Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1095-1106 ◽  
Author(s):  
I A Matus ◽  
P M Hayes
Keyword(s):  
Genetic Diversity ◽  
Hordeum Vulgare ◽  
Molecular Marker ◽  
Mapping Population ◽  
Allelic Diversity ◽  
Breeding Lines ◽  
Barley Germplasm ◽  
High Level ◽  
Elite Breeding Lines ◽  
Simple Sequence

Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp. spontaneum, SSR, genetic diversity, germplasm.

scholarly journals Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 752
Author(s):  
Kyung Jun Lee ◽  
Raveendar Sebastin ◽  
Gyu-Taek Cho ◽  
Munsup Yoon ◽  
Gi-An Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Solanum Tuberosum L ◽  
Allelic Diversity ◽  
Wild Relatives ◽  
Phenotypic Traits ◽  
Breeding Lines ◽  
Potato Germplasm ◽  
Potato Improvement ◽  
Simple Sequence

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

scholarly journals Microsatellite-Based Analysis of Genetic Diversity and Population Structure of Rainbow Trout (Oncorhynchus mykiss) Cultured in Ukraine

2020 ◽  
Vol 5 (1) ◽  
pp. 29-39
Author(s):  
Оlena Bielikova ◽  
Serhii Тarasjuk ◽  
Antonina Mruk ◽  
Olga Zaloilo ◽  
Alexander Didenko
Keyword(s):  
Genetic Diversity ◽  
Rainbow Trout ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Principal Coordinates ◽  
High Level ◽  
High Degree ◽  
Simple Sequence

The genetic structure of rainbow trout farmed in Ukraine were characterized based on microsatellite loci. The selected set of SSR-markers (Simple-sequence repeatsmarkers) had a high degree of polymorphism that allowed determining the specificity of each local stock (average PIC value = 0.785 ± 0.034). The microsatellite analysis of rainbow trout from the studied stocks showed a high level of genetic diversity (uHe = 0.825 ± 0.030, PIC = 0.785 ± 0.034, I = 1.836 ± 0.127). The level of allelic diversity of the selected loci was high, where the average number of alleles per locus was 7.833, the effective number of alleles per locus was 5.687. The range of amplicon sizes of the studied loci and private alleles for each local group was determined. The cluster analysis showed the presence of three clusters. The range of genetic variability was presented in the graphical interpretation of the principal coordinates analysis (PCoA). Based on unbiased genetic distances, the Kharkiv and Transcarpathian local stocks were found to be the closest, while the Chernivtsi stock was the most distant from them.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Genome Analysis of Mungbean [Vigna radiata (L.) Wilczek] using Simple Sequence Repeats (SSR) Mapping Data

2021 ◽  
Author(s):  
Babita Rani ◽  
Renu Singh ◽  
Minakshi Jattan ◽  
Shubham Kumar ◽  
Ram Kumar
Keyword(s):  
Genetic Diversity ◽  
Agricultural Research ◽  
Ammonium Bromide ◽  
Breeding Lines ◽  
Iron And Zinc ◽  
Zinc Concentrations ◽  
Increase Productivity ◽  
Cetyltrimethyl Ammonium ◽  
Simple Sequence

Background: Agricultural research chiefly focuses on the ways to increase productivity of staple food crops like wheat and rice, but still there are crops where research focus is meagre like nutritionally important mungbean crop grown by marginal farmers in crop rotation systems. Mungbean is leguminous crop which is high in protein content thus it offers health benefits at cheaper rates. The present work emphasizes on finding genetic diversity in mungbean germplasm on the basis of chemical and molecular analysis for micronutrients variation (iron and zinc). The identified molecular markers having linkage with high iron and zinc concentrations in the seeds can prove helpful in expansion of biofortification programme.Methods: Fifty-one green gram genotypes viz. varieties released from CCS Haryana Agricultural University (HAU), Hisar, Punjab Agricultural University (PAU), Ludhiana, Indian Institute of Pulse Research (IIPR), Kanpur and some advanced breeding lines were included in the study. Acid digested samples were used for determination of Fe and Zn by Atomic Absorption Spectrophotometer. Young seedlings leaves were used for isolation of genomic DNA using 2% CTAB (cetyltrimethyl ammonium bromide). Result: Total of fifty-one mungbean genotypes were tested using fifty simple sequence repeat (SSR) primers. Out of fifty primers screened, 16 primers generated 35 bands. Iron (Fe) and zinc (Zn) in mungbean lines was 36.90 to 107.1 mg/kg and 14.2 to 53.8 mg/kg respectively. The molecular studies based on SSR markers also indicates existence of ample genetic diversity at molecular level.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

