Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Evaluation of genetic diversity in 19 Glycine max (L.) Merr. accessions included in the Czech National Collection of soybean genotypes

Czech Journal of Genetics and Plant Breeding ◽

10.17221/6114-cjgpb ◽

2012 ◽

Vol 38 (No. 2) ◽

pp. 69-74 ◽

Cited By ~ 2

Author(s):

M. Baránek ◽

M. Kadlec ◽

J. Raddová ◽

M. Vachůn ◽

M. Pidra

Keyword(s):

Genetic Diversity ◽

Glycine Max ◽

Random Amplified Polymorphic Dna ◽

Breeding Programs ◽

Low Level ◽

Low Degree ◽

Soybean Genotypes ◽

Glycine Max L ◽

Rapd Polymorphism ◽

Selection Of

The random amplified polymorphic DNA (RAPD) technique was used to evaluate both genetic diversity among 19 soybean accessions included in the Czech National Collection of Soybean Genotypes and their potential as a new source of genetic variations for soybean breeding programs. Only 22 of all the 40 random primers used in RAPD reactions showed polymorphism acceptable for an effective characterisation of these accessions. Altogether 122 highly reproducible RAPD fragments were generated, 55 of them were polymorphic (46%). However, because of the previously observed low degree of RAPD polymorphism in the case of Glycine max, fragments with low level of informativeness were evaluated, too. Presented results enable the selection of genetically distinct individuals. Such information may be useful to breeders willing to use genetically diverse introductions in soybean improvement process. 

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Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm

Legume Research - An International Journal ◽

10.18805/lr-401 ◽

2018 ◽

Author(s):

Sajjad Ahmad ◽

Rajvinder Kaur ◽

Mark Lefsrud ◽

Jaswinder Singh

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Dna Polymorphism ◽

Breeding Programs ◽

Molecular Analyses ◽

Marker System ◽

Varietal Identification ◽

D Values ◽

Mean Similarity ◽

Germplasm Accessions

Retrotransposons diversity has been extensively studied in monocots, but it is not well documented in dicot species. Transposition activity of transposons creates DNA polymorphism and their abundant presence in genomes is making transposons a promising marker system for varietal identification and fingerprinting. In this study, four transposon-based markers (two DNA- and two RNA-transposons) were employed to evaluate the effectiveness of Inter-Retrotransposon Amplified Polymorphism (IRAP) transposon system in assessing genetic diversity in pea germplasm accessions. A total of 28 alleles were detected across the 35 pea accessions with number of alleles per locus ranged from 5 (Mutator) to 9 (Cyclops). RNA transposons produced a higher number of polymorphic alleles (Ogre: 8, Cyclops: 9) than DNA transposon markers (Mutator: 5, MITE: 6). Overall mean PIC value and D values for these transposon markers were 0.810 and 0.817 respectively. Genetic similarity values ranged from 0.143 to 0.823 with a mean similarity value of 0.403. Cluster analysis classified pea genotypes into six major groups that were somewhat consistent with their geographical origins. The molecular analyses differentiated all the 35 accessions and generated higher PIC and D values that can be useful for MAS-based breeding programs in pea.

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Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

Australian Journal of Agricultural Research ◽

10.1071/ar01178 ◽

2002 ◽

Vol 53 (6) ◽

pp. 629 ◽

Cited By ~ 17

Author(s):

J. M. Musial ◽

K. E. Basford ◽

J. A. G. Irwin

Keyword(s):

Genetic Diversity ◽

Population Genetic ◽

Random Amplified Polymorphic Dna ◽

Population Diversity ◽

Breeding Programs ◽

Population Genetic Diversity ◽

Medicago Sativa L ◽

Components Analysis ◽

High Level ◽

Selection Of

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

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Genetic diversity assessment of Rice (Oryza sativa L.) germplasm using ssr markers

Research in Agriculture Livestock and Fisheries ◽

10.3329/ralf.v1i1.22354 ◽

2015 ◽

Vol 1 (1) ◽

pp. 37-46 ◽

Cited By ~ 1

Author(s):

