Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm

2003 ◽  
Vol 54 (12) ◽  
pp. 1197 ◽  
Author(s):  
A. Karakousis ◽  
A. R. Barr ◽  
K. J. Chalmers ◽  
G. A. Ablett ◽  
T. A. Holton ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Strong Association ◽  
Variety Identification ◽  
Improvement Program ◽  
Breeding Programs ◽  
Partial Correlations ◽  
Trait Locus ◽  
Barley Germplasm ◽  
Barley Genotypes

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs. A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS). The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker. SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS. The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags. A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm. PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes. Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset. It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes. From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes. These markers all show high and/or consistent PIC values among Australian and European barley genotypes.

scholarly journals Genetic diversity among tropical maize inbred lines as revealed by SSR markers

2020 ◽  
pp. 2010-2019
Author(s):  
Maizura Abu Sin ◽  
Ghizan Saleh ◽  
Nur Ashikin Psyquay Abdullah ◽  
Pedram Kashiani
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Maize Inbred Lines

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

scholarly journals DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes

2017 ◽  
Vol 15 (1) ◽  
pp. 123-137 ◽  
Author(s):  
MM Islam ◽  
HA Begum ◽  
MS Ali ◽  
M Kamruzzaman ◽  
S Hoque ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Allelic Diversity ◽  
Breeding Programs ◽  
Chord Distance ◽  
Genetic Dissimilarity

The allelic diversity and relationship among 120 Aus rice landraces were determined through DNA fingerprinting using microsatellite (SSR) markers. A total of 85 SSR markers were used to characterize and discriminate all tested Aus rice genotypes, 45 of which were polymorphic for different chromosome numbers. The number of alleles per locus varied from 6 alleles (RM484 and RM541) to 30 alleles (RM519) with an average of 13 alleles per locus. The polymorphic information content (PIC) values varied ranged from 0.5211 (RM536) to 0.9369 (RM519) with an average 0.8217. The highest PIC value (0.9369) was obtained for RM519 followed by RM286 (0.9357). The genetic distance-based results seen in the unrooted neighbor-joining tree clustering revealed nine genetic groups. Being grouped into distant clusters and with highest genetic distance, eleven genotypes viz., Atithi dhan, Kadar chap, Pankiraj, Japanese-7, Jamri saity, Logi jota, Joba, Lada moni, Manik Mondal-2, Boilum and Brmulka-2 could be selected as potential parents for crop improvement for their distinctive characters. Panchash and Parija had closest distance in the SSR based CS-Chord distance (0.000) might have same genetic background. The highest genetic dissimilarity (1.000) was found among the nineteen Aus genotypes combinations followed by the second highest (0.9778) among 94 Aus rice combinations. Whereas lowest genetic dissimilarity was found between Kala and Kalo Hizli (0.1778) followed by Holat and Holae (0.2667). This information will be useful in the selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in the near future.SAARC J. Agri., 15(1): 123-137 (2017)

scholarly journals Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260651
Author(s):  
Sintayehu Admas ◽  
Kassahun Tesfaye ◽  
Teklehaimanot Haileselassie ◽  
Eleni Shiferaw ◽  
K. Colton Flynn
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Geographic Region ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Breeding Programs

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

scholarly journals Using SSR Markers For Assessment Genetic Diversity And Detection Drought Escape Candidate Genes In Barley Lines (Hordeum Vulgare L.)

2014 ◽  
Vol 70 (1) ◽  
pp. 3-14 ◽  
Author(s):  
Vahideh Gougerdchi ◽  
Sara Dezhsetan ◽  
Mohammad Ali Ebrahimi ◽  
Behzad Sadeghzadeh ◽  
Sona Savari
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Candidate Genes ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Marker Assisted Breeding ◽  
Hordeum Vulgare L ◽  
Breeding Programs ◽  
Mapping Analysis

Abstract Assessment of genetic diversity using molecular markers is one of the primary and important steps in breeding programs. In this study, genetic diversity of 52 barley lines evaluated using 68 SSR primer pairs and 47 primer pairs produced clear and polymorphic banding pattern. In general, 153 polymorphic alleles detected. The number of observed polymorphic alleles varied from 2 to 9, with an average of 3.26 alleles per locus. Polymorphic Information Content (PIC) ranged from 0.07 to 0.81, with an average of 0.45. In this research, SSR markers differentiated the studied lines efficiently. Using cluster analysis, studied barley lines divided into two groups. Genetic diversity was relatively corresponding with geographical origins, because the lines related to a country somewhat diverged from each other. Two-rowed Iranian and Chinese barleys classified in one subgroup. Also, most six-rowed barleys classified in one subgroup. Association mapping analysis was used to identify candidate genes for drought escape in barley lines and 16 informative markers were identified after which confirmation in other tests could be suitable for marker assisted breeding drought escape.

Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Rajinder Singh ◽  
Noorhariza Zaki ◽  
Ngoot-Chin Ting ◽  
Rozana Rosli ◽  
Soon-Guan Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Polymorphic Information Content ◽  
Strong Association ◽  
Geographic Location ◽  
Group Method ◽  
Pair Group ◽  
High Level ◽  
Nucleotide Repeats

AbstractA total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

Genetic diversity in accessions of lima bean (Phaseolus lunatus L.) determined from agro-morphological descriptors and SSR markers for use in breeding programs in Brazil

2021 ◽  
Author(s):  
Carolline de Jesús Pires ◽  
Marcones Ferreira Costa ◽  
Maria Imaculada Zucchi ◽  
Regina Lucia Ferreira-Gomes ◽  
José Baldin Pinheiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Lima Bean ◽  
Phaseolus Lunatus ◽  
Morphological Descriptors ◽  
Breeding Programs

scholarly journals Optimal use of SSR markers for varietal identification of upland cotton

2015 ◽  
Vol 50 (7) ◽  
pp. 571-581 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Ana Luíza Ramos Cazé ◽  
Michelle Garcia da Silva ◽  
Vanessa Cavalcante Almeida ◽  
Fernanda Oliveira da Cunha Magalhães ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Discrimination Power ◽  
Arithmetic Average ◽  
Pair Group ◽  
Varietal Identification ◽  
The World ◽  
The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

scholarly journals Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2668
Author(s):  
Zahid Nabi Sheikh ◽  
Vikas Sharma ◽  
Rafiq Ahmad Shah ◽  
Shilpa Raina ◽  
Maha Aljabri ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Genetic Parameter ◽  
Nutritional Composition ◽  
Prunus Armeniaca ◽  
Jammu And Kashmir ◽  
Expected Heterozygosity ◽  
Wild Apricot ◽  
Prunus Armeniaca L

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program.

scholarly journals Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

2017 ◽  
Vol 1 (01) ◽  
pp. 46-51
Author(s):  
OUMER SHERIFF ◽  
KEFYALEW ALEMAYEHU
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Domestic Sheep ◽  
Breeding Programs ◽  
Sheep Breeding ◽  
Population Structures ◽  
The Mean ◽  
Tree Building ◽  
Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

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