What Is One Explanation For The Wide Discrepancies In Genome Sizes From Species To Species?
Genome size variation in the genus Avena
Abstruse
Genome size is an indicator of evolutionary distance and a metric for genome label. Here, nosotros written report authentic estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the boilerplate genome size of C genome diploid species (2C = ten.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this departure likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from iii hexaploid species with the ACD genome configuration had similar genome sizes (boilerplate 2C = 25.74 pg). Genome size was more often than not consequent inside species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality command for species identification in germplasm collections, especially in cases where diploid and polyploid species take similar morphology.
Résumé
La taille du génome est un indicateur de la distance évolutive et constitue un paramètre pour la caractérisation des génomes. Ici, les auteurs rapportent des estimés précis de la taille du génome chez 99 accessions appartenant à 26 espèces du genre Avena. Les auteurs montrent que la taille moyenne du génome chez les espèces diploïdes ayant un génome C (2C = 10,26 pg) est xv % supérieure à celui des espèces ayant united nations génome A (2C = 8,95 pg), et que cette différence explique vraisemblablement la progression dans la taille des génomes parmi les espèces tétraploïdes, où AB < AC < CC (en moyenne, 2C = 16,76, eighteen,60 et 21,78 pg, respectivement). Toutes les accessions des trois espèces hexaploïdes ayant une composition génomique ACD présentaient des tailles de génome comparables (en moyenne, 2C = 25,74 pg). La taille du génome était généralement stable au sein d'une espèce, et conforme aux connaissances actuelles en ce qui a trait aux distances évolutives entre elles. Les résultats suggèrent également que la plupart des espèces polyploïdes du genre Avena ont connu une réduction de la taille du génome par rapport aux espèces diploïdes ancestrales. Les mesures de la taille du génome pourraient fournir une source additionnelle de contrôle de qualité lors de 50'identification des espèces au sein de collections de ressources génétiques, particulièrement dans les cas où des espèces diploïdes et polyploïdes présentent une morphologie semblable. [Traduit par la Rédaction]
Introduction
The genus Avena of the family Poaceae (Gramineae) is comprised of approximately xxx species (Baum 1977; Baum and Fedak 1985a, 1985b; Ladizinsky 1998) including iii natural ploidy levels (diploid, tetraploid, and hexaploid) with 7 basic haploid chromosomes (Rajhathy and Morrison 1959; Rajhathy and Thomas 1974; Thomas 1992). The diploid species take either an A or C genome, while tetraploid species have an Air-conditioning or AB genome and hexaploid species an ACD genome. There are no described diploid species with the B or D genome, although some oat workers accept postulated A. canariensis is a candidate D genome. Based on cytogenetic testify, both the D genome (Rajhathy and Thomas 1974) and B genome (Katsiotis et al. 1997) are highly similar to the A genome. All species of Avena except for A. macrostachya, a perennial out-crossing oat, are self-pollinated annuals.
The virtually usually cultivated oat is A. sativa L., a hexaploid species. It is an important cereal crop for both feed and homo consumption with global production that ranks 6th amongst cereal crops (Ahmad et al. 2014). Increased oat consumption is often promoted due to nutritional attributes, including antioxidants and high soluble fiber (Rasane et al. 2015). The genus Avena is considered to be an of import genetic pool for oat improvement (Loskutov and Rines 2011), and many alleles conferring disease resistance take been introgressed from wild oat germplasm into cultivated oat (Thomas et al. 1975; Rooney et al. 1994). Other traits such as plant height (Frey 1991) and spikelet number (Loskutov and Rines 2011) show potentially useful genetic variation in wild oat species.
Utilization of the rich genetic diversity in wild oat relatives would be facilitated by better knowledge of genome structure and relationships among these species. Genome size is a basic and important metric that can provide insight into the evolutionary history of a species. Genome size is commonly measured using the C-value, defined equally the Deoxyribonucleic acid mass in picograms (pg) within an united nations-replicated gametic nucleus (Greilhuber et al. 2005); thus the 2C value represents the weight of an entire somatic nucleus, regardless of ploidy level. The Kew Plant DNA C-value database (http://data.kew.org/cvalues/) is a widely used resource that incorporates many historic and electric current estimates of genome size. As of the concluding release, the Kew database holds C-value estimates from more than 8500 found species (Bennett and Leitch 2012).
