Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker

Seyedimoradi, Hiva; Talebi, Reza

doi:10.1007/s12298-014-0253-3

Cited by 22 publications

(11 citation statements)

References 31 publications

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“…A total of 10 SCoT [47] and 10 [59] DAMD primers were used in this study. Polymerase chain reaction amplification was performed in volume of 25 μL consisting of 2.0 μL 100 ng DNA, 2.5 μL of 10 x Buffer (Bioline), 1.5 μL of 50 mM MgCl 2 (Bioline), 2.0 μL of 2.5 mM dNTPs (Bioline), and 0.2 μL 500 U Taq DNA polymerase (Bioline), 1.0 μL of 10 μM each of the SCoT and DAMD primers (Additional file 2: Table S2) and 15.80 μL of 500 ml diethylpyrocarbonate (DEPC)-treated water (Invitrogen Corporation, USA).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

et al. 2019

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Background Identification of high resolving DNA-based markers is of paramount importance to unlock the potential of genetic diversity and selection of unique accessions of Capsicum annuum L., within Cross River and Ebonyi States of Nigeria, for breeding and conservation. Therefore, we comparatively explored the effectiveness of start codon targeted (SCoT) and directed amplified minisatellite DNA (DAMD) markers for diversity analysis of the accessions. Fifteen accessions were collected for DNA extraction and amplifications with the markers. Results Dendrograms from SCoT and DAMD categorized the accessions into five and three genetic groups, respectively, while the principal component analysis identified five genetic clusters, each from the markers. The average values of allele, gene diversity and polymorphic information content detected with SCoT and DAMD demonstrate that the two markers were effective and efficient, especially, SCoT in genetic diversity study of the accessions of pepper. Number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) from SCoT (NPL = 64, PPL = 80.00–95.73%) and DAMD (NPL = 56, PPL = 53.33–86.67%) were high, but higher in SCoT markers. Other effective genetic parameters (effective number of alleles, Nei’s genetic diversity and Shannon’s information indices) identified with the two marker systems elucidated the allelic richness, rich genetic diversity within the populations and informative nature of the markers, especially SCoT. The intraspecific genetic diversity, interspecific genetic diversity, and coefficient of differentiation obtained with SCoT and DAMD further exposed the genetic structure with more genetic divergence within than among the populations of the accessions. Estimate of gene flow from the SCoT markers was 3.8375 and 0.6.2042 for the DAMD markers. The estimate of gene flow values from the markers indicated extensiveness with SCoT (Nm = 3.8375) and extremely extensive with DAMD (Nm = 6.2042) among the populations. Conclusion This study shows that SCoT markers may be more useful and informative than DAMD in measuring genetic diversity and differentiation of the accessions of the genus Capsicum. Genetic parameters obtained with SCoT showed that the accessions from Cross River were more genetically diverse than the ones from Ebonyi State. Therefore, SCoT may be a preferred marker in evaluating genetic diversity for improvement and conservation of this spicy crop, C. capsicum.

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Section: Methodsmentioning

confidence: 99%

Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

et al. 2019

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“…Inter simple sequence repeats (ISSR) tool has been widely used in phylogenetic and genetic variation analysis of plant species [12,13,14,15,16,17]. Inter simple sequence repeats markers were used for analysis of genetic structure and population differentiation in Plantago brutia [18].…”

