Analysis of Genome Size of Sixteen Coffea arabica Cultivars Using Flow Cytometry

Coffee is an important crop worldwide, grown on about 10 million hectares in tropical regions including Latin America, Africa, and Asia. The genus Coffea includes more than 100 species; most are diploid, except for C. arabica, which is allotetraploid and autogamous. The genetic diversity of commercial coffee is low, likely due to it being self-pollinating, in addition, the widespread propagation of few selected cultivars, such as Caturra, Bourbon, and Typica. One approach is the analysis of genome size in these cultivars as a proxy to study its genetic variability. In the present work, genome size of 16 cultivars was assessed through high-resolution flow cytometry (FCM). Nuclear DNA was analyzed using a modified procedure that uses propidium iodide (PI) and 4′,6′-diamino-2-phenylindole dihydrochloride hydrate (DAPI) staining. The C. arabica cultivars investigated possessed a nuclear DNA content ranging from 2.56 ± 0.016 pg for Typica, to 3.16 ± 0.033 pg for ICATU, which had the largest genome size. All cultivars measured using both fluorochromes had greater estimates with DAPI than PI. The proportion of the genome composed of guanosine and cytosine (GC%) among the cultivars evaluated in this study ranged from 37.03% to 39.22%. There are few studies of genome size by FCM of distinct important C. arabica cultivars, e.g., hybrids and artificial crosses. Thus, this work could be valuable for coffee breeding programs. The data presented here are intended to expand the genomic understanding of C. arabica and could link nuclear DNA content with evolutionary relationships such as diversification, hybridization and polyploidy.

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The genome sizes of Hordeum species show considerable variation

Genome ◽

10.1139/g96-092 ◽

1996 ◽

Vol 39 (4) ◽

pp. 730-735 ◽

Cited By ~ 18

Author(s):

Juha Kankanpää ◽

Alan H. Schulman ◽

Leena Mannonen

Keyword(s):

Flow Cytometry ◽

Hordeum Vulgare ◽

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Dna Content ◽

Meiotic Pairing ◽

Genome Size Variation ◽

Dapi Staining ◽

Hordeum Vulgare Ssp

Hordeum, distributed worldwide in temperate zones, is the second largest genus in the tribe Triticeae and includes diploid, tetraploid, and hexaploid species. We determined, by DAPI staining and flow cytometry, the nuclear DNA content for 35 accessions of the genus Hordeum, from a total of 19 species, including specimens of 2 cultivars and 2 landraces of Hordeum vulgare ssp. vulgare as well as samples of 12 Hordeum vulgare ssp. spontaneum populations. Genome sizes ranged from 5.69 to 9.41 pg for the G1 nuclei of the diploids, and from 13.13 to 18.36 pg for those of the tetraploids. This constitutes a 1.7-fold variation for the diploids, contrasting with a 4% variation previously reported. For H. vulgare ssp. vulgare (barley), the accessions examined differed by 18%. These variations in genome size cannot be correlated with meiotic pairing groups (I, H, X, Y) or with proposed phylogenetic relationships within the genus. Genome size variation between barley accessions cannot be related to status as cultivated or wild, or to climatic or geological gradients. We suggest these data may indicate rapid but sporadic changes in genome size within the genus. Key words : barley, Hordeum, Triticeae, genome size, flow cytometry.

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Nuclear DNA content of the whitefly Bemisia tabaci (Aleyrodidae: Hemiptera) estimated by flow cytometry

Bulletin of Entomological Research ◽

10.1079/ber2005361 ◽

2005 ◽

Vol 95 (4) ◽

pp. 309-312 ◽

Cited By ~ 22

Author(s):

J.K. Brown ◽

G.M. Lambert ◽

M. Ghanim ◽

H. Czosnek ◽

D.W. Galbraith

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Bemisia Tabaci ◽

Dna Content ◽

Blood Cells ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Chromosome Counting ◽

Male And Female ◽

Haploid Genome Size

AbstractThe nuclear DNA content of the whitefly Bemisia tabaci (Gennnadius) was estimated using flow cytometry. Male and female nuclei were stained with propidium iodide and their DNA content was estimated using chicken red blood cells and Arabidopsis thaliana L. (Brassicaceae) as external standards. The estimated nuclear DNA content of male and female B. tabaci was 1.04 and 2.06 pg, respectively. These results corroborated previous reports based on chromosome counting, which showed that B. tabaci males are haploid and females are diploid. Conversion between DNA content and genome size (1 pg DNA = 980 Mbp) indicate that the haploid genome size of B. tabaci is 1020 Mbp, which is approximately five times the size of the genome of the fruitfly Drosophila melanogaster Meigen. These results provide an important baseline that will facilitate genomics-based research for the B. tabaci complex.

