Genetic diversity analysis in different genotypes of black gram [Vigna mungo (L.) Hepper] using RAPD marker

2016 ◽  
Author(s):  
Divya Vyas ◽  
Arunabh Joshi ◽  
Ganesh Rajamani ◽  
Devendra Jain ◽  
Gunnjeet Kaur
Keyword(s):  
Genetic Diversity ◽  
Rapd Marker ◽  
Crop Improvement ◽  
Molecular Classification ◽  
Similarity Coefficient ◽  
Black Gram ◽  
Randomly Amplified Polymorphic Dna ◽  
Marker Assisted Breeding ◽  
Average Percentage ◽  
Minimum Genetic Distance

Amongst the various DNA fingerprinting methodologies, randomly amplified polymorphic DNA (RAPD) was used to estimate genetic diversity and relationship amongst 22 black gram genotypes. A total of 25 randomly selected decamers were screened, out of which only 16 got amplified. A total of 133 amplified bands were obtained, out of which 120 were polymorphic. The average percentage of polymorphism was 90.23. The total number of amplified bands varied between 3 (primer OPK-03) and 15 (primer OPC-08) with an average of 9 bands per primer. The overall size of PCR amplified products ranged between 200 bp to 2600 bp. The average PIC was 0.30 ranging from 0.17 to 0.43. Five unique bands (ranging from 200-1200 bp) were detected in four genotypes using 5 RAPD primers. Jaccard's similarity coefficient values for RAPD primers ranged from 0.58-0.85 with an average of 0.71. Based on dendrogram generated through UPGMA method and PCA, most of the genotypes got divided into three main clusters. Genotypes U-17 and STY-2289 were lying close and thus showed minimum genetic distance while genotypes UH-177 and IPU99-233 had minimum similarity value of 0.42, thus showing maximum divergence. Thus, these results could be used to assess other black gram accessions in the Vigna germplasm pool that can provide useful information towards molecular classification and the genetic marker assisted breeding for crop improvement.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

A comparative performance of clustering procedures for mixture of qualitative and quantitative data – an application to black gram

2011 ◽  
Vol 9 (4) ◽  
pp. 523-527 ◽  
Author(s):  
Rupam Kumar Sarkar ◽  
A. R. Rao ◽  
S. D. Wahi ◽  
K. V. Bhat
Keyword(s):  
Genetic Diversity ◽  
Quantitative Trait ◽  
Quantitative Data ◽  
Quantitative Traits ◽  
Qualitative Data ◽  
Crop Improvement ◽  
Weighted Average ◽  
Black Gram ◽  
Comparative Performance ◽  
Qualitative And Quantitative

Knowledge of the genetic diversity of germplasm of breeding material is invaluable in crop improvement programmes. Frequently, qualitative and quantitative data are used separately to assess genetic diversity of crop genotypes. While assessing diversity based on qualitative and quantitative traits separately, there may occur a problem when the degree of correspondence between the clusters formed does not agree with each other. This study compares five different procedures of clustering based on the criterion of weighted average of observed proportion of misclassification in black gram genotypes using qualitative, quantitative traits and mixture data. The INDOMIX- and PRINQUAL-based clustering procedures, i.e. INDOMIX and PRINQUAL methods in conjunction with the k-means clustering procedure, show better performance compared with other clustering procedures, followed by clustering based on either quantitative or qualitative data alone. The use of the INDOMIX- and PRINQUAL-based procedures can help breeders in capturing the variation present in both qualitative and quantitative trait data simultaneously and solving the problem of ambiguity over the degree of correspondence between clustering based on either qualitative or quantitative traits alone.

scholarly journals Genetic Diversity of a Capsicum Germplasm Collection from Nepal as Determined by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (3) ◽  
pp. 318-324 ◽  
Author(s):  
J. Baral ◽  
P.W. Bosland
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Similarity Index ◽  
Germplasm Collection ◽  
Western Hemisphere ◽  
Randomly Amplified Polymorphic Dna ◽  
Index Value ◽  
Single Cluster

Domesticated chile (Capsicum annuum L. var. annuum) is a widely cultivated spice and vegetable crop. It originated in the Western Hemisphere, but spread rapidly throughout the globe after the voyage of Columbus. However, very little is known about the genetic diversity of chile in Asia and especially in Nepal. Thus, research was conducted to document morphological as well as molecular characterization of C. annuum var. annuum landraces collected from Nepal. Genetic diversity in C. annuum var. annuum landraces from Nepal was investigated using randomly amplified polymorphic DNA (RAPD) markers and compared with that of C. annuum var. annuum landraces from the center of diversity, Mexico. RAPD marker based cluster analysis of C. annuum var. annuum clearly separated each accession. All accessions of C. annuum var. annuum from Nepal grouped into a single cluster at a similarity index value of 0.80, whereas, accessions from Mexico grouped into eight different clusters at the same similarity level indicating greater genetic diversity in Mexican accessions. RAPD analysis indicated that the Nepalese chile population went through an additional evolutionary bottleneck or founder effect probably due to intercontinental migrations. Some Nepalese accessions had unique RAPD markers suggesting that additional sources of genetic variation are available in Nepalese germplasm.

