scholarly journals Use of Molecular Markers to Assist the Development of Inbred Lines under Open Field Conditions: the Case of Criollo Peppers (Capsicum annuum L.) from Mexico

2017 ◽  
Vol 45 (2) ◽  
pp. 365-368
Author(s):  
Leandro PEREIRA-DIAS ◽  
Gustavo CHÁVEZ-GONZÁLEZ ◽  
Miguel BRACHO-GIL ◽  
Ana M. FITA ◽  
Santiago VILANOVA ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Molecular Markers ◽  
Capsicum Annuum ◽  
Open Field ◽  
Ssr Markers ◽  
Inbred Lines ◽  
Open Pollination ◽  
Adaptation To Climate Change ◽  
Chile Peppers

Chile peppers are one of the most important crops in Mexico and a plethora of ecotypes can be found there. Most of them are ancient open-pollinated (OP) landraces selected by farmers for uniform phenotype but with an inherent level of genetic diversity, called criollos. In this work 15 pepper accessions, encompassing 2 criollo lines, their open-pollinated progenies, and 5 controls, were characterized with a set of 36 IPGRI descriptors and 23 SSR markers to assess the effect of open pollination in the inbreeding process. Heterozygosity levels were comprised between 12 and 47% in the progenies, which were similar or lower than those values from parent plants and similar or higher than control cultivars. Also, both progenies and parents showed similar levels of agronomic and morphological uniformity. Our results suggest that this OP program is efficient in terms of reaching enough agronomic uniformity in criollo Ancho peppers while preserving certain genetic diversity to confer adaptation to climate change.

scholarly journals Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers

2008 ◽  
Vol 51 (1) ◽  
pp. 183-192 ◽  
Author(s):  
Silvia Graciele Hülse de Souza ◽  
Valéria Carpentieri-Pípolo ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Paulo Maurício Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Zea Mays L ◽  
Inbred Lines ◽  
Pedigree Data ◽  
Dice Coefficient ◽  
Quantitative Characters ◽  
Maize Inbred Lines ◽  
Ssr Primers ◽  
Selection Of

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.

scholarly journals Applications of molecular markers in Genetic Diversity Studies of maize

2020 ◽  
Vol 37 (1) ◽  
pp. 101-108
Author(s):  
Degife Asefa Zebire
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Diversity Analysis ◽  
Crop Species ◽  
Heterotic Groups ◽  
Genetic Diversity Analysis ◽  
Diversity Studies ◽  
Genetic Diversity Study

Molecular markers are efficient for exploiting variations in genotypes as they are not influenced by environmental factors and also speed up breeding programs. They are used to detect large numbers of distinct divergence between genotypes at the DNA level. Genetic diversity study helps to estimate the relationship between inbred lines to make the best hybrid combinations. Lines which are clustered in different heterotic groups are considered as the best hybrid combinations to carry out further breeding activities. Molecular markers are used to meet a number of objectives, including genetic diversity analysis and prediction of hybrid performances in divergent crop species. Agro-morphological and molecular markers have been utilized to study genetic diversity so far. In maize, the uses of molecular markers are important for the evaluation of genetic diversity of inbred lines and in clustering them into heterotic groups. These markers determine genetic similarity of the lines and are used to assess the genetic diversity of maize. Molecular markers have proven valuable for genetic diversity analysis of many crop species and genetically diverse lines are important to improve hybrid breeding. Keyword: Molecular marker; Genetic diversity; Genetic variation, Diversity Array technology; cluster analysis

Genetic Diversity among CIMMYT Maize Inbred Lines Investigated with SSR Markers

Crop Science ◽  
2004 ◽  
Vol 44 (6) ◽  
pp. 2230-2237 ◽  
Author(s):  
X. C. Xia ◽  
J. C. Reif ◽  
D. A. Hoisington ◽  
A. E. Melchinger ◽  
M. Frisch ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Inbred Lines ◽  
Maize Inbred Lines

Analysis of genetic diversity and relationships among waxy maize inbred lines in Korea using SSR markers

2010 ◽  
Vol 32 (4) ◽  
pp. 375-384 ◽  
Author(s):  
Kyu Jin Sa ◽  
Jong Yeol Park ◽  
Ki Jin Park ◽  
Ju Kyong Lee
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Inbred Lines ◽  
Waxy Maize ◽  
Maize Inbred Lines

scholarly journals Genetic diversity may help evolutionary rescue in a clonal endemic plant species of Western Himalaya

