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 GENETIC DIVERSITY OF LIMA BEAN (PHASEOLUS LUNATUS L.) FROM TIMOR ISLAND BASED ON MOLECULAR MARKER INTER-SIMPLE SEQUENCE REPEATS (ISSR)

Floribunda ◽  
2021 ◽  
Vol 6 (7) ◽  
Author(s):  
Emilia Juliyanti Bria ◽  
Polikarpia Wilhelmina Bani
Keyword(s):  
Genetic Diversity ◽  
Lima Bean ◽  
Phaseolus Lunatus ◽  
Breeding Programs ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Group Methods ◽  
Lima Beans ◽  
Issr Molecular Markers ◽  
Simple Sequence

Lima bean (Phaseolus lunatus L.) is one of the important legume vegetables in Indonesia. However, genetic information for these plants is still minimalized, especially on Timor Island. This study aims to analyze the genetic diversity of lima beans from Timor Island based on ISSR molecular markers. A total of 4 accessions of lima beans were analyzed using 3 ISSR primers to produce 15 polymorphic bands with an average of 68.18% polymorphism. The cluster analysis results use the Unweighted Pair Group Methods using Arithmetic averages (UPGMA) method to create a dendrogram that produces two main clusters. There were plain seed and pattern seed group with a similarity coefficient of 0.52. These results indicated that the genetic variation of the lima beans from Timor Island was high. Moreover, the result provides a sutable method for evaluating the genetic diversity of lima beans using the ISSR marker and important information of future lima bean breeding programs.

scholarly journals SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 449 ◽  
Author(s):  
Jiantao Wu ◽  
Qinnan Wang ◽  
Jing Xie ◽  
Yong-Bao Pan ◽  
Feng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Capillary Electrophoresis ◽  
Population Structure ◽  
Ssr Markers ◽  
High Performance ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Parental Lines ◽  
Assisted Management ◽  
High Performance Capillary Electrophoresis

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

scholarly journals Genetic diversity assessment of Rice (Oryza sativa L.) germplasm using ssr markers

2015 ◽  
Vol 1 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Ahasanul Hoque ◽  
Shamsun Nahar Begum ◽  
Lutful Hassan
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Growth Duration ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Days To Heading ◽  
Early Maturing ◽  
Rice Genotypes ◽  
Selection Of

Diversity at molecular level among thirty rice genotypes, selected based on earliness and morphometric diversity was evaluated through five SSR markers associated with days to heading. Three primers viz., RM147, RM167 and RM215 showed polymorphism for growth duration related traits. A total of 17 alleles were detected among the 30 rice genotypes with an average of 5.66 alleles per locus. Polymorphism Information Content (PIC) ranged from 0.356 to 0.798 with an average of 0.543. A dendrogram based on total microsatellite polymorphism grouped 30 genotypes into four major clusters at 0.39 similarity coefficient differentiating early maturing genotypes from others. This information about the genetic diversity will be very useful for proper identification and selection of appropriate parents for future breeding programs, including gene mapping. The results also showed that microsatellite markers associated to genes or QTLs controlling growth duration properties are suitable tools for marker assisted selection (MAS) to select rice lines with short growth duration. DOI: http://dx.doi.org/10.3329/ralf.v1i1.22354 Res. Agric., Livest. Fish.1(1): 37-46, Dec 2014

scholarly journals Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

2020 ◽  
pp. 46-58 ◽  
Author(s):  
Ahmed Medhat Mohamed Al-Naggar ◽  
Mohamed Abd El-Maboud Abd El-Shafi ◽  
Mohamed Helmy El-Shal ◽  
Ali Hassan Anany
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Triticum Aestivum L ◽  
Genetic Progress ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
High Polymorphism Information Content ◽  
Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

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 Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers

2020 ◽  
Vol 22 (1) ◽  
Author(s):  
Halimatus Sadiyah ◽  
Sumeru Ashari ◽  
Budi Waluyo ◽  
Andy Soegianto
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Small Groups ◽  
Evaluation Studies ◽  
Geographic Isolation ◽  
Breeding Programs ◽  
Significant Difference ◽  
Future Evaluation ◽  
Relationship Of ◽  
Husk Tomato

Abstract. Sadiyah H, Ashari S, Waluyo B, Soegianto A. 2021. Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers. Biodiversitas 22: 184-192. This study aimed to investigate the genetic diversity and relationship of Physalis spp. from East Java province, Indonesia. A total of the 33 Physalis accessions was analyzed employing 16 SSR markers. AMOVA, UPGMA clustering, and non-parametric ANOVA analyses were applied. The results showed Genetic diversity in this sample showed lower levels (He =0.171), as compared to other studies of Physalis that used different molecular markers. The dendrogram revealed the presence of five groups, the different species belong to different small groups. The two major groups consist of accessions originated from eastern Java and Madura Island, indicating that there is no significant difference between accessions from both areas although there is geographic isolation in the form of the strait. It is consistent with the low population differentiation and high genetic drift. The AMOVA revealed that 96% of the total variation came from the within-population (among accession), reflect that the accessions used in this study have high variation and valuable for plant improvement through breeding programs. It is recommended that future evaluation studies include more accession from minor accessions detected in the sample of this study to better represent the genetic diversity available in this crop.