Section: Introductionmentioning

confidence: 99%

Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection ofPlantgaospecies

Bagheri

Heidari

Shahriari

et al. 2020

Preprint

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AbstractAnalysis of genetic diversity in medicinal plants assists germplasm conservation and selection for use in breeding schemes. The aims of the present study were to assess genetic diversity and differentiation of several Plantago species using Inter Simple Sequence Repeats (ISSR) markers and identify marker-trait associations (MTAs). Thirty-one Plantago accessions belonging to eight species with various mating system and chromosome number were collected from geographical regions of Iran environments. Polymorphism in the DNA of Plantago accessions were analyzed using polymerase chain reaction (PCR) of 25 ISSR primers. The data for number of polymorphic bands were analyzed on the basis of several genetic diversity parameters. The results of gel analysis indicated that the ISSR primers amplified 5 to 21 polymorphic bands with 100 to 3000 bp size. The mean polymorphism was 83.83% and five primers showed 100% polymorphism among Plantago accessions. The Polymorphism Information Content (PIC) for ISSR as a dominant marker ranged from 0.1103 to 0.3829 with the mean 0.2727 in the species tested. Accessions in P. amplexicaulis and P. pysillum species represented the highest Nei’s and Shannon’s genetic diversity whilst the lowest obtained for P. lagopus. Analysis of phylogenetic network generated by the Neighbor-Net Algorithm showed moderate split of the eight species tested and the network depicted moderate conflict. The principal coordinate analysis (PCoA) results showed lower conflict in separation of accessions of the eight species. Fifty-six significant MTAs were detected for the traits tested in Plantago accessions, of which six were shared between three seed and mucilage traits and 24 were common between two traits. The coefficient of determination (R2) for the identified MTAs varied between 32 and 73%. In conclusion, the results of genetic diversity analysis suggested that ISSR marker could efficiently differentiate Plantago species and the information of genetic diversity might assist Plantago improvement and conservation.

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“…Until today, many studies have been conducted on genetic diversity of lentil varieties, species and landraces utilizing several approaches, including physiological and morphological markers (Erskine and Choudhary, 1986;Erskine et al, 1989), isozymes (Erskine and Muehlbauer, 1991), storage proteins of seed (Sultana et al, 2006) and DNA based molecular markers such as restriction fragment length polymorphism (RFLP) (Havey and Muehlbauer, 1989), random amplified polymorphic DNA (RAPD) (Abo-Elwafa et al, 1995;Ahmad et al, 1996;Ford et al, 1997;Ferguson et al, 1998;Sonnante and Pignone, 2001;Yuzbasioglu et al, 2006), amplified fragment length polymorphism (AFLP) (Sharma et al, 1996;Toklu et al, 2009;Alghamdi et al, 2014), intersimple sequence repeat (ISSR) (Fikiru et al, 2007;Scippa et al, 2008;Toklu et al, 2009;El-Nahas et al, 2011;Seyedimoradi and Talebi, 2014), simple sequence repeat (SSR) (Jin et al, 2008;Babayeva et al, 2009;Kaur et al, 2011;Zaccardelli et al, 2012;Kushwaha et al, 2013;Dikshit et al, 2015;Idrissi et al, 2015;Idrissi et al, 2018;Tsanakas et al, 2018) and single nucleotide polymorphism (SNP) (Lombardi et al, 2014;Basheer-Salimia et al, 2015;Khazaei et al, 2016). On the other hand, Turkish lentil landraces which take a significant role in breeding offer rich genetic sources and farmers in Turkey still cultivated on a small scale landrace preferred for their ability of adaptation to regional environmental conditions (Toklu et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

GENETIC DIVERSITY IN LENTIL LANDRACES REVEALED BY DIVERSITY ARRAY TECHNOLOGY (DArT)

Ateş¹

2019

Turkish Journal of Field Crops

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Lentil is annual, autogamous and diploid (2n = 2x= 14) food legume with ~4 Gbp genome in size. Turkey is well known for its species richness with "diversity hot spots" for different legumes including lentil. In previous studies, various DNA markers were utilized but genetic diversity of lentil landraces have not yet been clarified. For this reason, present study aimed to identify genetic diversity of 94 Turkish lentil landraces utilizing 16,383 SNPs based on DArT technology. Results from "fastSTRUCTURE" analysis indicated that the unweighted pair group analysis with the arithmetic mean (UPGMA) dendrogram including a heat map and also principal component analysis (PCoA) showed that Turkish lentil landraces were classified into five main groups in current study, indicating the existence of a large genetic variation among landraces. Highest genetic variation was between geno34 and geno76 (0.9126) while the lowest genetic variation was between geno7 and geno1 (0.0104) and the average genetic variation among 94 lentil landraces was 0.63. The data obtained from current study can be utilized to increase genetic diversity of cultivated species and establish suitable conservation and breeding strategies of lentil.

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Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker

Cited by 22 publications

References 31 publications

Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection ofPlantgaospecies

GENETIC DIVERSITY IN LENTIL LANDRACES REVEALED BY DIVERSITY ARRAY TECHNOLOGY (DArT)

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