Genetic diversity and structure found in samples of Eritrean bread wheat

Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat.

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A Microsatellite Map of Wheat

Genetics ◽

10.1093/genetics/149.4.2007 ◽

1998 ◽

Vol 149 (4) ◽

pp. 2007-2023 ◽

Cited By ~ 8

Author(s):

Marion S Röder ◽

Victor Korzun ◽

Katja Wendehake ◽

Jens Plaschke ◽

Marie-Hélène Tixier ◽

...

Keyword(s):

Bread Wheat ◽

Reference Population ◽

Triticum Aestivum L ◽

Wheat Genome ◽

D Genome ◽

B Genome ◽

Microsatellite Map ◽

A Genome ◽

Polymorphic Microsatellite ◽

Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

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Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

Plant Genetic Resources ◽

10.1017/s147926212100040x ◽

2021 ◽

pp. 1-9

Author(s):

Atefeh Nouri ◽

Maryam Golabadi ◽

Alireza Etminan ◽

Abdolmajid Rezaei ◽

Ali Ashraf Mehrabi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Aegilops Tauschii ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Start Codon ◽

D Genome ◽

Breeding Programmes ◽

High Level ◽

Effective Multiplex Ratio

Abstract Aegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

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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 ◽

10.3390/plants10061116 ◽

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.

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Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

Plant Genetic Resources ◽

10.1017/s1479262114000343 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S91-S94 ◽

Cited By ~ 7

Author(s):

Puji Lestari ◽

Sue Kyung Kim ◽

Reflinur ◽

Yang Jae Kang ◽

Nurwita Dewi ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Vigna Radiata ◽

Diversity Index ◽

Polymorphic Information Content ◽

Conservation Strategy ◽

Low Genetic Diversity ◽

Breeding Programmes ◽

The Mean ◽

Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Genetic structure of annual ryegrass (Lolium multiflorum) populations estimated by RAPD

Scientia Agricola ◽

10.1590/s0103-90162004000400009 ◽

2004 ◽

Vol 61 (4) ◽

pp. 407-413 ◽

Cited By ~ 8

Author(s):

Eduardo Alano Vieira ◽

Caroline Marques Castro ◽

Antônio Costa de Oliveira ◽

Fernando Irajá Félix de Carvalho ◽

Paulo Dejalma Zimmer ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Diversity Index ◽

Lolium Multiflorum ◽

Rio Grande ◽

Conservation Strategies ◽

Temperate Climate ◽

Annual Ryegrass ◽

Rio Grande Do Sul ◽

Genetic Diversity And Structure

Annual ryegrass is a temperate climate annual foraging grass, grown mostly in the South of Brazil, especially in the state of Rio Grande do Sul. Despite its importance, little is known about its genetic diversity, both within and among the populations cultivated. This knowledge is of fundamental importance for developing breeding and conservation strategies. The aim of this study was to characterize the genetic diversity and structure of four populations of annual ryegrass. Three of the populations were located in Rio Grande do Sul and the fourth in Uruguay. RAPD markers were used to study the genetic diversity and structure of these populations. Analysis of 375 individuals sampled from the populations, using six RAPD primers, generated a total of 82 amplified bands. They included 73 polymorphic bands (89,02%). The value of the total genetic diversity index obtained, <IMG SRC="/img/revistas/sa/v61n4/22157s1.gif">(0,71) was high, indicating the presence of wide genetic diversity in the four populations. Genetic structure analysis revealed that 98% of total diversity is intrapopulational, whereas interpopulational genetic diversity was only 2%. These results suggest that before these populations separated, they had gone through a period of gene exchange and, even after the separation event, gene frequency stayed at levels similar to the original levels, with no differential selection for these genes in the different cultivation areas.

