The study by Thakur et al. [24] highlighted that there exist batch-to-batch variations in medicine lots in the traditional Indian medicine system known as Ayurveda, causing distrust in the effectiveness of the traditional medicines. The authors looked into a popular medicinal plant, Tinospora cordifolia, known as ‘Giloy’, and observed that this plant exists in two distinct morphotypes with significant differences in yield. Using various cytological techniques, such as flow cytometry for DNA quantification and cytogenetic and molecular analysis, they showed the somatic cells of morphotype 2 possess 1.5-fold more DNA than morphotype 1, as morphotype 2 carries a triploid chromosome number and morphotype 1, a diploid chromosome number and with DNA markers established T. cordifolia morphotype 1 as the maternal progenitor of the triploid cytotype. Further, the wild triploid Giloy cytotype characterized in this study exhibited significantly higher biomass. Hence, culturing this novel cytotype is expected to exhibit improved yield and minimize batch-to-batch variations commonly observed in Ayurvedic drugs due to unintentional mix-ups of plant types.

The research paper by Yamamoto and Mukai [28] focuses on yet another orphan crop, orchids. Orchids represent a diverse group of plants with stable genomes and diverse phenotypes with the ability to produce interspecific/intergeneric hybrids and polyploids by genetic crossing. These hybrids exhibit genomic flexibility. As the conventional method of studying genomic affinities based on chromosome pairing during meiosis remains a bottleneck for orchids, the authors developed a multi-color Genomic in situ Hybridization (GISH) method to visualize genomes of donor species to determine hybridization history in artificial hybrids. The authors also developed an immune-FISH method to study chromosomal distribution patterns of chromatin modifications, specifically histone methylation, acetylation, phosphorylation, and centromere-specific histone. The study revealed 5mC distribution differences among species and ploidy variants; for instance, intergenomic hybrids of species with large chromosomes and elevated ploidy levels exhibit enhanced methylation. The technical developments reported in this study will alleviate the limitation of the meiotic analysis and allow the development of means to analyze interspecific orchid hybrids with desirable floral patterns.

Likewise, in the research paper, Ji et al. [8] have dealt with a common problem of aberrant numerical variants or aneuploidy observed in cauliflower (Brassica oleracea L. var. botrytis) by developing assays that allow the identification of specific chromosomes. For this purpose, the authors developed two FISH procedures: (1) FISH painting with diagnostic repetitive DNA and (2) cross-species chromosome painting. The first method involved a five-color FISH with 5S rDNA, 45S rDNA, two centromere-specific repeats from B. rapa, CentBr1 and CentBr2, and a B. rapa BAC clone (KBrH092N02). The second strategy consists of FISH based on DNA probes of a related species used under relaxed stringency conditions to allow identification of the homoeologous loci. Since B. oleracea carries several chromosome rearrangements due to genome triplication, its genome differs from Arabidopsis; hence, the authors used a computation tool, MUMmer, to identify a set of BAC clones to identify B. oleracea chromosomes uniquely. Further, the authors highlighted the pros and cons of each method in identifying numerical aberrations in cauliflower populations.

In this direction, the manuscript by Doležel et al. [3] elaborated on chromosome flow sorting methods. These methods rely on sorting mitotic chromosomes based on their fluorescence and light scattering patterns as they rapidly move across a narrow liquid stream in a queue. Chromosome flow sorting was used in the past for karyotyping and allowed the detection of structural and numerical chromosome changes. The purified chromosomes were also used to study the three-dimensional chromosome organization at the nanometer scale. More recently, flow sorting was used extensively to isolate specific chromosomes that allow the targeted development of DNA markers and the construction of chromosome-specific DNA libraries, physical mapping, and draft genome sequencing.