Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Elit Domuz Ayrığı (Dactylis glomerata L.) Genotiplerinde Genetik Çeşitliliğin SSR Markörleri ile Belirlenmesi

2019 ◽  
Vol 7 (1) ◽  
pp. 127
Author(s):  
Gonul Cömertpay ◽  
Hüseyin Özpınar
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Agricultural Research ◽  
Dactylis Glomerata ◽  
Distance Matrix ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Group A ◽  
Dactylis Glomerata L

Orchardgrass (Dactylis glomerata L.) is an economically important, and widely cultivated perennial forage grass. The aim of this study was to determine the genetic diversity and genetic relationship among the orchardgrass breeding lines developed in Aegean Agricultural Research Institute, using simple sequence repeat (SSR, microsatellite) molecular markers. The genetic diversity of 32 orchardgrass was assessed using a set of 24 SSR markers. SSR primer pair combinations yielded 126 alleles for all genotypes. The number of alleles per locus ranged from three to seven with an average of 5.25 alleles across 24 loci. The alleles size ranged from 101 to 354 and the polymorphism rate was 100%. Jaccard genetic distance coefficient varied from 0.21 to 0.84 among genotypes. The degree of genetic diversity among the genotypes was high. Total number of rare alleles was 28 alleles across 126 loci. Dendrogram constructed using neighbor-joining analysis based on Jaccard genetic distance matrix were clustered into three main groups A, B and C. Group A was the largest group contained 15 genotypes, while B had 13 genotypes originated mainly from same region. The group C was the smallest group contained genotypes originated from northern part of Turkey. The molecular analysis revealed that a significant genetic variation existed in this orhardgrass collection, and the genotypes studied have potential for ensure rich genetic resources in orchardgrass breeding program. In addition to this, it was concluded that SSR markers are suitable markers for the molecular identification of different orchardgrass genotypes.

scholarly journals Genetic Relationships between Elite Oil Palms from Nigeria and Selected Breeding and Germplasm Materials from Malaysia via Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (2) ◽  
pp. 159 ◽  
Author(s):  
M. N. Okoye ◽  
C. Bakoumé ◽  
M. I. Uguru ◽  
R. Singh ◽  
C. O. Okwuagwu
Keyword(s):  
Ssr Markers ◽  
Oil Palm ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Coefficient Matrix ◽  
High Genetic Diversity ◽  
Breeding Lines ◽  
Natural Oil ◽  
Materials Used

<p>Nine SSR markers were used to study the genetic relationships among 26 elite oil palm materials from Nigeria and Malaysia. The Nigerian elite materials comprised 15 Nigerian Institute for Oil Palm Research (NIFOR) oil palm parental genotypes. The 11 Malaysian genotypes included 2 <em>dura</em> and 2 <em>pisifera</em> advanced breeding lines, 3 palms from natural populations of Nigeria, and 2 from each of the Angola, and Madagascar natural oil palm collections maintained at the Malaysian Palm Oil Board (MPOB). The results revealed a high percentage of polymorphic loci (83.3%) in the entire materials with average polymorphic information content (PIC) of 0.7325. Two SSR markers showed relatively high PIC namely sMg00016 and sMg00179 (0.8018 and 0.8509, respectively). The mean number of alleles varied from 1.333 in Madagascar germplasm material to 4.889 in NIFOR <em>tenera </em>materials (mean = 2.958). The observed heterozygosity varied from 0.167 in Madagascar material to 0.778 in Nigeria germplasm materials (mean = 0.575) and the expected heterozygosity from 0.153 to 0.643. The various oil palm provenances showed significant genetic differentiation (F<sub>ST</sub> = 0.177, P = 0.001) indicating the existence of a genetic structure among the materials used. UPGMA analysis based on Rogers’ dissimilarity coefficient matrix displayed two main clusters, one separating Madagascar accessions from the rest. PCoA showed that the NIFOR breeding parents clustered closely with MPOB’s Nigeria and Angola-derived materials suggesting a common origin of mainland genotypes. The high genetic diversity observed among the MPOB’s germplasm materials highlights the need for proper characterization of entire NIFOR oil palm germplasm with SSR markers to facilitate effective utilization in the breeding programme.</p>

scholarly journals Molecular characterization of papaya genotypes using AFLP markers