Ahasanul Hoque ◽

Shamsun Nahar Begum ◽

Lutful Hassan

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Oryza Sativa L ◽

Growth Duration ◽

Breeding Programs ◽

Diversity Assessment ◽

Days To Heading ◽

Early Maturing ◽

Rice Genotypes ◽

Selection Of

Diversity at molecular level among thirty rice genotypes, selected based on earliness and morphometric diversity was evaluated through five SSR markers associated with days to heading. Three primers viz., RM147, RM167 and RM215 showed polymorphism for growth duration related traits. A total of 17 alleles were detected among the 30 rice genotypes with an average of 5.66 alleles per locus. Polymorphism Information Content (PIC) ranged from 0.356 to 0.798 with an average of 0.543. A dendrogram based on total microsatellite polymorphism grouped 30 genotypes into four major clusters at 0.39 similarity coefficient differentiating early maturing genotypes from others. This information about the genetic diversity will be very useful for proper identification and selection of appropriate parents for future breeding programs, including gene mapping. The results also showed that microsatellite markers associated to genes or QTLs controlling growth duration properties are suitable tools for marker assisted selection (MAS) to select rice lines with short growth duration. DOI: http://dx.doi.org/10.3329/ralf.v1i1.22354 Res. Agric., Livest. Fish.1(1): 37-46, Dec 2014

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Genetic diversity in sunflower (Helianthus annuus L.) as revealed by random amplified polymorphic DNA analysis

Australian Journal of Agricultural Research ◽

10.1071/ar9941319 ◽

1994 ◽

Vol 45 (7) ◽

pp. 1319 ◽

Cited By ~ 23

Author(s):

WR Lawson ◽

RJ Henry ◽

JK Kochman ◽

GA Kong

Keyword(s):

Genetic Diversity ◽

Ribosomal Rna ◽

Dna Analysis ◽

Random Amplified Polymorphic Dna ◽

Efficient Tool ◽

Breeding Programs ◽

Breeding Lines ◽

Sunflower Genome ◽

Pair Wise Comparison ◽

Selection Of

A cross-section of sunflower genotypes grown in Australia including commercial cultivars (Suncross 40R, Hysun 33, Hysun 45CQ, Advance, DK3873), breeding lines (Sunfola, S37- 388, PhRR3, HA-R2, MC29, MC69, S37-388RR), wild sunflower varieties (H. annuus, H. argophyllus), a distantly related species (Tithonia diversifolia), and a hexaploid/diploid cross (H. tuberosus L.x H. annuus L.) were assessed for genetic diversity using RAPD (Random Amplified Polymorphic DNA) analysis. A considerable amount of polymorphism was revealed. Of the total of 158 markers amplified, 133 were polymorphic for at least one pair-wise comparison within the 16 genotypes. Overall, 33% dissimilarity was detected, with an average of 27% dissimilarity revealed among the hybrids and breeding lines, which exhibited 38% dissimilarity to the wild varieties H. annuus and H. tuberosus, and 51% dissimilarity to Tithonia and H. tuberosus x H, annuus. PCR of the 5S ribosomal RNA gene spacer region did not reveal any polymorphisms among the cultivated and breeding lines, but did distinguish between H. tuberosus and the other wild species. This survey of a selection of sunflower genotypes indicates that the genetic base of domesticated sunflower may be quite wide. These results suggest that RAPD methodology will provide an efficient tool for the analysis of the sunflower genome, in particular in breeding programs.