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Genome Sizes in Hepatica Mill: (Ranunculaceae) Show a Loss of DNA, Not a Gain, in Polyploids

Journal of Botany ◽

10.1155/2010/758260 ◽

2010 ◽

Vol 2010 ◽

pp. 1-7 ◽

Cited By ~ 7

Author(s):

B. J. M. Zonneveld

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Close Relationships ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Dna Contents ◽

Asiatic Species ◽

Nuclear Dna Contents ◽

Allotetraploid Species

Genome size (C-value) was applied anew to investigate the relationships within the genus Hepatica (Ranunculaceae). More than 50 samples representing all species (except H. falconeri), from wild and cultivated material, were investigated. Species of Hepatica turn out to be diploid (), tetraploid ( ), and a possible pentaploid. The somatic nuclear DNA contents (2C-value), as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14%) loss of nuclear DNA in the natural allopolyploids was found.

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Evolution of Genome Size in Duckweeds (Lemnaceae)

Journal of Botany ◽

10.1155/2011/570319 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 45

Author(s):

Wenqin Wang ◽

Randall A. Kerstetter ◽

Todd P. Michael

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Propidium Iodide ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Continuous Increase ◽

Spirodela Polyrhiza ◽

Wolffia Arrhiza ◽

Basic Reference

To extensively estimate the DNA content and to provide a basic reference for duckweed genome sequence research, the nuclear DNA content for 115 different accessions of 23 duckweed species was measured by flow cytometry (FCM) stained with propidium iodide as DNA stain. The 1C-value of DNA content in duckweed family varied nearly thirteen-fold, ranging from 150 megabases (Mbp) in Spirodela polyrhiza to 1,881 Mbp in Wolffia arrhiza. There is a continuous increase of DNA content in Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia that parallels a morphological reduction in size. There is a significant intraspecific variation in the genus Lemna. However, no such variation was found in other studied species with multiple accessions of genera Spirodela, Landoltia, Wolffiella, and Wolffia.

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Genome size, fluorochrome banding, and karyotype evolution in some Hypochoeris species

Genome ◽

10.1139/g95-087 ◽

1995 ◽

Vol 38 (4) ◽

pp. 689-695 ◽

Cited By ~ 24

Author(s):

M. Cerbah ◽

J. Coulaud ◽

B. Godelle ◽

S. Siljak-Yakovlev

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Nucleolar Organizer ◽

Phylogenetic Position ◽

Nucleolar Organizer Regions ◽

Fluorochrome Banding ◽

South American

Four South American and two European species of Hypochoeris (Asteraceae) were studied using fluorochrome banding, and genome size was determined by flow cytometry, in order to obtain information about microevolution in this genus and about its primary origin. Fluorochrome banding patterns showed GC-rich repeated sequences, particularly around the nucleolar organizer regions. Few differences appeared among the South American species. Nevertheless, determination of nuclear DNA content and base composition revealed significant differences among these species. The phylogenetic position of Hypochoeris robertia, which has the smallest DNA content, is discussed with regard to chromosome evolution in this genus.Key words: Hypochoeris, Asteraceae, fluorochromes, flow cytometry, nucleolar organizer regions, microevolution.

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Genome size differences in Hyalella cryptic species

Genome ◽

10.1139/g11-085 ◽

2012 ◽

Vol 55 (2) ◽

pp. 134-139 ◽

Cited By ~ 12

Author(s):

Roland Vergilino ◽

Kaven Dionne ◽

Christian Nozais ◽

France Dufresne ◽

Claude Belzile

Keyword(s):

Flow Cytometry ◽

Cryptic Species ◽

Dna Barcoding ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Complex Species ◽

Numerous Species ◽

Freshwater Habitats

The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex.

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Nuclear DNA content variation within four species of Asian catfish of family Pangasidae and their two interspecific hybrids by flow cytometry

Jurnal Akuakultur Indonesia ◽

10.19027/jai.19.2.142-152 ◽

2020 ◽

Vol 19 (2) ◽

pp. 142-152

Author(s):

Imron ◽

Evi Tahapari ◽

Jadmiko Darmawan ◽

Muhammad Luthfi Abdurachman

Keyword(s):

Flow Cytometry ◽

Phylogenetic Relationship ◽

Dna Content ◽

Interspecific Hybrid ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Pure Line ◽

Dapi Staining ◽

Dna Content Variation ◽

Parental Lines

Nuclear DNA content (NDC) of species or population is believed to have been formed naturally by many mechanisms such chromosomal mutation, insertion and deletion, transposable element, and duplication. Additionally, hybridizations and species’ phylogenetic relationship may also contribute to the NDC diversity. This study was aimed to investigate the profile of NDC in four species Asian catfishes of the genera Pangasius including Pangasionodon hypophthalmus, Pangasius djambal, Pangasius nasusutus, Pangasius nieuwenhuisii, interspecific hybrid of female P. hypophthalmus and male P. djambal (Hybrid HD), and female P. hypophthalmus and male P. nasutus (Hybrid HN). Red blood cells (RBC) were taken from the respective species/groups and NDC measurement was performed in an Attune acoustic flowcytometer (ABI) using DAPI staining and chicken, Gallus domesticus, RBC was used as size reference. The results showed that the mean NDC of P. hypophthalmus, P. djambal. P. nasusutus, P. nieuwenhuisii, were 0.960±0.0254 pg, 1.017±0.0510 pg, 1.000±0.0410 pg, 1.074±0.0231 pg, which are within the range of NDC in the other catfish families The NDC values of Hybrid HD and Hybrid HN were1.005±0.0358 and 0.956± 0.0089, respectively. Among the pure line species, the NDC of P. hypophthalmus was the lowest and was different (P<0.05) from those of P. djambal and P. nieuwenhuisii but was not different (P>0.05) from that of the P. nasutus. The NDC of both Hybrid HD and Hybrid HN were not different form their respective parental lines. However, the NDC profiles of both hybrids were different in that the NDC of the former was in between while the latter was below their respective parental lines. Phylogenetically, the NDC diversity within Pangasiid catfish in this study was independent of their phylogenetic relationship based on cytoplasmic and nuclear markers. Keywords: Flow cytometry, nuclear DNA content, P.hypophthalmus, P. djambal, P. nasutus, P. nieuwenhuisii, interspecific hybrid.

