Deciphering the genetic diversity and population structure of Turkish bread wheat germplasm using iPBS-retrotransposons markers

2021 ◽  
Author(s):  
Muhammad Azhar Nadeem
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Bread Wheat ◽  
Wheat Germplasm

scholarly journals Genomic Analysis of Spanish Wheat Landraces Reveals Their Huge Potential for Breeding

2019 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Geographic Origin ◽  
Local Conditions ◽  
Reference Set ◽  
Wheat Landraces

Abstract Background One of the main goals for the XXI century breeding is the development of crop cultivars that can maintain current yields under unfavorable environments. Landraces that have been grown under varied local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a wide collection of wheat landraces. These accessions, locally adapted to a really wide diversity of eco-climatic conditions, represent a highly valuable material for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results DArTseq GBS approach generated 10K SNPs and 40K DArT high-quality markers that were mapped against the currently available bread wheat reference genome. The markers with known location were distributed in all the chromosomes, having a relatively well-balanced genome-wide coverage. The genetic analysis showed that Spanish wheat landraces are clustered in different groups, thus representing genetic pools capable to provide different allelic variation. The subspecies had a major impact on the population structure of durum wheat landraces, identifying three different clusters that corresponded to subsps. durum, turgidum and dicoccon. The population structure of bread wheat landraces was more biased by geographic origin. Conclusions The results showed a wider genetic diversity in landraces when compared to a reference set that included commercial varieties, and a higher divergence between landraces and the reference set in durum wheat than in bread wheat. Some genomic regions with patterns of variation that differ between landraces and reference varieties could be detected, pointing out loci under selection during crop improvement that could help to target breeding efforts. The results obtained from this work will be highly valuable for future GWAS analysis.

scholarly journals Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

2021 ◽  
Vol 12 ◽  
Author(s):  
Pooja Sihag ◽  
Vijeta Sagwal ◽  
Anuj Kumar ◽  
Priyanka Balyan ◽  
Reyazul Rouf Mir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Wheat Varieties ◽  
Wheat Genotypes ◽  
Wheat Germplasm ◽  
Heat Tolerant

A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR markers (miRNA-SSRs) in wheat, which were found as key players in various abiotic stresses. In the present study, we identified 104 heat-stress-responsive miRNAs reported in various crops. Out of these, 70 miRNA-SSR markers have been validated on a set of 20 terminal heat-tolerant and heat-susceptible wheat genotypes. Among these, only 19 miRNA-SSR markers were found to be polymorphic, which were further used to study the genetic diversity and population structure. The polymorphic miRNA-SSRs amplified 61 SSR loci with an average of 2.9 alleles per locus. The polymorphic information content (PIC) value of polymorphic miRNA-SSRs ranged from 0.10 to 0.87 with a mean value of 0.48. The dendrogram constructed using unweighted neighbor-joining method and population structure analysis clustered these 20 wheat genotypes into 3 clusters. The target genes of these miRNAs are involved either directly or indirectly in providing tolerance to heat stress. Furthermore, two polymorphic markers miR159c and miR165b were declared as very promising diagnostic markers, since these markers showed specific alleles and discriminated terminal heat-tolerant genotypes from the susceptible genotypes. Thus, these identified miRNA-SSR markers will prove useful in the characterization of wheat germplasm through the study of genetic diversity and population structural analysis and in wheat molecular breeding programs aimed at terminal heat tolerance of wheat varieties.

Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

2019 ◽  
Vol 60 (3-4) ◽  
pp. 283-289 ◽  
Author(s):  
Madhav Bhatta ◽  
Vladimir Shamanin ◽  
Sergey Shepelev ◽  
P. Stephen Baenziger ◽  
Violetta Pozherukova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Bread Wheat ◽  
Structure Analysis ◽  
Western Siberia ◽  
Population Structure Analysis

scholarly journals Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e94000 ◽  
Author(s):  
Nanna Hellum Nielsen ◽  
Gunter Backes ◽  
Jens Stougaard ◽  
Stig Uggerhøj Andersen ◽  
Ahmed Jahoor
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Population Structure ◽  
Bread Wheat ◽  
Structure Analysis ◽  
Triticum Aestivum L ◽  
Population Structure Analysis

scholarly journals Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1116
Author(s):  
Vladimir Aleksandrov ◽  
Tania Kartseva ◽  
Ahmad M. Alqudah ◽  
Konstantina Kocheva ◽  
Krasimira Tasheva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Bread Wheat ◽  
Clustering Algorithm ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Geographic Region ◽  
Snp Markers ◽  
Genetic Diversity And Structure

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r2), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

scholarly journals Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 340
Author(s):  
Muhammad Massub Tehseen ◽  
Deniz Istipliler ◽  
Zakaria Kehel ◽  
Carolina P. Sansaloni ◽  
Marta da Silva Lopes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Bread Wheat ◽  
Structure Analysis ◽  
Geographic Origin ◽  
Climatic Conditions ◽  
Population Structure Analysis ◽  
North Eastern ◽  
Wheat Landraces

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

scholarly journals Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

2020 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Reference Set ◽  
Genome Wide ◽  
Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.)

2016 ◽  
Vol 54 (4) ◽  
pp. 421-437 ◽  
Author(s):  
Tulin Tascioglu ◽  
Ozge Karakas Metin ◽  
Yildiz Aydin ◽  
Muhammet Sakiroglu ◽  
Kadir Akan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Bread Wheat ◽  
Triticum Aestivum L

scholarly journals Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

2019 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Reference Set ◽  
Genome Wide ◽  
Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were mapped against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

Sign in / Sign up

Export Citation Format

Share Document