Assessment of inter- and intra-inbred line variability in sunflower (Helianthus annuus) by RFLPs

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 1040-1048 ◽  
Author(s):  
Y. X. Zhang ◽  
L. Gentzbittel ◽  
F. Vear ◽  
P. Nicolas
Keyword(s):  
Genetic Distance ◽  
Inbred Line ◽  
Gene Diversity ◽  
Principal Component ◽  
Restriction Enzymes ◽  
Inbred Lines ◽  
Absolute Difference ◽  
Cdna Clones ◽  
Average Gene Diversity ◽  
Average Gene

The restriction fragment length polymorphism (RFLP) between 26 sunflower inbred lines was evaluated with 81 probe–enzyme combinations involving 51 cDNA clones and 4 restriction enzymes (HindIII, EcoRI, EcoRV, and BglII). An average of 4.6 fragments and 4.9 profiles was detected per probe–enzyme combination, across all inbred lines. The RFLPs revealed were characterized by a high percentage (>70%) of multifragment profiles. Nei's average gene diversity was calculated to measure the genetic variability within cultivated sunflower; the average gene diversity computed with 81 probe–enzyme combinations was 0.59. The relationships between the 26 sunflower inbred lines were analysed by estimates of Nei's F index, which ranged from 0.50 to 0.91, as well as Nei's genetic distance, d, which varied from 0.05 to 0.41. A UPGMA (unweighted pair-group arithmetic average clustering) dendrogram was constructed using the genetic distance matrix; likewise, a principal component analysis was performed using the F matrix. The results obtained from the two clustering analyses allowed the separation of maintainer lines (females) from restorer lines (males). After partitioning the 26 lines into a pool of maintainer lines and a pool of restorer lines, the estimation of gene differentiations showed that the absolute difference (Dm) between females and males was only about 5%. Intraline variability was also examined in 4 sunflower inbred lines, using 30 probe–enzyme combinations. Heterogeneity at varying levels was detected in 3 of the 4 lines studied. The RFLPs detected by this set of selected clones in the 26 inbred lines suggests that RFLPs could be very useful descriptors for sunflower inbred line and variety studies.Key words: RFLPs, sunflower, inbred lines, genetic diversity.

scholarly journals Grouping and clustering of maize Lancaster germplasm inbreds according to the results of SNP-analysis

2017 ◽  
Vol 8 (3) ◽  
pp. 343-348 ◽  
Author(s):  
K. V. Derkach ◽  
T. M. Satarova ◽  
V. V. Borysova ◽  
V. Y. Cherchel ◽  
B. V. Dzyubeckiy
Keyword(s):  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Total Variation ◽  
Inbred Line ◽  
Gene Diversity ◽  
Principal Component ◽  
Component Analysis ◽  
Inbred Lines ◽  
Snp Markers ◽  
Snp Analysis

The objective of this article is grouping and clustering of maize inbred lines based on the results of SNP-genotyping for the verification of a separate cluster of Lancaster germplasm inbred lines. As material for the study, we used 91 maize (Zea mays L.) inbred lines, including 31 Lancaster germplasm lines and 60 inbred lines of other germplasms (23 Iodent inbreds, 15 Reid inbreds, 7 Lacon inbreds, 12 Mix inbreds and 3 exotic inbreds). The majority of the given inbred lines are included in the Dnipro breeding programme. The SNP-genotyping of these inbred lines was conducted using BDI-III panel of 384 SNP-markers developed by BioDiagnostics, Inc. (USA) on the base of Illumina VeraCode Bead Plate. The SNP-markers of this panel are biallelic and are located on all 10 maize chromosomes. Their range of conductivity equals >0.6. The SNP-analysis was made completely in automated regime on Illumina BeadStation equipment at BioDiagnostics, Inc. (USA). The grouping of the studied set of 91 inbred lines according to allelic state of SNP-markers and identifying cluster of Lancaster germplasm inbred lines in general selection of inbreeds used principal component analysis. The clustering and determining hierarchy in 31 Lancaster germplasm inbreds used quantitative cluster analysis. The share of monomorphic markers in the studied set of 91 inbred lines equaled 0.7%, and the share of dimorphic markers equaled 99.3%. Minor allele frequency (MAF) > 0.2 was observed for 80.6% of dimorphic markers, the average indicator of shift of gene diversity equaled 0.2984, PIC on average reached 0.3144. The index of gene diversity of markers varied from 0.1701 to 0.1901, pairwise genetic distances between inbred lines ranged from 0.0316–0.8000, the frequencies of major alleles of SNP-markers were within 0.5085–0.9821, and the frequencies of minor alleles were within 0.0179–0.4915. The average homozygosity of inbred lines was 98.8%. The principal component analysis of SNP-distances confirmed the isolation of the Lancaster group within the general set of analyzed inbred lines. Two-dimensional component analysis showed that the first principal component (PCA1) accounted for 36.0% of total variation and divided the investigated set of 91 inbred lines into two fractions, while all the inbred lines which are considered Lancaster based on pedigree information were included in one of the fractions. The second principal component (PCA2), which accounted for 12.1% of total variation, separated most of the Lancaster germplasm inbred lines from the others in this fraction, although the overlapping of the locations of Lancaster and non-Lancaster inbred lines was observed. Qualitative cluster analysis of 31 Lancaster germplasm inbred lines allowed us to identify two clusters: the first one includes 23 inbred lines of Ukrainian selection and the well known Mo17 (77.4% of total number of analysed lines) inbred line, and the second cluster included 6 inbred lines of Ukrainian selection and the well known Oh43 (22.6% of total number of analysed lines) inbred line. The isolation of two clusters within Lancaster germplasm indicates the genetic diversity in this plasm. The evaluation of genome similarities through allelic states of SNP-markers can successfully be used as a data source for classification and systematization of the gene pool of maize inbred lines.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