Historically, and in the Kew database, genome size was well-nigh commonly estimated using the technique of Feulgen microdensitometry (McLeish and Sunderland 1961). Still, this arroyo is laborious and boring (Doležel et al. 2007). Since the development of menstruation cytometry in the 1980s, and due to its increased convenience, speed, and accuracy, menstruation cytometry has go the ascendant method used in genome size estimates (Doležel et al. 2007; Greilhuber et al. 2007). Based on electric current results in Kew Found Deoxyribonucleic acid C-values database (release half-dozen.0, December 2012) described past Bennett and Leitch (2012), 57% of C-values have been estimated by catamenia cytometry while 37% have been estimated using Feulgen microdensitometry. In the nearly recent literature, 85% of genome size estimates were fabricated using flow cytometry versus xv% past microdensitometry (Bai et al. 2012).
Genome size is constant within an individual, and usually inside a species (Lysák et al. 2000; Greilhuber 2005), although there are notable exceptions such equally flax (Linum usitatissimum) where rapid evolution of genome size causes variation of up to 15% amidst accessions within the species (Cullis 2005). However, genome size can vary over several orders of magnitude in eukaryotes (Bennett and Leitch 2005; Pellicer et al. 2010a). In Angiosperms, 2C values range from 0.thirteen pg in Genlisea aurea (Greilhuber et al. 2006) to 304.4 pg in Paris japonica (Pellicer et al. 2010b). Even amidst species having the same ploidy level within a single genus, genome size can differ by >xl-fold (Bennett and Leitch 2012). Molecular investigations accept shown that changes in repetitive DNAs such as retrotransposon and satellite DNA (Piegu et al. 2006), as well as depression-abundance repeat-derived Dna (Kelly et al. 2015), are responsible for some of the more substantial differences in genome size observed amidst related species.
Genome size can have profound furnishings on many aspects of found biology. For example, variations in genome size are related to phenotypic traits such every bit leaf size (Sugiyama 2005), leaf architecture and metabolic rates (Beaulieu et al. 2007a), seed mass (Beaulieu et al. 2007b), and prison cell size (Henry et al. 2014). Genome size can likewise be associated with adaptation to environmental weather (Kang et al. 2014) and related phenology such every bit weediness and lifecycle (Leitch and Bennett 2007). Genome size has been used as an indicator for taxonomic and evolutionary studies. For example, in wild peanuts, it is believed that larger genome size is associated with species having more recent origin (Lavia and Fernández 2008). A combination of genome size, morphologic traits, and SSR markers provided robust evidence in back up of the taxonomy and development of the genus Miscanthus (Chae et al. 2014). In addition, an accurate estimate of genome size provides critical information for genome sequencing and for the calibration of genetic maps (Leitch and Bennett 2007; Ochatt 2008).
Genome size has been estimated in 16 species of Avena (Bullen and Rees 1972; Iiyama and Grant 1972; Bennett and Smith 1976; Crosby et al. 2014) excluding iii that are considered to be homotypic with others in the Kew database (Baum 1977). Nigh estimates in the Kew database were provided by Bennett and Smith (1976) who made additional estimates and attempted to calibrate these with prior estimates. However, some apparent discrepancies and uncertainties amid early estimates that were based on Feulgen microdensitometry remain in the Bennett and Smith (1976) publication, and therefore in the Kew database. For instance, the Kew database provides very different estimates (eight.0 vs. x.ii pg) for 2 closely related species with similar A genomes: A. strigosa and A. wiestii, respectively. At that place is as well substantial and unexpected variation in C-value estimates among the species having ACD genomes. Recent estimates based on multiple accessions of A. barbata propose that its genome size is approximately 16.2 pg (Crosby et al. 2014), which differs substantially from the reported value of 17.8 pg in Kew. Some discrepancies may be due to variable methodologies and to lack of appropriate internal standards, but information technology is also notable that the works prior to and including 1976 investigated an average of simply two accessions per species, counting an average of just 45 nuclei per replicate. Furthermore, C-value estimates for many of the 30 species of Avena described past Baum (1977), Baum and Fedak (1985a, 1985b), and Ladizinsky (1998) take non been reported. A thorough reassessment of genome sizes in all species of Avena using electric current flow cytometric methodology would provide a critical criterion for further genome assay, including studies of speciation and genome evolution.
