabetta Mazzucotelli ◽  
Giuseppe Sciara ◽  
Anna M. Mastrangelo ◽  
Francesca Desiderio ◽  
Steven S. Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Triticum Turgidum ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Breeding Program ◽  
Fixation Index ◽  
Breeding Programs ◽  
Genetic Clusters ◽  
Modern Breeding

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94–97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970–2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (Fst) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.

scholarly journals Strategic Identification of New Genetic Diversity to Expand Lentil (Lens culinaris Medik.) Production (Using Nepal as an Example)

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1933
Author(s):  
Sandesh Neupane ◽  
Rajeev Dhakal ◽  
Derek M. Wright ◽  
Deny K. Shrestha ◽  
Bishnu Dhakal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Field Experiments ◽  
Breeding Programs ◽  
Genetic Base ◽  
The World ◽  
History Of ◽  
Production Area

Although lentil has a long history of cultivation, cultivars rely on a narrow genetic base, indicating room for broadening the diversity. Two field experiments were conducted at Bardiya, Nepal, during winter 2016 and 2017, with 324 diverse lentil genotypes obtained from genebanks and breeding programs around the world. Phenological traits related to adaptation, particularly days to flower, were assessed. A photothermal model was used to predict days to flower in new environments to identify genotypes that may be suitable for additional growing regions in Nepal, allowing for the expansion of the production area. Many putatively adapted genotypes were identified for terai, mid-hill, and high-hill growing regions. The list includes large-seeded or yellow cotyledon lines, representing new market classes of lentils for Nepal.

scholarly journals Characterization of Annur and Bedakam Ecotypes of Coconut from Kerala State, India, Using Microsatellite Markers

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
M. K. Rajesh ◽  
K. Samsudeen ◽  
P. Rejusha ◽  
C. Manjula ◽  
Shafeeq Rahman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
West Coast ◽  
Clustering Analysis ◽  
Climatic Conditions ◽  
Breeding Programs ◽  
Wide Range ◽  
History Of ◽  
Kerala State

The coconut palm is versatile in its adaptability to a wide range of soil and climatic conditions. A long history of its cultivation has resulted in development of many ecotypes, which are adapted to various agro-eco factors prevalent in a particular region. These ecotypes usually are known by the location where they are grown. It is important to explore such adaptation in the coconut population for better utilization of these ecotypes in coconut breeding programs. The aim of the present study was to identify the genetic diversity of the Bedakam and Annur ecotypes of coconut and compare these ecotypes with predominant West Coast Tall (WCT) populations, from which they are presumed to have been derived, using microsatellite markers. All the 17 microsatellite markers used in the study revealed 100% polymorphism. The clustering analysis showed that Annur and Bedakam ecotypes were two separate and distinct populations compared to WCT. It was also evident from the clustering that Annur ecotype was closer to WCT than Bedakam ecotype.

scholarly journals Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247787
Author(s):  
Antonios Kominakis ◽  
Eirini Tarsani ◽  
Ariadne L. Hager-Theodorides ◽  
Ioannis Mastranestasis ◽  
Ioannis Hadjigeorgiou
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Genetic Distances ◽  
Admixture Analysis ◽  
Ecosystem Integrity ◽  
Genetic History ◽  
Aegean Islands ◽  
History Of ◽  
North Aegean ◽  
Historic Data

Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.

Sign in / Sign up

Export Citation Format

Share Document