Genome size variation in Corchorus olitorius (Malvaceae s.l.) and its correlation with elevation and phenotypic traits

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L

Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals.

Altitudinal Patterns in Adaptive Evolution of Genome Size and Inter-Genome Hybridization Between Three Elymus Species From the Qinghai–Tibetan Plateau

Genome size variation and hybridization occur frequently within or between plant species under diverse environmental conditions, which enrich species diversification and drive the evolutionary process. Elymus L. is the largest genus in Triticeae with five recognized basic genomes (St, H, P, W, and Y). However, the data on population cytogenetics of Elymus species are sparse, especially whether genome hybridization and chromosomal structure can be affected by altitude are still unknown. In order to explore the relationship between genome sizes, we studied interspecific hybridization and altitude of Elymus species at population genetic and cytological levels. Twenty-seven populations at nine different altitudes (2,800–4,300 m) of three Elymus species, namely, hexaploid E. nutans (StHY, 2n = 6x = 42), tetraploid E. burchan-buddae (StY, 2n = 4x = 28), and E. sibiricus (StH, 2n = 4x = 28), were sampled from the Qinghai–Tibetan Plateau (QTP) to estimate whether intraspecific variation could affect the genomic relationships by genomic in situ hybridization (GISH), and quantify the genome size of Elymus among different altitude ecological groups by flow cytometry. The genome size of E. nutans, E. burchan-buddae, and E. sibiricus varied from 12.38 to 22.33, 8.81 to 18.93, and 11.46 to 20.96 pg/2C with the averages of 19.59, 12.39, and 16.85 pg/2C, respectively. The curve regression analysis revealed a strong correlation between altitude and nuclear DNA content in three Elymus species. In addition, the chromosomes of the St and Y genomes demonstrated higher polymorphism than that of the H genome. Larger genome size variations occurred in the mid-altitude populations (3,900–4,300 m) compared with other-altitude populations, suggesting a notable altitudinal pattern in genome size variation, which shaped genome evolution by altitude. This result supports our former hypothesis that genetic richness center at medium altitude is useful and valuable for species adaptation to highland environmental conditions, germplasm utilization, and conservation.

Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem

The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.

Sympatric genome size variation and hybridization of four oak species as determined by flow cytometry genome size variation and hybridization

The Quercus species serve as a powerful model for studying introgression in relation to species boundaries and adaptive processes. Coexistence of distant relatives, or lack of coexistence of closely relative oak species, introgression may play a role. In the current study, four closely related oak species were found in Zijinshan, China. We generated a comprehensive genome size (GS) database for 120 individuals of four species using flow cytometry-based approaches. We examined GS variability within and among the species and hybridization events among the four species. The mean GSs of Q. acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata were estimated to be 1.87, 1.92, 1.97, and 1.97 pg, respectively. The intraspecific and interspecific variations of GS observed among the four oak species indicated adaptation to the environment. Hybridization occurred both within and between the sections. A hybrid offspring was produced from Q. fabri and Q. variabilis, which belonged to different sections. The GS evolutionary pattern for hybrid species was expansion. Hybridization between the sections may be affected by habitat disturbance. This study increases our understanding of the evolution of GS in Quercus and will help establish guidelines for the ecological protection of oak trees.

Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip

Genome size (GS) was proposed as proxy for gross phenotypic and environmental changes in plants. GS organismal complexity is an enigma in evolutionary biology. While studies pertaining to intraspecific GS variation are abundant, literatures reporting the adaptive significance of GS are largelymissing. During food shortage, Brassica rapa var. rapa (turnip) is used as food and fodder for sustaining the livelihood of residents in the Qinghai Tibetan Plateau (QTP), which is also known as “the roof of the world”. Thus, climatic extremities make this region a natural environment to test adaptive significance of GS variation in turnip landraces. Therefore, from the QTP and its adjacent regions (the Hengduanshan and the Himalayas), we investigated adaptive evolution of GS in turnip landraces. Tuber diameter of turnip landraces was found to be significantly correlated with most of the environmental factors. GS was also shown not to be associated with morphological traits, temperature, and precipitation. Moreover, principal component analyses based on the whole dataset trisected the landraces into three distinct populations based on landrace usage—Hengduanshan, QTP, and the Himalayas. Nonetheless, our cumulative dataset showed evidence of adaptation of turnip landrace to different environments throughnonassociated genomic and phenomic plasticity.