The objectives of the nowadays study were to provide accurate estimates of genome size for 26 available species of Avena using multiple accessions per species, to evaluate intra- and interspecific genome size variation, to explore possible evolutionary models of genome size in Avena, and to evaluate flow cytometry equally a diagnostic tool for use in Avena germplasm characterization.
Materials and methods
Found materials
A total of 99 accessions of Avena, including 14 diploid species, viii tetraploid species, and 4 hexaploid species, were used in this study (Tabular array S11), with at least three accessions per species when adequate viable accessions were available. Seeds were provided by Plant Cistron Resources of Canada (PGRC) or USDA-Grinning when non bachelor in PGRC. The species A. matritensis, A. atherantha, A. hybrida, and A. trichophylla described in Baum'due south (1977) monograph and A. prostrata described by Ladizinsky (1971) were not included due to lack of viable materials, and species that we considered to be homotypic are noted in Table 1.
Tabular array 1.
a
Species that are considered in this work to be homotypic include the post-obit: A. nudi-brevis (=A. nuda), A. pilosa (=A. eriantha), A. magna (=A. maroccana), A. ludoviciana (=A. sterilis), and A. byzantina (=A. sativa). The incorrect utilize of A. nuda to refer to a hulless hexaploid species has been corrected to the accustomed classification inside A. sativa.
b
Comparison amongst species was performed based on accessions every bit biological replicates, except for A. murphyi where but 1 viable accession was bachelor and multiple plants were grown instead. For A. macrostachya, merely one viable institute was available and statistical inferences were non made.
c
Species followed by identical lowercase messages are not significantly different at α = 0.05, based on an unadjusted Fisher'southward least significant difference (LSD) test.
d
Species followed by identical lowercase messages are not significantly different at α = 0.05, based on an unadjusted Tukey's honest significance departure (HSD) test.
eastward
The characters V and P stand for the internal reference standard species Vicia faba and Pisum sativum, respectively.
f
Avena insularis has occasionally been designated CD (e.g., Loskutov 2008). Although this constitution has non been substantiated, the similarity between A and D genomes remains a potential source of revision.
Sample grooming
Accessions and standards were grown in cabinets. Internal standards were selected based on appropriate not-overlapping genome size and availability of self-pollinated seed from contempo definitive work (Doležel et al. 1992). Seed of Vicia faba (26.90 pg/2C) originating from Doležel et al. (1992) was used as the internal standard for diploid species and tetraploid species, and seed of Pisum sativum (9.09 pg/2C) originating from Doležel et al. (1998) was used for hexaploid species. Seed from both standards was supplied by The Center of Establish Structural and Functional Genomics (Šlechtitelů 31, 783 71 Olomouc - Holice, Czech republic). Fresh leaf tissue was harvested from immature plants and kept on water ice until assays were conducted, unremarkably inside three days. A leaf surface area of approximately 0.5 cm2 of standard and 2 cmii of Avena species were co-chopped with a razor blade for about 2–iv s in a petri dish containing 0.75 mL ice-cold LB01 chopping buffer (Doležel et al. 2007). The buffer was and so homogenized past several repeated pipette actions, and the solution was passed through 30 μm Celltrics nylon filters (Sysmex, Lincolnshire, Ill., USA) into 5 mL round-bottom Falcon tubes (Corning, New York, N.Y., USA). A volume of 0.25 mL (100 μg/mL) propidium iodide (PI) staining buffer was and so added and mixed by gentle shaking. Samples were incubated with the staining solution at four °C for 30 min prior to period cytometry. Samples from both standards were co-chopped and analyzed on each twenty-four hour period on which samples were analyzed for final aligning to a single standard.