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Estimating Nuclear DNA Content in Peach and Related Diploid Species Using Laser Flow Cytometry and DNA Hybridization

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.119.6.1312 ◽

1994 ◽

Vol 119 (6) ◽

pp. 1312-1316 ◽

Cited By ~ 56

Author(s):

W. Vance Baird ◽

Agnes S. Estager ◽

John K. Wells

Keyword(s):

Flow Cytometry ◽

Chromosome Number ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Diploid Species ◽

Nuclear Genome ◽

Nuclear Dna Content ◽

Gene Copy ◽

Polyploid Series

Using laser flow cytometry, nuclear DNA amounts were estimated for 12 Prunus species, representing three subgenera [Prunophora (Prunus), Amygdalus, and Cerasus (Lithocerasus)], two interspecific hybrids, four cultivars, and a synthetic polyploid series of peach consisting of haploids, diploids, triploids, and tetraploids (periclinal cytochimeras). Peach nuclear DNA content ranged from 0.30 pg for the haploid nuclei to 1.23 pg for the tetraploid nuclei. The diploid genome of peach is relatively small and was estimated to be 0.60±0.03 pg (or 5.8×108 nucleotide base pairs). The polyploid series represented the expected arithmetic progression, as genome size positively correlated with ploidy level (i.e., DNA content was proportional to chromosome number). The DNA content for the 12 diploid species and two interspecific diploid hybrids ranged from 0.57 to 0.79 pg. Genome size estimates were verified independently by Southern blot analysis, using restriction fragment length polymorphism clones as gene-copy equivalents. Thus, a relatively small and stable nuclear genome typifies the Prunus species investigated, consistent with their low, basic chromosome number (× = 8).

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Determination of DNA content and relative 2C genome sizes of some promising commercial varieties of sugarcane using flow cytometer

Current Botany ◽

10.19071/cb.2017.v8.3207 ◽

2017 ◽

Vol 8 ◽

Author(s):

A. Mondal S.K. Ghosal ◽

T. Pal Kalyan Kumar De

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Cane Yield ◽

Sugarcane Varieties ◽

Yield Information ◽

A Genome ◽

2C Dna Content

In the present study, 2C DNA content and the genome sizes (in picograms-pg and megabase pairs-Mbp respectively) of 19 promising commercial varieties of sugarcane, the derivatives of man-made interspecific hybrids between cultivated and wild species were analyzed using flow cytometry. In this work, 2C nuclear DNA content was determined. Knowing the 2C nuclear DNA content, the unknown chromosome numbers of the varieties could be predicted. Large differences (65 % variation) in DNA content (2C) of 19 varieties were detected, ranging, from 3.80 pg to 10.96 pg, which corresponds to a genome size ranging from 3724.00 Mbp to 10740.80 Mbp due to the variation of ploidy level and are considered the most complex genomes among crop plants. However, the relationship between chromosome number and genome size was highly significant (P < 0.001). In the present study, internode diameter, Sugar juice content and cane yield/ha are also positively correlated with DNA content. The estimated genome sizes would also yield information critical for sugarcane breeding and genome sequencing programs. Keywords: Genome size, Sugarcane varieties, Flow cytometry, DNA content.

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Genome size in 21 Artemisia L. species (Asteraceae, Anthemideae): Systematic, evolutionary, and ecological implications

Genome ◽

10.1139/g01-004 ◽

2001 ◽

Vol 44 (2) ◽

pp. 231-238 ◽

Cited By ~ 27

Author(s):

Montserrat Torrell ◽

Joan Vallès

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Life Forms ◽

Dna Amount ◽

Ploidy Levels ◽

Ecological Selection ◽

Ecological Implications

Genome size was estimated by flow cytometry in 24 populations belonging to 22 Artemisia taxa (21 species, 1 with two subspecies), which represent the distinct subgenera, life forms, basic chromosome numbers, and ploidy levels in the genus. 2C nuclear DNA content values range from 3.5 to 25.65 pg, which represents a more than sevenfold variation. DNA content per haploid genome ranges from 1.75 to 5.76 pg. DNA amount is very well correlated with karyotype length and ploidy level. Some variations in genome size have systematic and evolutionary implications, whereas others are linked to ecological selection pressures.Key words: Artemisia, Asteraceae, flow cytometry, genome size, nuclear DNA amount variation, systematics, evolution, ecology.

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