scholarly journals Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers

2011 ◽  
Vol 62 (2) ◽  
pp. 177 ◽  
Author(s):  
Tadesse Sefera ◽  
Bekele Abebie ◽  
Pooran M. Gaur ◽  
Kebebew Assefa ◽  
Rajeev K. Varshney
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Dna Fingerprint ◽  
Pedigree Information ◽  
Sequence Repeat ◽  
Dissimilarity Matrix ◽  
Breeding Programs ◽  
Simple Sequence ◽  
Chickpea Cultivars

The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR diversity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic diversity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.

scholarly journals Reaction of lima bean genotypes to Macrophomina phaseolina

2019 ◽  
Vol 45 (1) ◽  
pp. 11-17
Author(s):  
Mynor Efraín Munguía García ◽  
Enayra Silva Sousa ◽  
Jayara Dayany da Costa Silva ◽  
Maruzanete Pereira de Melo ◽  
José Monteiro da Mota ◽  
...  
Keyword(s):  
Integrated Management ◽  
Lima Bean ◽  
Macrophomina Phaseolina ◽  
Phaseolus Lunatus ◽  
Breeding Programs ◽  
Charcoal Rot ◽  
Stability Of Resistance ◽  
Resistance Reaction ◽  
Resistance Stability ◽  
Promising Source

ABSTRACT Charcoal rot, caused by Macrophomina phaseolina, is an important disease of lima bean (Phaseolus lunatus L.) in the Northeast of Brazil. Considering that there are no reports of resistance to this disease in Brazil, 37 lima bean accessions were evaluated for their resistance reaction and resistance stability against isolates of M. phaseolina in two periods of the year (February-March and July-August 2016), with the aim of selecting genotypes with the potential for use in the management of this disease. Seeds were inoculated at sowing, using rice grains with husk that were colonized by the pathogen. The evaluations of genotypes were carried out at every five days, from the tenth day after sowing, using a score scale and dividing them into six reaction classes. From a population of 37 accessions of P. lunatus, no immunity reaction to M. phaseolina was seen; however, thirteen accessions presented the lowest severity levels and greatest stability in the two seasons: UFPI 892, UFPI 908 and UFPI 905, which were considered resistant to the isolate COUFPI 06. The resistance reaction of accessions considered resistant varied depending on the isolate of M. phaseolina. Accession UFPI 908 expressed the most promising results for resistance and stability of resistance against the isolates COUFPI 06, COUFPI 08 and COUFPI 10. Therefore, accession UFPI 908 constitutes a promising source of resistance to M. phaseolina, making possible its use in breeding programs and in integrated management of charcoal rot.

scholarly journals SSR Based Genetic Diversity in Magic Lines of Soybean (Glycine max (L.) Merrill)

2021 ◽  
pp. 8-16
Author(s):  
V. Swarnalatha ◽  
Bidush Ranjan Swar ◽  
M. Rajendar Reddy ◽  
S. Vanisree
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Level ◽  
Genetic Recombination ◽  
Abiotic Stress Tolerance ◽  
Similarity Coefficient ◽  
Biotic And Abiotic Stress ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Glycine Max L

Soybean MAGIC lines are recently developed by tailor made source of germplasm that have undergone heavy genetic recombination. The present study was carried out in Kharif 2018 to Rabi 2019 - 20 to assess its extent of genetic diversity at molecular level in 95 soybean MAGIC lines along with six checks by using 30 SSR markers from which 27 were found polymorphic. A total of 106 alleles were generated with an average of 3.53 and a range of two to six alleles per loci. The value of observed heterozygosity was varying from 0.00 to 0.099 indicating a higher frequency of homozygotes among the accessions. Maximum PIC was 0.955 for Staga001 followed by 0.948 (Satt168, Satt453, Satt534), 0.947(Satt565) and 0.945(Satt371). The range of Jaccard’s similarity coefficient was varying from 0.089 to 1, most of the values were between 0.2 to 0.3 with an average of 0.3 indicating considerable diversity exists among the genotypes. A total of six main clusters were formed by UPGMA clustering method. Cluster II was the largest comprising 48 genotypes which were grouped into four sub-clusters. Clustering based on SSR markers revealed a very precise grouping of the genotypes based on their relatedness than their phenotypic data alone. Hence it can be successfully deployed for selecting desirable genotypes which can be utilized in future breeding programs for exploiting heterosis or in the introgression of genes for biotic and abiotic stress tolerance in soybean crop.

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