Flow cytometry analysis
Flow cytometry was performed using a Beckman Coulter (Miami, Fla., USA) Gallios catamenia cytometer. The positions of peaks and the distributions of nuclei were estimated using Modfit LT version 4.0 (Verity Software Firm, Topsham, Maine, U.s.). Several samples were initially tested with >5000 nuclei to evaluate the coefficient of variation among nuclei (CVn) where CVn = SD/M, SD is the standard departure of the cell distribution, and G is the mean channel number (Ormerod and Novo 2008). If the CVn value of a sample or standard was more 5%, further estimates were done until chopping techniques were optimized and the CVn values were consistently less than 5%. Near samples were then estimated with total nuclei numbers (including sample and internal standard) exceeding 1500. Some results with good quality (modest CVns and good peak shape) were kept even if nuclei counts were less than 1500 but not less than 1000. All samples were analyzed with at least three replicates of the aforementioned individual (technical replicates) conducted over three different days. The formula used to calculate the absolute 2C value of each sample was (mean of sample G1 top/mean of standard G1 peak) × 2C DNA content (pg) of the standard. Since two internal standards were used in this study, we used P. sativum as standard to calculate the 2C values of V. faba based on the average of each cess.
Statistical analysis
The residuals from a model plumbing equipment means by accession were used to monitor homogeneity of variance, and the average coefficient of variance (CVt), calculated equally the standard divergence of residuals divided by thou mean, was estimated. A nested analysis of variance (ANOVA) testing replicates within accessions within species within genomes within ploidy-levels was conducted using REML in the SPSS software (IBM, Armonk, N.Y., USA). Differences among species, considering accessions every bit replicates, were tested using one-way ANOVA followed by multiple comparison using Fisher'due south least significant departure (LSD) test and Tukey'due south honest significance difference (HSD) test within the package agricolae in R.
Results
All measured values were calibrated to the published value of the P. sativum standard (9.09 pg/2C). After adjustment, the average 2C value of V. faba based on 29 technical replicates was 26.82 ± 0.44 pg, which is very shut to the published value of 26.9 pg (Doležel et al. 1992). The average genome sizes (2C) of 99 accessions of Avena were estimated (Tabular array S11), and information were summarized past species (Table 1). All of the menses cytometric analyses generated high-resolution histograms (e.g., Fig. 1) with CVdue north of the G0/G1 peaks ranging from 1.14% to iii.80% (mean two.14%). The average CVt among technical replications on separate days was i.25%, which was lower than previous reported variation (1.53%) in diploid species of Triticeae (Eilam et al. 2007). The mean 2C values of individual accessions varied 3.one-fold, ranging from 8.41 to 26.24 pg. The residuals of a model fitting the accession mean to each sample were inspected in relation to this large progression in genome size (Fig. S11), and it was concluded that there was no systematic bias in variance in relation to genome size. Thus statistical methods bold equality of variance were used in further analyses. The box plot of genome size by species (Fig. 2) suggested that size variation within species is minimal and that accessions were correctly assigned to species.
Fig. 1.
Fig. 2.
The nested ANOVA (Tabular array 2) revealed that significant variance tin exist attributed to all levels of our sampling blueprint. The differences between ploidy levels were highly significant, as expected, but there was also substantial variation among genome types with the aforementioned ploidy, as well equally meaning variation among species with the same genome type. Variation amongst accessions within a species, though actualization meaning by this test, was the smallest component of the variance. Because technical replicates conducted on different days were sampled from the same plants, they cannot exist considered independent samples of individuals within accessions. Variance among individuals may likewise exist attributable to differences amongst plants, such as differences in the presence of dye inhibitors (Greilhuber 2005; Bennett et al. 2008). Thus, we were non able to infer true statistical differences amongst accessions, and this test is presented primarily as guidance to the relative scales of variance. Variance among technical replicates was substantially larger than the variation among accessions, and comparable to the variance among species within genome types.
Table 2.
a
Ploidy is a stock-still factor with three levels (diploid, tetraploid, and hexaploid) and ii degrees of freedom (df). Remaining factors are considered random (as required to judge variance components of a nested design) with df equal to one less than the number of observed levels minus the df used in the preceding level. For example, the 10 genome levels (As, Ac, Advertising, Al, Cp, Cv, AB, AC, CmCm, and ACD) within three ploidy levels leaves 7 df.
b
The significance exam of accessions is not entirely valid because technical replicates, which form the mistake term, were non randomly assigned. This variance ratio and significant test are reported as guidance to the scale of variance components.
c
Variance components were estimated by REML in SPSS. A parallel analysis using the package nlme in R gave similar results.