Highly polymorphic microsatellite markers in Chamaecyparis obtusa

2001 ◽  
Vol 31 (12) ◽  
pp. 2248-2251 ◽  
Author(s):  
Y Nakao ◽  
H Iwata ◽  
A Matsumoto ◽  
Y Tsumura ◽  
N Tomaru
Keyword(s):  
Microsatellite Loci ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Chamaecyparis Obtusa ◽  
Mendelian Inheritance ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene

Nine microsatellite loci in hinoki, Chamaecyparis obtusa (Sieb. et Zucc.) Endl., were identified and characterized. A genomic library, developed using enrichment with magnetic beads, was screened to identify microsatellite repeats (CT/AG). The microsatellite loci, where the alleles were segregated, displayed codominant Mendelian inheritance. Genetic analysis of 16 plus trees and two unrelated individuals of Chamaecyparis obtusa revealed that all loci were highly polymorphic, with an average of 10.3 alleles per locus, and an average gene diversity of 0.77. The applicability of these microsatellite loci was also tested in other species of the Cupressaceae and in Cryptomeria japonica (L.f.) D. Don (Taxodiaceae, a family closely related to Cupressaceae). Polymerase chain reaction (PCR) amplification was successful for about half of the loci of the species in the genus Chamaecyparis. However, the PCR amplification patterns of the 11 species of Cupressaceae showed no clear correlations with their molecular phylogeny. The highly polymorphic microsatellite loci in Chamaecyparis obtusa, identified here, will be useful in studies of hinoki breeding and population genetics.

scholarly journals Randomly Amplified Polymorphic DNA (RAPD) Variation among and within Artichoke (Cynara scolymus L.) Cultivars and Breeding Populations

1996 ◽  
Vol 121 (5) ◽  
pp. 783-788 ◽  
Author(s):  
Jan Tivang ◽  
Paul W. Skroch ◽  
James Nienhuis ◽  
Neal De Vos
Keyword(s):  
Rapd Markers ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Phenotypic Variability ◽  
Population Sample ◽  
Relationship Matrix ◽  
Globe Artichoke ◽  
Breeding Populations ◽  
Average Gene Diversity ◽  
Average Gene

The magnitude of genetic differences among and heterogeneity within globe artichoke cultivars is unknown. Variation among individual heads (capitula) from three artichoke cultivars and two breeding populations were evaluated using RAPD markers. One vegetatively propagated cultivar (`Green Globe'), two seed-propagated cultivars (`Imperial Star' and `Big Heart') and two breeding populations were examined. Two to thirteen polymorphic bands were observed for 27 RAPD primers, which resulted in 178 scored bands. Variation was found within and among all cultivars, and breeding populations indicating that all five groups represent heterogeneous populations with respect to RAPD markers. The genetic relationships among individual genotypes were estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed five independent clusters corresponding to the three cultivars and two breeding populations. The integrity of the five clusters was confirmed using pooled chi-squares for fragment homogeneity. Average gene diversity (Hs) was calculated for each population sample, and a one-way analysis of variance showed significant differences among populations. `Big Heart' had an Hs value equivalent to the two breeding populations, while clonally propagated `Green Globe' and seed propagated `Imperial Star' had the lowest Hs values. The RAPD heterogeneity observed within clonally propagated `Green Globe' is consistent with phenotypic variability observed for this cultivar. Overall, the results demonstrate the utility of the RAPD technique for evaluating genetic relationships and contrasting levels of genetic diversity among populations of artichoke genotypes.