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Introduction of the D-genome chromosomes from bread wheat into hexaploid triticale with a complete rye genome

Genome ◽

10.1139/g87-074 ◽

1987 ◽

Vol 29 (3) ◽

pp. 425-430 ◽

Cited By ~ 25

Author(s):

A. J. Lukaszewski ◽

B. Apolinarska ◽

J. P. Gustafson

Keyword(s):

Key Words ◽

Bread Wheat ◽

Hexaploid Triticale ◽

Genome Chromosome ◽

D Genome ◽

Homozygous Condition ◽

C Banding ◽

B Genome ◽

Chromosome Substitutions ◽

Triticosecale Wittmack

Hexaploid triticale (× Triticosecale Wittmack) lines selected from the progeny of octoploid × tetraploid triticale hybrids were karyotyped using C-banding. The number of D-genome chromosome pairs substituted for A- and (or) B-genome chromosomes ranged from 0 to 4, averaging 2.1 substitutions per line. Every D-genome chromosome was present in at least 1 of the 70 lines analyzed. The most frequent were chromosomes 3D and 6D, followed by 1D. Of the 14 possible substitutions, 12 were present in the homozygous condition, 1 (4D/4B) was still segregating, and 6D/6B was absent. With the exception of one 1D/1R substitution and one 7RS/4DS translocation, all lines had a complete rye genome. Key words: triticale, chromosome substitutions, D genome.

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Over-expression of HMW glutenin subunit Glu-B1 7x in hexaploid wheat varieties (Triticum aestivum)

Australian Journal of Agricultural Research ◽

10.1071/ar03227 ◽

2004 ◽

Vol 55 (5) ◽

pp. 577 ◽

Cited By ~ 52

Author(s):

M-J. Vawser ◽

G. B. Cornish

Keyword(s):

Bread Wheat ◽

Expression Profiles ◽

Major Effect ◽

Dough Strength ◽

D Genome ◽

Wheat Varieties ◽

B Genome ◽

Rp Hplc ◽

Hmw Glutenin ◽

Different Origin

In Canada in 1993, a special market class of wheat, Canada Western Extra Strong (CWES), was established to segregate wheat varieties known to produce very strong and extensible doughs. These exceptional dough properties enable CWES cultivars to be blended with wheats of lesser quality as well as being suited to the manufacture of frozen dough products. The high molecular weight (HMW) glutenin allele (Glu-B1al) that confers these properties, particularly dough strength, has now been identified. Typically, the presence of the Glu-B1al (7+8*) allele is associated with the overexpression of HMW-GS 1Bx 7. RP-HPLC was used to quantify the proportion (% area) of individual HMW-GS relative to total HMW-GS in wheat varieties of different origin. The B genome contributed the highest percentage of HMW-GS, with the exception of Glu-B1d (6+8*) where the D genome contributed the most. Cultivars that possessed the Glu-B1al allele contained a significantly higher (P < 0.001) proportion of HMW-GS (56.80 ± 3.25%) encoded by the B genome. This suggests that the proportion of Glu-B1 subunits, relative to the total amount of HMW-GS expressed, has a major effect on dough strength. We also identified germplasm, of different origin, that contains the Glu-B1al allele and overexpresses subunit 7, including the most likely source of this allele in bread wheat cultivars. The Glu-B1al allele in the varieties identified in this paper could be traced, at least through one parent, to the Argentinean bread wheat cultivar Klein Universal II. RP-HPLC elution and expression profiles of various common HMW-GS are also discussed.

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Genetic diversity and structure of improved indica rice germplasm

Plant Genetic Resources ◽

10.1017/s1479262113000579 ◽

2014 ◽

Vol 12 (2) ◽

pp. 248-254 ◽

Cited By ~ 3

Author(s):