Assessment of molecular diversity of greengram [Vigna radiata (L.) Wilzek] through RAPD

2016 ◽  
Author(s):  
Gunnjeet Kaur ◽  
Arunabh Joshi ◽  
Devendra Jain ◽  
Ganesh Rajamani ◽  
Divya Vyas
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Polymorphism Information Content ◽  
Vigna Radiata ◽  
Molecular Diversity ◽  
Rapd Analysis ◽  
Similarity Coefficient ◽  
Green Gram ◽  
Randomly Amplified Polymorphic Dna ◽  
Legume Crop

A total twenty three genotypes of green gram (Vigna radiata) were subjected to Randomly amplified polymorphic DNA (RAPD) analysis for molecular characterization. A total of 25 randomly selected decamers were screened, out of which only 15 generated 126 amplification products from which 117 bands were found polymorphic, the average polymorphism being 93.48%. The total number of amplified bands varied between 2 (primer OPP-09) to 17 (primer OPA-1) with an average of 9.5 bands per primer. The overall size of PCR amplified products ranged between 200 bp to 2900 bp. The average Polymorphism Information Content(PIC) was 0.32 ranging from 0.17 to 0.46. Primer OPA-01 and OPP-06 detected two unique bands ranged between 250 bp to 2500 bp in two genotypes (PUSA-672 and HUM-12). Jaccard's similarity coefficient values ranged from 0.28-0.90 with an average of 0.59. Based on dendrogram generated through UPGMA method and PCA, most of the genotypes got divided into four main clusters. Genotype EC-398885 lay far apart and thus showed maximum genetic distance. The assessment of genetic diversity is a prerequisite and important step for the improvement of any legume crop. Thus, present results of the present study could be further extrapolated to other green gram accessions in Vigna germplasm.

STUDI PERAKITAN KELAPA HIBRIDA GSK x DMT BERDASARKAN PENANDA RAPD (RANDOMLY AMPLIFIED POLYMORPHIC DNA)

EUGENIA ◽  
2008 ◽  
Vol 14 (1) ◽  
Author(s):  
Semuel D. Runtunuwu ◽  
Hengky Novarianto ◽  
Heldering Tampake ◽  
Edy F. Lengkong
Keyword(s):  
Dna Marker ◽  
Rapd Marker ◽  
High Yield ◽  
Randomly Amplified Polymorphic Dna ◽  
Germination Time ◽  
Flower Production ◽  
Short Time

ABSTRACT   Runtunuwu, S.D. et al. 2008. Assembling Hybrid Coconut of GSK x DMT Based on RAPD (RANDOMLY AMPLIFIED POLYMORPHIC DNA) Marker. Eugenia 14 (1) : 134-152.   The aimed of this research was : 1. assembling hybrid coconut GSK x DMT (Genjah Salak x Dalam Mapanget) that seeds growth was relatifly homogeneous based on RAPD (Randomly Amplified Polymorphic DNA) marker and 2. to found the assembling method of hybrid coconut that will produce massive seeds relatifely short time will homogeneous plant. It was 65 individu trees observe for the average of famale flower per bunch. The result was 25 individu of coconut GSK has the average flower production > 40 per bunch was analyze the homogeneous genetic with the RAPD marker. Based on the analyze RAPD that were 25 individu of GSK coconut trees have the same genetic average 88 % and 14 individu among that was 100 % have same genetic. Further more that 14 individu of GSK was crossing with the 3 individu of DMT that have high yield per year its was DMT 1188, 1172 and 781. Based on the evaluation for the color of buds, high of buds, the steam circle, the petiole color and the germination time of hybrid coconut seeds from the crossing of GSK x DMT 1188 produce more than    70 % seeds that have same genetic, also for crossing of GSK x DMT 1172 have 9 combination and have more than 70 % that same genetic, 10 combination from crossing GSK x DMT 781 have more than 80 % same seeds growth. Therefore, using the RAPD marker were successfully produced 28 crossing of the hybrid coconut GSK x DMT that have relatifly homogeneous seeds growth.   Keywords : assembling, hybrid coconut GSK x DMT, RAPD.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 118
Author(s):  
Ljiljana Brbaklić ◽  
Dragana Trkulja ◽  
Sanja Mikić ◽  
Milan Mirosavljević ◽  
Vojislava Momčilović ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Hordeum Vulgare ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Breeding Period ◽  
Phenotypic Variance ◽  
Hordeum Vulgare L ◽  
Phenotypic Data ◽  
Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

Randomly amplified polymorphic DNA linkage relationships in different Norway spruce populations

2001 ◽  
Vol 31 (8) ◽  
pp. 1456-1461
Author(s):  
M Troggio ◽  
T L Kubisiak ◽  
G Bucci ◽  
P Menozzi
Keyword(s):  
Rapd Markers ◽  
Rapd Marker ◽  
Population Based ◽  
Italian Population ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Consensus Map ◽  
Norwegian Population ◽  
Marker Loci ◽  
Linkage Relationships

We tested the constancy of linkage relationships of randomly amplified polymorphic DNA (RAPD) marker loci used to construct a population-based consensus map in material from an Italian stand of Picea abies (L.) Karst. in 29 individuals from three Norwegian populations. Thirteen marker loci linked in the Italian stand did show a consistent locus ordering in the Norwegian population. The remaining 16 unlinked marker loci were spread over different linkage groups and (or) too far apart both in the population map and in this study. The limited validity of RAPD markers as genomic "hallmarks" resilient across populations is discussed. We also investigated the reliability of RAPD markers; only 58% of the RAPD markers previously used to construct the consensus map in the Italian population were repeatable in the same material. Of the repeatable ones 76.3% were amplified and found polymorphic in 29 megagametophyte sibships from three Norwegian populations.

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