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Irshad Ahmad Sofi ◽  
Irfan Rashid ◽  
Javaid Yousuf Lone ◽  
Sandhya Tyagi ◽  
Zafar A. Reshi ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Population Structure ◽  
Plant Species ◽  
Ssr Markers ◽  
Sequence Data ◽  
Endemic Plant ◽  
Single Marker Analysis ◽  
Endemic Plant Species ◽  
Trait Associations

AbstractHabitat loss due to climate change may cause the extinction of the clonal species with a limited distribution range. Thus, determining the genetic diversity required for adaptability by these species in sensitive ecosystems can help infer the chances of their survival and spread in changing climate. We studied the genetic diversity and population structure of Sambucus wightiana—a clonal endemic plant species of the Himalayan region for understanding its possible survival chances in anticipated climate change. Eight polymorphic microsatellite markers were used to study the allelic/genetic diversity and population structure. In addition, ITS1–ITS4 Sanger sequencing was used for phylogeny and SNP detection. A total number of 73 alleles were scored for 37 genotypes at 17 loci for 8 SSRs markers. The population structural analysis using the SSR marker data led to identifying two sub-populations in our collection of 37 S. wightiana genotypes, with 11 genotypes having mixed ancestry. The ITS sequence data show a specific allele in higher frequency in a particular sub-population, indicating variation in different S. wightiana accessions at the sequence level. The genotypic data of SSR markers and trait data of 11 traits of S. wightiana, when analyzed together, revealed five significant Marker-Trait Associations (MTAs) through Single Marker Analysis (SMA) or regression analysis. Most of the SSR markers were found to be associated with more than one trait, indicating the usefulness of these markers for working out marker-trait associations. Moderate to high genetic diversity observed in the present study may provide insurance against climate change to S. wightiana and help its further spread.

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

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

2018 ◽  
Vol 17 (03) ◽  
pp. 280-284 ◽  
Author(s):  
Katina F. Olodo ◽  
Mame C. Gueye ◽  
Caroline Calatayud ◽  
Baye M. Diop ◽  
Ndjido A. Kane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
West Africa ◽  
Ssr Markers ◽  
Related Species ◽  
Evolutionary History ◽  
Genetic Difference ◽  
Transcriptome Sequences ◽  
Ssr Development ◽  
Digitaria Exilis

AbstractDigitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

scholarly journals Assessment of genetic diversity and wilt disease resistance in hot pepper (Capsicum annuum) germplasm from Ethiopia

2021 ◽  
Vol 63 (1) ◽  
pp. 31-40
Author(s):  
Dawit Bedane Woubit ◽  
Shiferaw Eleni ◽  
Sileshi Fitsum ◽  
Assefa Mekonnen ◽  
Aklilu Shimeles
Keyword(s):  
Genetic Diversity ◽  
Disease Resistance ◽  
Capsicum Annuum ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Disease Incidence ◽  
In Situ Conservation ◽  
Wilt Disease ◽  
Hot Pepper ◽  
Diversity Assessment

Abstract Hot pepper (Capsicum annuum L.) is an economically important crop in Ethiopia. Wide variability in hot pepper germplasm in Ethiopia is expected due to the presence of diverse environmental conditions and variation in farming systems. The present study was carried out to evaluate the resistance of 75 hot pepper accessions to wilt disease and assess their genetic diversity using SSR markers. Out of 75 accessions tested, the present study identified 23 accessions that showed resistance (R) with the value of 1-10% disease incidence. The genetic diversity assessment using 13 polymorphic SSR markers allowed the detection of 111 clear and scorable bands. The number of alleles per locus ranged from 5 to 13, with an average of 8.54. The PIC value ranged from 0.27 to 0.87 with an average of 0.59. The gene diversity indices were highly variable across SSR loci and ranged from 0.29 to 0.88 with mean genetic diversity of 0.62. Observed heterozygosity was also highly variable between loci (0.01-0.45) indicating that the accessions were not fixed to homozygosity. Furthermore, genetic diversity parameters were estimated among populations by grouping accessions based on their origin. Within populations, the PIC value ranged from 0.31 to 0.77. The genetic distances among the eight populations ranged from 0.15 to 0.48. The observed highest genetic diversity (0.80) in the Amhara region (Gojam) may indicate this area as the primary site for designing in situ conservation for this crop in Ethiopia. The research findings provide baseline information on disease resistance germplasm sources to be used for the breeding program, as well as the status of genetic diversity of the accessions for efficient conservation and proper utilization of the existing genetic resources in the country.

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