Kai Wang ◽

Fulin Qiu ◽

Madonna Angelita Dela Paz ◽

Jieyun Zhuang ◽

Fangming Xie

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Latin American ◽

Hybrid Rice ◽

Hybrid Breeding ◽

Model Based ◽

Population Structure Analysis ◽

Wide Range ◽

Genetic Diversity And Structure ◽

Breeding Programmes

The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improved indica varieties/lines developed recently and/or widely used by present indica breeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improved indica varieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/lines through germplasm exchanges. Distance-based clustering revealed that Latin-American cultivated indica lines have tended to form their own ecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding, although they are still closely related to Asian indica lines. African cultivated indica lines, on the other hand, have not yet formed their own ecological cline. It was also observed that the most well-known hybrid rice parents, Zhenshan97B and Minghui63, were unexpectedly clustered in the same SG with a relatively narrow genetic distance, which suggests that a significant genetic distance between parents is not a prerequisite for all elite hybrid rice lines with high heterosis.

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DNA barcode reference libraryconstruction and population genetic diversity and structure analysis of Amomum villosum Lour. in Daodi production area

10.21203/rs.3.rs-133546/v1 ◽

2020 ◽

Author(s):

Zhang Danchun ◽

Xiaoxia Ding ◽

Wan Guan ◽

Juan Huang ◽

He Su ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Diversity Index ◽

Gene Diversity ◽

Dna Barcode ◽

Guangdong Province ◽

Shannon Index ◽

Success Rates ◽

Genetic Diversity And Structure ◽

Amomum Villosum

Abstract Background: The Amomum villosum has the situation that it is inferior and other other varieties are used as A. villosum in the market. In order to develop and utilize the genuine medicinal materials A. villosum, this experiment aims to carry out the identification and research of variety of the A. villosum and analyze its genetic diversity, constructing the DNA barcode database of the genuine medicinal materials A. villosum in Guangdong Province and providing recommendations for populations planting, which will be critical to the further research of A. villosum. (2) Methods: A total of 141 samples of A. villosum were analyzed by DNA barcoding to construct DNA barcode database. The genetic diversity of A. villosum sampled from 7 populations in Guangdong Province was detected based on ISSR molecular marker technology. (3) Results: The success rates of PCR amplification and sequencing of five barcodes of A. villosumwas rbcL> ITS > ITS2 >psbA-trnH>matK. 141 samples of A. villosum from 7 populations in Guangdong Province were used to construct a reference DNA barcode database containing 531 sequences. The results of genetic diversity were as follow, the number of alleles Na ranged from 1.2879 to 1.7121, the effective number of alleles Ne ranged from 1.1848 to 1.4240, the gene diversity index (H) ranged from 0.2536 to 0.1117, and the Shannon index (I) ranged from 0.3816 to 0.1658, whichindicatedthegenetic diversity of A.Villosum was rich. The total genetic diversity among the 7 populations (Ht) was 0.3299, the genetic diversity within the populations (Hs) was 0.1819, and the gene differentiation coefficient (Gst) was 0.4487. AMOVA showed that the genetic variation within the populations and the genetic variation between the populations accounted for 68.74% (P<0.05) and 31.26% (P<0.05) respectively, indicating that the genetic variation of A. villosum was mainly within the populations. The gene flow Nm was 0.6143.The genetic distance of the 7 populations was 0.0844 - 0.3347, and the genetic identity was 0.7156 - 0.9191, confirming that the genetic relationship of each population was relatively close. The 7 populations were significantly grouped in the cluster analysis and the genetic level of each population from high to low was as follow: ZY (National Highway Roadside) > ZJD (Zhongjiaodong) > GY (Geopark) >MM (Dianbai) > YC (Dadong Village) > XFC (Xingfu Village) > TK (Tankui Village). There was no correlation between the geographic distance and the degree of genetic differentiation among populations. Conclusion: By amplifying and sequencing five barcodes of ITS2, psbA-trnH, ITS, matK and rbcL, a reference DNA barcode database of A. villosum with 531 sequences was constructed. The results of genetic diversity showed that it is necessary to take appropriate in situ protection measures for the populations of A. villosum in Yangchun City and increase the genetic exchange between populations to improve the genetic diversity of A. villosum.

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