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SWEETPOTATO FLAVOR - EXISTING STATUS AND FUTUREOUTLOOK

HortScience ◽

10.21273/hortsci.28.4.262a ◽

1993 ◽

Vol 28 (4) ◽

pp. 262A-262

Author(s):

J. Kays ◽

Wayne J. McLaurin

Keyword(s):

Genetic Diversity ◽

Current Understanding ◽

Breeding Programs ◽

Flavor Chemistry ◽

Staple Crops ◽

Baked Potato ◽

New Cultivars ◽

Selection Of

Flavor is a primary trait in the selection of foods. The role of flavor in acceptance of the sweetpotato, flavors status as a selection trait in existing breeding programs, and our current understanding of the flavor chemistry of the sweetpotato was reviewed. The sweetpotato, unlike most staple crops, has a very distinct and dominant flavor. In typical breeding programs, however, flavor is generally one of the last traits screened. A tremendous diversity and range of flavors has been reported within the sweetpotato germplasm (e.g., acidic, bland, baked potato, boiled potato. carrot, chalky, chemical, citrus, earthy, Ipomoeo/terpene, lemon, musty, pumpkin, salty, squash (titer type), starchy, sweet, sweetpotato (traditional), terpene, and turnip. These results indicate that the genetic diversity for flavor present in sweetpotato germplasm will allow making substantial changes in the flavor of new cultivars, thus potentially opening previously unexploited or under-exploited markets. Implementation involves solving two primary problems: 1) identification of desirable flavor ideotypes; and development of procedures that allow maximizing the selection of specific flavor types.

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Evaluation of Genetic Diversity and Identification of Huperzia Species Collected in Some Different Areas in Vietnam by Molecular Markers

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.80.13 ◽

2020 ◽

Vol 80 ◽

pp. 13-23

Author(s):

Tran Thi Thu Ha ◽

Tran Dang Khanh ◽

Khuat Huu Trung

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Phylogenetic Tree ◽

Genetic Similarity ◽

High Quality ◽

Plant Sources ◽

High Genetic Similarity

The objective of this study was to evaluate genetic diversity of 35 Huperzia samples collected from the different ecological areas in Vietnam by using rbcL markers. The results revealed that the samples were genetically diverse in high genetic similarity which ranged from 98.0 to 99.0%, respectively. Based on the Genbank data in comparison, it was ascertained that only one sample (BK3) is a member of H.phlegmarioides group, and others belonged H. squarrosa group as divided into two main groups by phylogenetic tree analyses. It suggests that some Huperzia samples may plausibly descend from the same origin, evolution and arising relations. This study has provided useful information for further identifying the high-quality genetic plant sources for propagation, development and conservation of the high-valued medicinal materials of Huperzia plants in this country.

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Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

Jurnal Tanaman Industri dan Penyegar ◽

10.21082/jtidp.v5n2.2018.p77-86 ◽

2018 ◽

Vol 5 (2) ◽

pp. 77

Author(s):

Budi Martono ◽

Syafaruddin Syafaruddin

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Similarity ◽

Binary Data ◽

Rapd Markers ◽

Group Method ◽

Breeding Programs ◽

Pair Group ◽

Monomorphic Band ◽

And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

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(235) Genetic Diversity Analysis of Five Passiflora Genotypes

HortScience ◽

10.21273/hortsci.40.4.1002a ◽

2005 ◽

Vol 40 (4) ◽

pp. 1002A-1002

Author(s):

Eric Stafne ◽

Jon Lindstrom ◽

John Clark

Keyword(s):

Genetic Diversity ◽

North American ◽

Genetic Similarity ◽

The Other ◽

Diversity Analysis ◽

Breeding Programs ◽

Genetic Diversity Analysis ◽

Native North American ◽

Cold Hardy ◽

High Degree

Passiflora is an important ornamental genus, mainly within tropical zones. However, two cold-hardy, North American Passiflora species exist. Previous work has been done to incorporate these species into breeding programs with some success. The intent of this study was to evaluate the extent of genetic diversity among five different Passiflora genotypes, including the two native North American species, P. incarnata L. and P. lutea L. Results indicate low genetic similarity among all genotypes with none at 50% or greater. P. incarnata and the ornamental cultivar `Lady Margaret' displayed the highest relationship at 49%. P. incarnata averaged 35.5% similarity with the other genotypes and P. lutea was 29.5%. Average overall similarity among all genotypes was 31.1%. These and other results show that the Passiflora genus has a high degree of genetic variation and breeding efforts could expand interest within North America.

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