The highly significant exam showing variance among species justified further inspection of species means by LSD and HSD, both performed at P < 0.05 (Tabular array 1). Average values by ploidy level were 9.23, xviii.08, and 25.74 pg for diploid, tetraploid, and hexaploid species, respectively, and boundaries betwixt ploidy levels were all statistically separated. In addition, some groups of species inside ploidy levels were statistically separated. Near notably, the C genome diploids had higher C-values (≥10.18 pg) than all A genome diploids (≤9.23 pg), and tetraploids containing the Ac genomes (eighteen.51 to xviii.70 pg) had college C-values than those containing the AB genomes (16.38 to 17.49 pg), while the single CC genome tetraploid (21.78 pg) had a markedly higher C-value than any other tetraploid species. Furthermore, there were some significant differences amidst A genome diploid species as well equally amid AB genome tetraploid species. For example, the diploid A. damascena had a lower 2C value (viii.43 pg) than all other species, while A. agadiriana had a higher 2C value (17.49 pg) than other AB genome species. In that location were no significant differences among Air-conditioning genome tetraploid species, nor amid ACD genome hexaploid species.
Word
Reliability and completeness of genome size estimates in Avena
We consider these reported 2C values in 26 species, including 10 previously unreported species, to exist the most accurate and comprehensive genome size estimates in the genus Avena available to engagement. Variations among nuclei (CVn) and variations amid technical replications (CVt) were lower than, or comparable to, values found in current literature. Although genome sizes in 16 species of Avena have been reported previously (Table 3), all except for the recently published estimates in A. barbata (Crosby et al. 2014) were estimated by using Feulgen microdensitometry. While Bennett and Smith (1976) attempted to correct a bias in previous studies, virtually previous estimates were essentially college than those in the current report (Table 3). This may be an inherent bias due to the apply of early Feulgen microdensitometry, every bit suggested by Moscone et al. (2003), only it may also relate to the use in the electric current piece of work of consistent internal standards as recommended past Leitch and Bennett (2007). Fifty-fifty with internal standards, there may still be slight systematic differences among studies caused by variable experimental factors such every bit the presence of dye inhibitors in institute fabric (Greilhuber 2005; Bennett et al. 2008), which might alter the measured summit of the standard (analogous to shifting the scale on a ruler). Thus a set of estimates such as those provided here may prove high degree of relative accuracy, just they could differ slightly from estimates in other similarly controlled experiments. Importantly, the credible discrepancies among previous estimates (mentioned in our introduction) have now been resolved. This includes the large variation amidst previous estimates of closely related A genomes, and the discrepancy in prior estimates for A. barbata. It also resolves the large variation in prior estimates amidst the hexaploid ACD species, all of which are statistically identical in this work. While not a substantial revision from previous estimates, this work suggests that an appropriate guess for the haploid genome of A. sativa is 12.85 pg, which corresponds to 12 567 Mbp (1 pg = 978 Mbp) (Doležel et al. 2003).
Table three.
a
The species A. nudi-brevis, A. pilosa, and A. magna used in previous studies are synonymous to A. nuda, A. eriantha, and A. maroccana, respectively, according to Baum'due south (1977) monograph.
b
The 2C estimates exterior parentheses are absolute DNA contents re-calibrated by Bennett and Smith (1976). The values in parentheses were original data obtained from Bullen and Rees (1972).
c
The 2C values displayed were re-calibrated by Bennett and Smith (1976).
Intraspecific variation in genome size
We found very niggling variation of genome size amid accessions inside a species. This was the smallest component of total variance, and it was markedly smaller than the fault variance measured among technical replicates. This finding is consistent with measurements past Bullen and Rees (1972). The existence of intraspecific variation in genome size is controversial. Although numerous studies have reported intraspecific variation (Schmuths et al. 2004; Wang et al. 2009; Díez et al. 2013), it is more common to find stability within species (Lysák et al. 2000; Greilhuber et al. 2005; Eilam et al. 2007), and some perceived intraspecific variation may be explained past other factors such every bit endogenous staining inhibitors or other methodical noise (Greilhuber 2005; Noirot et al. 2005; Loureiro et al. 2006). Thus, our results are consistent with the concept of intra-species stability in genome size. This is of import, as the test for differences among species requires the assumption that accessions stand for random samples from a population having a normal distribution. Whatsoever non-random biological differences within a species (including the misidentification of an accession) could violate this assumption, reduce the power of detecting a difference, and (or) reduce the accuracy of estimating the species mean. Our results suggest that these factors and consequences are minimal.