2008 ◽  
Vol 88 (2) ◽  
pp. 313-322 ◽  
Author(s):  
S. C. Debnath ◽  
S. Khanizadeh ◽  
A. R. Jamieson ◽  
C. Kempler
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Pair Group ◽  
Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

2016 ◽  
Vol 96 (5) ◽  
pp. 808-818 ◽  
Author(s):  
Neil Hobson ◽  
Habibur Rahman
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Low Cost ◽  
Pak Choi ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Genetic Pools ◽  
High Level ◽  
Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

Using soybean pedigrees to identify genomic selection signatures associated with long-term breeding for cultivar improvement

2018 ◽  
Vol 98 (5) ◽  
pp. 1176-1187 ◽  
Author(s):  
Christopher M. Grainger ◽  
Jocelyne Letarte ◽  
Istvan Rajcan
Keyword(s):  
In Silico Analysis ◽  
Selection Signatures ◽  
Selection Signature ◽  
Breeding Lines ◽  
Genomic Regions ◽  
Elite Breeding Lines ◽  
Silico Analysis ◽  
Simple Sequence ◽  
Introgressive Breeding

Genetic hitchhiking methods used to uncover selection signatures related to traits of agronomic importance in crops have primarily been used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, two groups of cultivars defined by an elite Canadian soybean cultivar, ‘OAC Bayfield’, were compared to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis compared the results in this study to quantitative trait loci (QTL) reported in SoyBase and showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield, or maturity. In addition, the number and type of QTL associated with the fixed versus selected loci differed, particularly for yield. Genomic regions exhibiting a selection signature may contain important loci that either need to be conserved for agronomic performance or be targeted for introgressive breeding and germplasm enrichment.

scholarly journals Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

2019 ◽  
Vol 18 (4) ◽  
pp. 93-109
Author(s):  
Ilaria Marcotuli ◽  
Andrea Mazzeo ◽  
Domenica Nigro ◽  
Stefania Lucia Giove ◽  
Angelica Giancaspro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ficus Carica ◽  
Accurate Information ◽  
Main Crop ◽  
Polymorphic Pattern ◽  
Genetic Diversity And Structure ◽  
The Mean ◽  
High Level ◽  
Simple Sequence ◽  
Modern Technologies

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

scholarly journals Molecular Identification Keys for Cultivars and Lines of Cornus florida and C. kousa Based on Simple Sequence Repeat Loci

2008 ◽  
Vol 133 (6) ◽  
pp. 783-793 ◽  
Author(s):  
Phillip A. Wadl ◽  
Xinwang Wang ◽  
Andrew N. Trigiano ◽  
John A. Skinner ◽  
Mark T. Windham ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Identification ◽  
Simple Sequence Repeat ◽  
Floral Display ◽  
Cornus Florida ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Flowering Dogwood ◽  
Identification Keys ◽  
Simple Sequence

Flowering dogwood (Cornus florida) and kousa dogwood (C. kousa) are popular ornamental species commonly used in the horticultural industry. Both trees are valued for their beautiful floral display and four-season appeal. Species-specific simple sequence repeat (SSR) loci were used to genotype and assess genetic diversity of 24 flowering dogwood cultivars and breeding lines and 22 kousa dogwood cultivars. Genetic diversity was determined by allele sharing distances and principal coordinate analysis and was high in both species. Molecular identification keys were developed for cultivars and breeding lines of each species using a few polymorphic SSRs loci (four in C. florida and five in C. kousa). Most (18 of 24) of the flowering dogwood and all (22 of 22) kousa dogwood accessions could be distinguished from each other using these SSRs; those that could not were resolved using DNA amplification fingerprinting. The reliability of both keys was assessed using five anonymous cultivars for each dogwood species, which were correctly identified using the molecular keys. The genetic information presented here will be useful for identification and verification of cultivars for nurseries and as molecular markers for breeders and researchers.

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