2011 ◽  
Vol 33 (3) ◽  
pp. 849-858 ◽  
Author(s):  
Eder Jorge de Oliveira ◽  
Juliana Leles Costa ◽  
Lucas Ferraz dos Santos ◽  
Fabiana Moraes de Carvalho ◽  
Aline dos Santos Silva ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Carica Papaya ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Inbred Lines ◽  
Genetic Distance Matrix ◽  
Pair Method ◽  
Polymorphic Bands

Due to the low genetic variability reported in the commercial plantations of papaya (Carica papaya L.), the objective of this study was analyze the genetic diversity of 32 genotypes including cultivars, landraces, inbred lines, and improved germplasm using the AFLP technique (Amplified Fragment Length Polymorphism). The genetic distance matrix was obtained using the Nei and Li genetic distance and clustering was performed using the unweighted pair-method with arithmetic mean (UPGMA). Using 11 combinations of EcoRI/MseI primers, 383 polymorphic bands were obtained. On average, 34.8 polymorphic bands were obtained per primer combination. Five clusters were formed. The traditional cultivar 'Sunrise' and the inbred line CMF-L30-08 were the closest genotypes, and the improved germplasm (CMF041) and landrace (CMF233) the most distant. The main papaya cultivars commercially grown in Brazil, as well as four inbred lines and three improved germplasm, were clustered together, however, were not grouped in the same branch. The genetic distance between the Sunrise and Golden cultivars was 0.329, and even arising from mutation and selection within the Sunrise variety, the Golden stores considerable genetic variability. Additional variability was observed in the inbred lines derived from papaya breeding program at Embrapa Cassava and Fruits.

Genetic and morphological evidence for a new cryptic species of Ectinogonia (Coleoptera: Buprestidae) from central Chile

Zootaxa ◽  
2017 ◽  
Vol 4303 (2) ◽  
pp. 284 ◽  
Author(s):  
SIMÓN ANGUITA-SALINAS ◽  
RODRIGO M. BARAHONA-SEGOVIA ◽  
ELIE POULIN ◽  
ALVARO ZÚÑIGA-REINOSO
Keyword(s):  
New Species ◽  
Genetic Distance ◽  
Cryptic Species ◽  
Distance Matrix ◽  
Morphological Evidence ◽  
Mountain Range ◽  
Central Chile ◽  
The Andes ◽  
Genetic Distance Matrix ◽  
Coi Sequences

The genus Ectinogonia Spinola, 1837 is a genus mainly found in Chile; it currently contains 17 species. Recent exploration in the Andes Mountain Range of the Bio Bio Region in Chile have resulted in the collection of specimens slightly different morphologically from all previously described species. The aim of this paper is to describe this new species of Ectinogonia using morphological and genetic evidence. To establish differences between species we described the external morphology and compared it to species that are morphologically similar (i.e. E. buqueti Spinola 1837 and E. intermedia Kerremans 1903). We also measured the genetic differences in COI sequences, constructing a distance matrix in which we compared it to species that are morphologically similar (E. buqueti and E. intermedia) and other species found in the same region (E. speciosa oscuripennis Moore 1994). We found that E. cryptica sp. n. differs from E. buqueti (which previously contained E. cryptica sp. n.) in pronotum and elytral patterns. The genetic distance matrix shows that E. cryptica sp. n. differs by 4.6% from all other Ectinogonia species compared, supporting the morphological evidence. 

scholarly journals Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 137-146 ◽  
Author(s):  
Martin Vivodík ◽  
Zelmíra Balázová ◽  
Zdenka Gálová ◽  
Lenka Petrovicová
Keyword(s):  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Start Codon ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Genetic Distance Matrix ◽  
Functional Genetic Variation ◽  
Amplicon Size

In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

scholarly journals Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

scholarly journals Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

2022 ◽  
Author(s):  
Huiling Wang ◽  
Kuan Yang ◽  
Liwei Guo ◽  
Lifen Luo ◽  
Chi He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Yunnan Province ◽  
Polymorphic Information Content ◽  
Polyacrylamide Gel Electrophoresis ◽  
Panax Notoginseng ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

scholarly journals Genetic diversity analysis of soybean (Glycine max (L.) Merr.) genotypes making use of SSR markers