A small variance amongst accessions was achieved partly through technical replication. Such replication may not exist necessary in all cases, depending on the goals of the study, simply when they are omitted, the associated error variance contributes to the perceived variation among individuals or accessions. For case, in A. barbata, we gauge the variance within and betwixt accessions at 0.017 and 0.009, respectively (standard deviations of 0.13 and 0.0976). Since variances are additive, if technical replicates were omitted, the apparent variance among accessions would be roughly 0.026. This is indeed comparable to the variance reported in A. barbata by Crosby et al (2014), who omitted technical replicates, every bit the initial goal of that study was to only verify ploidy. Thus, the broad range of estimates (15.99–sixteen.79 pg) reported in A. barbata by Crosby et al (2014) demand non imply intraspecific variation (Leitch and Bennett 2007; Bennett et al. 2008), and the contrast between native Old World and colonizing Californian A. barbata samples has yet to be verified in a strictly controlled comparing.
Interspecific variation in genome size
In contrast to intraspecific stability, numerous studies in plants have reported large variations in genome size among species within genera (Schmuths et al. 2004; Wang et al. 2009; Díez et al. 2013). Retro-elements and polyploidization are considered to be primary factors leading to the variations in genome size (Piegu et al. 2006; Grover and Wendel 2010). In this study, variation among ploidy levels was substantial, and was obviously driven past genome duplication, while variation inside ploidy levels was generally consistent with prior sub-genome designations. The 2C values of species with identical genomic constitutions were generally continuous with only small differences. This suggests that in that location have been no major events driving divergence inside a genome type, and this is consistent with observations in the related genera Triticeae (Eilam et al. 2007). Small only pregnant variations were detected, even among closely related diploids with identical sub-genome designations by the LSD exam. For instance, within the Asouth genome diploid species, the genome of A. lusitanica was significantly smaller (P ≤ 0.05) than all others except for A. hispanica, and it was close in size to the smallest Ad genome diploid A. damascena. Molecular evidence (Fu and Williams 2008; Peng et al. 2010; Yan et al. 2014) likewise showed that A. lusitanica was more closely related to A. damascena than to other As genome diploids. Yet, the differences between A. lusitanica and other Asouthward genome diploids were non judged pregnant past HSD, hence this outcome should be investigated further.
Most notably, our results showed that the C genome has a larger genome size than other sub-genomes. Based on averages inside the A and C genome diploids, the difference in size is approximately 15%. This difference was also observed by Iiyama and Grant (1972), although the large variation amid A genomes reported by these authors made this difference less hitting, and the average difference that they reported was closer to 10%. The apparent deviation between the A and C sub-genomes is supported by previous studies showing major cytogenetic differences between A and C genome chromosomes that are most likely due to differences in repetitive DNA content (Fominaya et al. 1988; Linares et al. 1992; Jellen et al. 1993). Within hexaploid species, the C genome contains a greater number of large heterochromatic regions than the A or D genomes (Fominaya et al. 1988; Linares et al. 1992; Jellen et al. 1993). In future work, it will be interesting to compare these variations in genome size with other genomic indicators of speciation.
Genome size as a diagnostic tool
Every bit species identification in Avena is difficult, it is possible to find misidentified accessions inside big genebank collections. Such misidentifications can result in wasted resources and erroneous scientific results. Some misidentifications can be corrected through morphological observation, simply this requires extensive field- or greenhouse-scale grow-outs, trained experts, and substantial investment in time. In contrast, flow-cytometric assays on seedlings are rapid and inexpensive, and these could be used to screen large collections in support of correct identification. This possibility was suggested through the piece of work of Crosby et al. (2014) in which unexpected variation in ploidy level was observed amongst accessions previously identified equally A. barbata. Hither, and elsewhere in the genus Avena (e.one thousand., A. sterilis vs. A. insularis), it appears that species having similar morphology only different ploidy levels is common. In such cases a single replication of flow cytometry would effectively identify errors. However, multiple replications together with a series of standard check varieties would be required to observe the smaller differences identified in this work. Catamenia cytometry could also exist used in parallel with high-throughput marker analysis, and it could alleviate anticipated problems in the apply of markers to distinguish among species that bear closely related sub-genomes in dissimilar combinations and ploidy levels.