DNA barcoding to promote social awareness and identity of neglected, underutilized plant species having valuable nutritional properties

It is estimated that about 7000 plant species and a large number of cultivars and varieties have been cultivated for consumption in human history. However, <0.5% of these currently provide the majority of human food energy needs worldwide (e.g., rice, wheat, maize, and potato). Global issues such as climate change, diffusion of pests, and resistance to agrochemical treatments are posing great concern about the sustainable cultivation of these major staples, especially in equatorial and tropical countries, such as Sub Saharan Africa. In addition, most of these regions contain malnutrition and micronutrient deficiencies, and the sum of such problems create serious implications at social, political, and economic levels. A possible solution relies on the exploitation of plant biodiversity and particularly on the so-called NUS (Neglected and Underutilized Species). These plants are traditionally grown in their centres of origin and continue to be maintained by sociocultural preferences, however they remain inadequately documented and neglected by formal research and conservation programs. Although they are important in terms of micronutrients and the ability to grow in harsh conditions, these species are falling into disuse due to agronomic, genetic, economic, and cultural reasons. To promote and spread their cultivation at the global scale, along with knowledge on their suitability for human nutrition, reliable identification systems are necessary to guarantee adequate authenticity along the entire supply chain and distribution network. A precise identification of the different species and their varieties is fundamental both to retrieve information on their origin and authenticate the raw materials (i.e., seeds, leaves and fruit) and related processed products that can be distributed at the local or global scale. DNA-based techniques can help achieve this mission. In particular, the DNA barcoding approach has gained a role of primary importance due to its universality and versatility. Here, we discuss the advantages in using DNA barcoding for the identification of some of the most representative NUS species, as well as their traceability and conservation of cultural practices around them.

Using k-NN to analyse images of diverse germination phenotypes and detect single seed germination in Miscanthus sinensis

BACKGROUND

Miscanthus is a leading second generation bio-energy crop. It is mostly rhizome propagated; however, the increasing use of seed is resulting in a greater need to investigate germination. Miscanthus seed are small, germination is often poor and carried out without sterilisation; therefore, automated methods applied to germination detection must be able to cope with, for example, thresholding of small objects, low germination frequency and the presence or absence of mould.

RESULTS

Machine learning using k-NN improved the scoring of different phenotypes encountered in Miscanthus seed. The k-NN-based algorithm was effective in scoring the germination of seed images when compared with human scores of the same images. The trueness of the k-NN result was 0.69-0.7, as measured using the area under a ROC curve. When the k-NN classifier was tested on an optimised image subset of seed an area under the ROC curve of 0.89 was achieved. The method compared favourably to an established technique.

CONCLUSIONS

With non-ideal seed images that included mould and broken seed the k-NN classifier was less consistent with human assessments. The most accurate assessment of germination with which to train classifiers is difficult to determine but the k-NN classifier provided an impartial consistent measurement of this important trait. It was more reproducible than the existing human scoring methods and was demonstrated to give a high degree of trueness to the human score.

Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)

Background and Aims

Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus.

Methods

Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa.

Key Results

The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra.

Conclusions

The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages.

Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae)

The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA⁺/DAPI⁻ bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

Comparative genomics of two jute species and insight into fibre biogenesis

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production¹. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species² in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae)

BACKGROUND AND AIMS

The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification.

METHODS

A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling.

KEY RESULTS

Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species.

CONCLUSIONS

The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.

Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

BACKGROUND AND AIMS

Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x-8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation.

METHODS

The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables.

KEY RESULTS

The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group.

CONCLUSIONS

Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different evolutionary origins of cytotypes via hybridization of parental combinations with different genome sizes in the south-western and south-eastern part of Europe, introgression between cytotypes, and antropic dispersal. The role of broad-scale and fine-scale environmental variables in shaping genome size is probably of minor importance in A. oleraceum.

Development of SSR markers and construction of a linkage map in jute

Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.