Genetic diversity between Italian and Greek buffalo populations

2001 ◽  
Vol 29 ◽  
pp. 31-40 ◽  
Author(s):  
B. Moioli ◽  
A. Georgoudis ◽  
F. Napolitano ◽  
G. Catillo ◽  
S. Lucioli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Allele Frequency Distribution ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene ◽  
Degree Of Differentiation ◽  
Two Populations ◽  
Global Project

SummaryThe present study is a first step of a global project aiming at the estimation of the genetic distances and relationships among buffalo breeds and sub-populations and the investigation of the production potential and adaptability of different buffalo genotypes in various environments.Genetic diversity of Italian and Greek buffalo populations was estimated on the basis of allele frequencies at nine polymorphic microsatellite loci: CSSM43, CSSM38, DRB3, D21S4, CYP21, CSSM47, CSSM60, CSSM36 and CSSM33. The number of detected alleles per locus varied from two (D21S4) to thirteen (CSSM47). Allele frequency distribution was similar in the two populations, which have the same alleles at the highest frequency at all loci, except loci CSSM47 and CSSM60. Average gene diversity over all loci was 0.60. Across-loci average gene diversity increased with the number of alleles. Observed average heterozygosity was 0.167 and 0.177 in the Italian and Greek populations, respectively. The degree of differentiation between Italian and Greek buffalo was moderate and estimated at 0.021 ± 0.009.

scholarly journals Genetic Diversity in Domestic and Introduced Wheats

2013 ◽  
Vol 59 (3) ◽  
pp. 101-110
Author(s):  
Martina Hudcovicová ◽  
Katarína Ondreičková ◽  
Pavol Hauptvogel ◽  
Ján Kraic
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Bread Wheat ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Markers ◽  
Wheat Genotypes ◽  
Average Gene Diversity ◽  
Average Gene

Abstract A set of 33 wheat EST-SSR markers was designed and 18 from them were polymorphic and used for assessment of genetic diversity within 36 introduced genotypes of hexaploid bread wheat. Altogether 105 alleles were detected, in average 3.18 alleles per locus. Maximum number of alleles 14 was detected at the locus TDI389708. Five the most polymorphic markers were used for the evaluation and comparison of genetic variation within 46 domestic (Slovak) wheat genotypes and 36 introduced (foreign) wheat genotypes. The number of alleles per used primer pair within domestic genotypes varied from 7 to 19, with an average of 13.2 alleles, an average gene diversity 0.846 and PIC 0.980 per locus. The number of alleles per primer within introduced genotypes varied from 7 to 14, with an average of 10.8 alleles, an average gene diversity 0.780 and PIC 0.958 per locus. The level of polymorphism in EST- SSRs was sufficient for discrimination between genotypes and variation within domestic genotypes was slightly higher than in introduced genotypes. Variation revealed by 5 selected EST-SSR markers clustered genotypes according to origin. Domestic and introduced wheats were grouped distinctly into two separate groups.

scholarly journals Assessment of Genetic Relationship Among Landraces of Bangladeshi Ridge Gourd (Luffa acutangula Roxb.) Using RAPD Markers

2009 ◽  
Vol 1 (3) ◽  
pp. 615-623 ◽  
Author(s):  
S. Hoque ◽  
M. G. Rabbani
Keyword(s):  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Relatedness ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Group Method ◽  
Pair Group ◽  
Average Gene ◽  
Luffa Acutangula

