Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas, Convolvulaceae) complex

Genome Size Variation in Sesamum indicum L. Germplasm from Niger

Sesamum indicum L. (Pedaliaceae) is one of the most economically important oil crops in the world, thanks to the high oil content of its seeds and its nutritional value. It is cultivated all over the world, mainly in Asia and Africa. Well adapted to arid environments, sesame offers a good opportunity as an alternative subsistence crop for farmers in Africa, particularly Niger, to cope with climate change. For the first time, the variation in genome size among 75 accessions of the Nigerien germplasm was studied. The sample was collected throughout Niger, revealing various morphological, biochemical and phenological traits. For comparison, an additional accession from Thailand was evaluated as an available Asian representative. In the Niger sample, the 2C DNA value ranged from 0.77 to 1 pg (753 to 978 Mbp), with an average of 0.85 ± 0.037 pg (831 Mbp). Statistical analysis showed a significant difference in 2C DNA values among 58 pairs of Niger accessions (p-value < 0.05). This significant variation indicates the likely genetic diversity of sesame germplasm, offering valuable insights into its possible potential for climate-resilient agriculture. Our results therefore raise a fundamental question: is intraspecific variability in the genome size of Nigerien sesame correlated with specific morphological and physiological traits?

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

Screening and optimisation of in vitro pollen germination medium for sweetpotato (Ipomoea batatas)

BACKGROUND

Sweetpotato is an important vegetable and food crop that is bred through sexual crosses and systematic selection. The use of in vitro germination of sweetpotato pollen to test its viability has important theoretical and practical implications for improving the efficiency of sweetpotato crossbreeding by controlling pollination and conducting research on sweetpotato pollen biology.

RESULTS

In this study, we observed the morphological structure of sweetpotato pollen under a scanning electron microscope (SEM), developed an effective method for the in vitro germination of sweetpotato pollen, and examined the viability of sweetpotato pollen after treating plants at different temperatures before blossoming. Sweetpotato pollen grains are spherical, with an average diameter of 87.07 ± 3.27 μm (excluding spines), with multiple germination pores and reticulate pollen surface sculpture. We applied numerous media to sweetpotato pollen germination in vitro to screen the initial medium and optimised the medium components through single-factor design. The most effective liquid medium for in vitro sweetpotato pollen germination contained 50 g/L Sucrose, 50 g/L Polyethylene glycol 4000 (PEG4000), 100 mg/L Boric acid and 300 mg/L Calcium nitrate, with a pH = 6.0. The optimum growth temperature for pollen development in sweetpotato was from 25 to 30 °C. Neither staining nor in situ germination could accurately determine the viability of sweetpotato pollen.

CONCLUSIONS

In vitro germination can be used to effectively determine sweetpotato pollen viability. The best liquid medium for in vitro germination of sweetpotato pollen contained 50 g/L Sucrose, 50 g/L Polyethylene glycol 4000 (PEG4000), 100 mg/L Boric acid and 300 mg/L Calcium nitrate, with the pH adjusted to 6.0. This study provides a reliable medium for the detection of sweetpotato pollen viability, which can provide a theoretical reference for sweetpotato genetics and breeding.

Pollen analysis using multispectral imaging flow cytometry and deep learning

Pollen identification and quantification are crucial but challenging tasks in addressing a variety of evolutionary and ecological questions (pollination, paleobotany), but also for other fields of research (e.g. allergology, honey analysis or forensics). Researchers are exploring alternative methods to automate these tasks but, for several reasons, manual microscopy is still the gold standard. In this study, we present a new method for pollen analysis using multispectral imaging flow cytometry in combination with deep learning. We demonstrate that our method allows fast measurement while delivering high accuracy pollen identification. A dataset of 426 876 images depicting pollen from 35 plant species was used to train a convolutional neural network classifier. We found the best-performing classifier to yield a species-averaged accuracy of 96%. Even species that are difficult to differentiate using microscopy could be clearly separated. Our approach also allows a detailed determination of morphological pollen traits, such as size, symmetry or structure. Our phylogenetic analyses suggest phylogenetic conservatism in some of these traits. Given a comprehensive pollen reference database, we provide a powerful tool to be used in any pollen study with a need for rapid and accurate species identification, pollen grain quantification and trait extraction of recent pollen.

Hazelnut Pollen Phenotyping Using Label-Free Impedance Flow Cytometry

Impedance flow cytometry (IFC) is a versatile lab-on-chip technology which enables fast and label-free analysis of pollen grains in various plant species, promising new research possibilities in agriculture and plant breeding. Hazelnut is a monoecious, anemophilous species, exhibiting sporophytic self-incompatibility. Its pollen is dispersed by wind in midwinter when temperatures are still low and relative humidity is usually high. Previous research found that hazelnut can be characterized by high degrees of pollen sterility following a reciprocal chromosome translocation occurring in some cultivated genotypes. In this study, IFC was used for the first time to characterize hazelnut pollen biology. IFC was validated via dye exclusion in microscopy and employed to (i) follow pollen hydration over time to define the best pre-hydration treatment for pollen viability evaluation; (ii) test hazelnut pollen viability and sterility on 33 cultivars grown in a collection field located in central Italy, and two wild hazelnuts. The accessions were also characterized by their amount and distribution of catkins in the tree canopy. Pollen sterility rate greatly varied among hazelnut accessions, with one main group of highly sterile cultivars and a second group, comprising wild genotypes and the remaining cultivars, producing good quality pollen. The results support the hypothesis of recurring reciprocal translocation events in Corylus avellana cultivars, leading to the observed gametic semi-sterility. The measured hazelnut pollen viability was also strongly influenced by pollen hydration (R adj 2 = 0.83, P ≤ 0.0001) and reached its maximum at around 6 h of pre-hydration in humid chambers. Viable and dead pollen were best discriminated at around the same time of pollen pre-hydration, suggesting that high humidity levels are required for hazelnut pollen to maintain its functionality. Altogether, our results detail the value of impedance flow cytometry for high throughput phenotyping of hazelnut pollen. Further research is required to clarify the causes of pollen sterility in hazelnut, to confirm the role of reciprocal chromosome translocations and to investigate its effects on plant productivity.

Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq

Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.