Genome size reduction after polyploidization
The availability of tetraploid and hexaploid species together with their diploid progenitor genomes provided an opportunity to exam for additivity in the size of sub-genome components. Since diploid representatives of the B and D genomes are not known, but the genomes are considered to be similar to the A genome (Rajhathy and Thomas 1974; Leggett and Markhand 1995; Katsiotis et al. 1997; Shelukhina et al. 2008; Peng et al. 2010), the average A and C genome sizes of the diploids were used to model predicted polyploid genome sizes (Fig. 3). These predictions suggest that polyploid species have genome sizes similar to the sum of their putative genome progenitors, but that a systematic downsizing has occurred in all of the polyploid species except for the perennial tetraploid species A. macrostachya. An alternate (or boosted) explanation could be that the unknown B and D genomes are actually smaller than the observed A genomes. The hypothesis that the B genome is smaller than the A genome was put forrard past Iiyama and Grant (1972) for this reason, although this was also in support of a proposed AABBDD genome constitution for the hexaploid, which has been subsequently rejected. Polyploid genome downsizing has been observed in most angiosperms, and it is assumed to be a general trend (Kellogg and Bennetzen 2004; Pellicer et al. 2010a). The mechanisms leading to loss of the DNA in polyploids include diff homologous recombination (Bennetzen et al. 2005), not-homologous recombination (Devos et al. 2002), full general elimination of redundant DNA (Ozkan et al. 2003; Leitch and Bennett 2004), and specific elimination of indistinguishable genes (Renny-Byfield and Wendel 2014; Evans et al. 2015). Information technology is interesting that A. macrostachya, the only known perennial outcrossing species in Avena, appears to show the reverse trend (genome aggrandizement). Yet, an alternate explanation for this deviation in A. macrostachya could exist that the Cm genome differs substantially in size from the diploid C genomes observed in this study. It has been suggested that Cm is ancestral to the C genome type (Rodionov et al. 2005; Badaeva et al. 2010), and large differences in chromosome morphology and heterochromatin distribution have been observed in A. macrostachya relative to other C genome diploids (Hutchinson et al. 1986; Rodionov et al. 2005; Badaeva et al. 2010). Furthermore, symmetrical chromosomes, every bit well as large heterochromatic blocks, are more apparent in A. macrostachya than in other species of Avena. Thus, Badaeva et al. (2010) suggested that A. macrostachya formed via chromosome duplication from an ancestral C genome diploid that is no longer extant, and that this occurred prior to the formation of the present C and A genomes. Our results support this hypothesis, although other explanations cannot exist excluded at this stage.
Fig. three.
In decision, the genome sizes reported here for most of the recognized species in the genus Avena should provide consequent and reliable benchmarks to assistance in farther characterization of the evolutionary relationships among these important species. Furthermore, these estimates volition facilitate the planning and scale of hereafter mapping and genome sequencing efforts. It is fortunate that substantial multifariousness in the genus Avena has been preserved in many national germplasm collections, simply the number of accessions from some species is quite limited. Further characterization of diversity in the genus Avena is needed to inform time to come decisions on germplasm collection, conservation, and utilization.
Acknowledgements
Nosotros give thanks Paul Kron for expert communication regarding catamenia cytometry, and members of the Canadian and Usa Genebank teams for practiced assistance in maintaining and providing germplasm. This work was made possible by outstanding technical assistance from Charlene Wight and Kathie Upton. This piece of work was funded by an AAFC Ingather Genomics project. Funding for H.Y. was provided by a Prc Ministry of Pedagogy scholarship.
Footnote
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Volume 59 • Number 3 • March 2016
Editor: G. Jenkins
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Received: 2 October 2015
Accustomed: eighteen December 2015
Published online: 17 January 2016
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© 2016.
Key Words
- oat
- flow cytometry
- nucleus
- polyploidy
Mots-clés
- avoine
- cytométrie en flux
- noyau
- polyploïdie
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Honghai Yan, Sara L. Martin, Wubishet A. Bekele, Robert Grand. Latta, Axel Diederichsen, Yuanying Peng, and Nicholas A. Tinker. Genome size variation in the genus Avena. Genome. 59(3): 209-220. https://doi.org/10.1139/gen-2015-0132
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