Information on genetic relatedness among ridge gourd (Luffa acutangula) genotypes from Bangladesh is currently not reported. Twenty eight accessions collected from different parts of Bangladesh were studied using random amplified polymorphic DNA (RAPD) technique. Four selected decamer primers, out of sixteen screened, could generate a total of 27 RAPD fragments of which 22 were polymorphic (81.5%). The bands ranged from 50 to 1500 bp in size. Genetic variation statistics for all loci estimated the average gene diversity (h) value as 0.278 and the Shannon’s Information Index (I) as 0.415. Dendrogram based on unweighted pair-group method with arithmetic averages (UPGMA) segregated the accessions into five clusters. Cluster III was the largest with 13 members followed by cluster II, V, I and IV with 6, 4, 3 and 2 members, respectively. Accession LA27 and LA29 were found very close to each other with the highest inter-variety similarity index (96.05%) and the lowest genetic distance (0.077); whereas accession LA40 and LA72 were more distant to each other with the lowest inter-variety similarity index (44.43%) and the highest genetic distance (0.73). A DNA extraction method has been standardized. The marker was found to be useful tool for assessing genetic variations in Luffa acutangula. Keywords: Genetic relationship; Germplasm; Ridge gourd; Luffa acutangula; RAPD.  © 2009 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v1i3.1968               J. Sci. Res. 1 (3), 615-623 (2009) 

scholarly journals Heterosis and Genetic Diversity of Yield and Its Some Components in F1 of Sunflower Inbred Lines

2021 ◽  
Vol 910 (1) ◽  
pp. 012025
Author(s):  
Zainab Mofak Musa ◽  
Saddam Hussein Abbas ◽  
Hamzah Mohsin Kadhim
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Distance ◽  
First Generation ◽  
Genetic Difference ◽  
Block Design ◽  
Principal Component ◽  
Inbred Lines ◽  
High Degree ◽  
Positive Heterosis

Abstract Fall season 2020, six inbred lines of sunflower were crossed by half-diallel crosses to obtain 15 single hybrids. The genotypes (parents and first-generation hybrids -F1) were planted in randomized comlete block design (RCBD) with three replications in a field/Babylon Governorate during the spring season 2021. The study aimed to estimate Heterosis of the first generation hybrids from the mean of the parents for the traits; stem diameter, head diameter, number of seeds per head, weight of 100 seeds, seed yield and oil yield per plant. Furthermore, estimation of genetic distance among genotypes using cluster analysis. The results of the analysis of variance showed that there were significant differences at the probability level (0.01) for all the studied traits of the parents and the first generation hybrids. The two hybrids (I×Q) and (Q×C) were distinguished a high significant positive heterosis for most of the traits measured. The cluster analysis showed that the two genotypes that include hybrids (Q×C) and (Q×F) had the highest Euclidean distance (175.92 and 183.66) respectively. This indicated to high degree of genetic diversity between the two hybrids and the rest of the studied hybrids, which it positively reflected on the performance of the hybrids for the studied traits. The results of Principal Component Analysis (PCA) and Dendrogram showed that (Q) genotype was far from the rest of the genotypes and isolated to a single group, whereas the remaining genotypes separated into groups to two separed branches, especially the two genotypes (C( and )Q). The reason may be due to the distinguish genetic difference of these interested genotypes which have the ablility to transfer from parents to the its progenies, which resulted from a presence of the clear genetic distance between them, while, other genotypes lacks the of this genetic variation case.

scholarly journals Development of Microsatellite Markers from Crape Myrtle (Lagerstroemia L.)

HortScience ◽  
2010 ◽  
Vol 45 (5) ◽  
pp. 842-844 ◽  
Author(s):  
Xinwang Wang ◽  
Deborah Dean ◽  
Phillip Wadl ◽  
Denita Hadziabdic ◽  
Brian Scheffler ◽  
...  
Keyword(s):  
Allelic Richness ◽  
Genomic Library ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Average Gene Diversity ◽  
Wide Range ◽  
Growth Habits ◽  
Average Gene ◽  
Breeding And Genetics ◽  
Ornamental Species

Lagerstroemia L. (crape myrtle) is an economically important woody plant genus with several deciduous flowering ornamental species. A wide range of flower colors, long flowering periods, growth habits ranging from miniature to tree sizes, and exfoliating bark characteristics provide horticulturists and nursery growers with a great deal of interest in the breeding and genetics of this genus. We report microsatellite marker development from a GT-enriched genomic library of the interspecific hybrid ‘Natchez’ (L. indica L. × L. fauriei Koehne). Twelve of 43 novel microsatellite loci were characterized on a collection of 33 Lagerstroemia cultivars and accessions. Four to eight alleles per locus (mean = 5.6 alleles) were detected. Allelic richness ranged from 3.9 to 7.2 with a mean of 5.3. The level of polymorphism detected (average gene diversity of 0.68) indicates moderately high genetic diversity within the selections of crape myrtle cultivars and accessions. The examined markers also exhibited high cross-species transferability to L. fauriei, L. limii Merr., and L. subcostata Koehne.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

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