Genome size in gymnosperms

Ohri, Deepak; Khoshoo, T. N.

doi:10.1007/bf00989421

Cited by 153 publications

(101 citation statements)

References 26 publications

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“…This may lead to overestimates for genetic distances and total map length. Maritime pine has 12 metacentric chromosomes of approximately equal size (Saylor, 1964 (Ohri & Khoshoo, 1986;Arumuganathan & Earle, 1991). Thus, on a chromosomal basis, maritime pine has approximately 57-fold more DNA per cM than Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

“…Pine genome organization Gynmosperm species are characterized by: (i) their antiquity (conifers appeared 140 millions years before the first angiosperm) and their longevity, (ii) the absence of ploidy level and chromosome number evolution (reviewed by Neale & Williams, 1991), and (iii) the very high and consistent amount of DNA per nucleus (Ohri & Khoshoo, 1986;Wakamiya et a!., 1993). The technique of DNA reassociation kinetics applied to Pinus species (Miksche & Hotta, 1973;Rake et at., 1980;Kriebel, 1985) showed that 25 per cent of total DNA is low-to single-copy, 75 per cent being middle to highly repetitive.…”

Section: Discussionmentioning

confidence: 99%

“…RAPDs have been used for genomic mapping in several conifer species (Neale & Sederoff, 1991;Tulsieram et a!., 1992;Nelson et a!., 1993;Bineffi & Bucci, 1994). Pinus species have a large genome (Ohri & Khoshoo, 1986;Wakamiya et a!., 1993) characterized by a high proportion of repetitive DNA (Miksche & Hotta, 1973;Rake et a!., 1980;Kriebel, 1985). Therefore, RAPDs and markers that are based on coding sequences could provide different coverage of the genome in pine.…”

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confidence: 99%

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Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

et al. 1995

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A detailed genomic map was constructed for one F1 individual of maritime pine, using randomly amplified polymorphic DNA (RAPD) and protein markers scored on megagametophytes of germinated seeds. Proteins allowed the localization of exclusively coding DNA in the large genome of this Pinus species, mapped with RAPD markers that essentially fail within repetitive (i.e. mostly noncoding) DNA. Dot blots experiments of 53 RAPD fragments showed that 89 per cent amplified from highly repetitive chromosomal regions. The map comprised 463 loci, including 436 RAPDs amplified from 142 10-mer oligonucleotide primers and 27 protein loci. Twelve major and one minor linkage groups were identified using a LOD score 5 and a recombination fraction ® 0.30. A framework map was ordered with an interval support 4, covering 1860 cM which provided almost complete coverage of the maritime pine genome. The average distance between two framework markers was 8.3 cM; only one interval was larger than 30 cM. Protein loci were well distributed throughout the map. Their potential use as anchor points to join RAPD-based maps is discussed. Finally, the genomic maps of Arabidopsis and maritime pine were compared. Linkage groups were shown to have similar total map lengths on a chromosomal basis, despite a 57-fold difference in DNA content.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

et al. 1995

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“…Natarajan et al 1961;Cesca and Peruzzi 2002) and C-bands (Borzan and Papeš 1978; MacPherson and Filion 1981) but they seem less reproducible and difficult to compare among studies or species. The difficulty of karyotype analysis in Pinus may be cause by their large genome size (Ohri and Khoshoo 1986;O'Brien et al 1996;Morse et al 2009) or long chromosomes. For karyotype analysis in species of Pinus having large genome, long-term pretreatment of the chemicals are required to get well contract chromosomes suitable for karyotype analysis.…”

Section: Discussionmentioning

confidence: 99%

Chromosome banding in the genus <i>Pinus</i> V. Fluorescent banding patterns in 16 diploxylon pines

et al. 2016

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ABSTRACT:In Pinus , Subgenus Pinus 16 species were investigated on their somatic chromosomes by a fluorescent banding technique using chromomycin A 3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI). The chromosome number of 2n=24 was commonly counted in all the species studied. Their karyotypes were composed of many long metacentric chromosomes and a few short submetacentric chromosomes, and two karyotypes were recognized in respect to number of short chromosomes in the subgenus. CMA-bands appeared at an interstitial and/or proximal region of chromosomes and DAPI-band did at a proximal region. Thin DAPI-bands appeared at interstitial regions and DAPI-dots appeared at a centromeric region in most chromosomes. In a chromosome complement each homologous chromosome was identified on the base of its shape and fluorescent banding pattern. The typical banding patterns were compared among the species studied. Many interstitial CMA-bands at the secondary constrictions appeared on many metacentric chromosomes. Proximal fluorescent bands varied in fluorescent nature and number and divided into several groups. Section Pinus short three chromosome pairs were two or three patterns of fluorescent banding. The section Trifolae species had many proximal DAPI-bands and less proximal CMA-bands than section Pinus. The shortest chromosome had proximal bands indicating two groups on the kinds of fluorescent band.

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“…However, the number of necessary SNP markers may not be as large if most of the genome is segregating as blocks, as found in the BAC regions studied here. Thus, genome-wide association studies may be feasible in conifers whose genome sizes are generally large (Ohri and Khoshoo 1986), although it would be difficult to locate the causal polymorphism if LD is extensive (Atwell et al 2010). Nevertheless, identifying Table S1).…”

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confidence: 99%

Extended Linkage Disequilibrium in Noncoding Regions in a Conifer, Cryptomeria japonica

et al. 2012

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We measured linkage disequilibrium in mostly noncoding regions of Cryptomeria japonica, a conifer belonging to Cupressaceae. Linkage disequilibrium was extensive and did not decay even at a distance of 100 kb. The average estimate of the population recombination rate per base pair was 1.55 · 10 25 and was ,1/70 of that in the coding regions. We discuss the impact of low recombination rates in a large part of the genome on association studies.

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Genome size in gymnosperms

Cited by 153 publications

References 26 publications

Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

Chromosome banding in the genus <i>Pinus</i> V. Fluorescent banding patterns in 16 diploxylon pines

Extended Linkage Disequilibrium in Noncoding Regions in a Conifer, Cryptomeria japonica

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