2019 ◽  
pp. 1113-1119
Author(s):  
Keitumetse Kujane ◽  
Moosa M Sedibe ◽  
Alina Mofokeng
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Dna Ladder ◽  
Ssr Primers ◽  
Soybean Genotypes ◽  
Glycine Max L ◽  
Simple Sequence ◽  
Selection Of

In this study, we aimed to investigate the genetic diversity and polymorphism among 30 soybean genotypes maintained by the ARC using simple sequence repeat (SSR) markers. Soybean genotypes were characterized using 20 SSR primers. DNA was extracted using the standard cetyl trimethylammonium bromide method and amplified using PCR. Allele size was determined via comparison with a 100 base pair (bp) DNA ladder. Molecular data were analyzed, and a dendrogram and matrix were generated using GGT 2.0 software. A total of 216 alleles with an average of 10.8 alleles per locus were detected. The allele sizes ranged between 2 and 33 bp with an average of 18.7 bp. The polymorphic information content among genotypes varied from 0.85 (Satt001) to 0.75 (Satt43) with an average of 0.716, and heterozygosity ranged from 0.87 to 0.78 with an average of 0.7485. The most diverse genotypes were B 66 S 31, 69S 7, and R5-4-2 M, which indicated the efficiency of the SSR markers for the detection of genetic diversity. The results of the current study revealed the diversity among the soybean genotypes tested, which might aid breeders in the future in the selection of parents for breeding.

scholarly journals Molecular characterization of elephantgrass accessions through RAPD markers

2005 ◽  
Vol 29 (3) ◽  
pp. 568-574 ◽  
Author(s):  
Leônidas Paixão Passos ◽  
Marco Antonio Machado ◽  
Maria Coletta Vidigal ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Binary Data ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Distance Matrix ◽  
Genetic Distances ◽  
Average Genetic Distance ◽  
Genetic Distance Matrix

Elephantgrass pastures are limited by yield variations and reductions in forage quality and availability, thus making the search for genotypes with reduced seasonality a major concern. In order to verify the extent of genetic variability among contrasting cultivars, ten elephantgrass accessions were analyzed through DNA amplification by RAPD technique. A total of 160 DNA bands were generated with the use of 44 random primers and 23% of these bands were monomorphic for all accessions. Gel-obtained binary data (1 for presence and 0 for absence) were used for generating a genetic distance matrix, which was utilized in a UPGMA grouping analysis. Elephantgrass cultivars Cameroon and Vruckwona were the accessions mostly divergent from the others, with an average genetic distance of 0.34. The accessions with the lowest average genetic distances from the others were Pioneiro and CNPGL 27-5, both with a distance of 0.25. Overall, genetic distances ranged from 0.06 to 0.43, indicating little genetic variability for the set of accessions, despite the contrasting morphology of the studied genotypes.

scholarly journals Establishment of Molecular Identity Cards for Cucumis melo Cultivars Using SSR Markers

HortScience ◽  
2018 ◽  
Vol 53 (2) ◽  
pp. 138-143 ◽  
Author(s):  
Li Li ◽  
Xiulan Xu ◽  
Ping Wu ◽  
Guo Zhang ◽  
Xiaobing Zhang
Keyword(s):  
Cucumis Melo ◽  
Ssr Marker ◽  
Polymorphic Information Content ◽  
Republic Of China ◽  
Molecular Identity ◽  
Ssr Primers ◽  
Unique Identity ◽  
Identity Card ◽  
Identity Cards ◽  
Simple Sequence

Twenty-four representative melon varieties and six parental cultivars were examined in this study. Among 159 pairs of simple sequence repeat (SSR) primers, 18 SSR core primers with rich polymorphic information, a large number of genotypes, and the ability to distinguish different melon varieties were selected. A total of 113 genotypes were detected among the 30 experimental materials, with an average of 6.28 genotypes for each pair of primers. The polymorphic information content was on average 0.6807, ranging from 0.5618 to 0.7885. Specific bands of the primers for the 30 experimental materials were analyzed, and by combining different primer loci, all 30 varieties were identified. Unique barcodes for molecular identity cards for the 30 experimental materials were established using the fingerprints formed with this SSR marker system. Each variety has a unique identity card that can be applied for the registration of the newly bred varieties, the protection of breeders’ rights, and the authenticity of breeds after promulgation of the new Seed Law of the People’s Republic of China.

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