Critical review maps cytogenetic variation and data gaps in Indian Allium taxa

A critical review in Comparative Cytogenetics consolidates published cytogenetic evidence for Allium species occurring in India, finding a predominant basic chromosome number of eight alongside variation in ploidy, nuclear genome size, chromosome morphology, ribosomal DNA sites and telomeric sequence. The authors describe the work as a literature compilation rather than a new genome-wide survey and emphasize that the assembled dataset is not exhaustive.

The review considers approximately 33 species for which chromosome counts are known and about 25 for which karyotype details are available, within a flora of roughly 35–40 Allium species reported from India. Its sources include original publications, chromosome atlases, the Database on Genome-Related Information of Indian Plants, the Index to Plant Chromosome Numbers, the Chromosome Counts Database, the Plant DNA C-values Database and the Plant rDNA Database. The compilation covers taxon distribution, chromosome numbers, ploidy, karyotypes, nuclear genome sizes and molecular cytogenetic reports, while retaining current taxonomic designations for synonyms.

Indian Allium flora is represented in nine subgenera: Cepa, Allium, Amerallium, Reticulatobulbosa, Polyprason, Anguinum, Butomissa, Melanocrommyum and Rhizirideum. Many species occupy temperate mixed forests or rocky slopes at elevations of 1,200–5,480 metres in the western Himalayas. Others occur in north-eastern hill habitats or at wild and semi-wild sites in the eastern and western Himalaya. Endemic examples include Allium gilgiticum, which is listed as endangered, Allium stracheyi and the recently described Allium negianum.

Across the Indian taxa, x=8 is the prominent basic chromosome number regardless of subgenus, section or distribution pattern. Divergent basic numbers of x=7, 10 and 11 occur in Indian members of Amerallium, which the review notes is consistent with recognition of that group as a separate subgenus. The greatest reported variation in ploidy occurs in A. tuberosum, A. przewalskianum, A. chinense, A. rubellum, A. ampeloprasum and A. griffithianum. Polyploidy has been reported in almost all subgenera, but the available data are insufficient to assess a correlation between chromosome size and ploidy across the full Indian flora.

Reported nuclear genome sizes differ substantially despite the predominant basic number of eight. Among diploid species, values range from 7.8 pg/1C in A. schoenoprasum to 30.0 pg/1C in A. sativum. For polyploid taxa, the reviewed range extends from 15.16 pg/1C in A. schoenoprasum to 40.5–41.78 pg/1C in A. victorialis, with A. chitralicum reported at 34.35 pg/1C. The compilation combines values produced through different published methods, and the authors state that the dataset is not exhaustive.

Chromosome-count and karyotype information remains unavailable for several taxa, including A. negianum, A. loratum, A. auriculatum, A. rhabdotum and A. gilgiticum. Meiotic studies have reported multivalents, univalents and occasional irregularities in A. chinense, A. hookeri, A. roylei, A. rubellum and A. tuberosum. In contrast, tetraploid A. ampeloprasum has regularly shown 16 bivalents without multivalents, together with localized pericentromeric chiasmata. The authors note that the recorded incidence of vivipary and hybridization in onion makes fuller meiotic analysis of agriculturally important species such as A. cepa and A. sativum a significant subject for future revision.

The reviewed karyotypes are characterized mainly by metacentric chromosomes, whereas Amerallium species predominantly possess submetacentric chromosomes. A. atrosanguineum, A. carolinianum, A. griffithianum and A. fasciculatum show a tendency toward asymmetry. Ribosomal DNA sites vary in number and position among species, populations and cultivars. In onion, conventional staining and C-banding commonly identified two satellite chromosomes, while silver staining showed one to four active nucleolus organizer regions and 45S rDNA hybridization showed two to five sites. Garlic has recorded secondary constrictions on two to six chromosomes.

A key distinction between the subgenera Allium and Cepa is the position of nucleolus organizer regions: the review reports them as interstitial in Allium and distal in Cepa, supported by heterochromatic CMA banding, Ag-NOR staining and rDNA fluorescence in situ hybridization. Allium also possesses the distinctive telomeric repeat sequence (TTATGGGCTCGG)n, which differs from both the Arabidopsis-type TTTAGGG and human-type TTAGGG sequences. Conservation of this sequence across the genus has been cited as supporting a monophyletic origin for Allium.

Tyramide-FISH and the SteamDrop protocol have enabled physical mapping of genes including bulb alliinase, chalcone synthase and expressed sequence tag markers. The bulb alliinase gene was located on the long arm of chromosome 4 in A. cepa and A. schoenoprasum, but on its short arm in several related and more distantly related species. These observations underpin a proposed pericentric-inversion model for chromosome 4 rearrangements. Overall, the review identifies missing chromosome and karyotype information, population-level variation and molecular evidence from wild and endemic Indian species as limitations of the present evidence base, despite the crop importance of onion and garlic and the diversity of Himalayan Allium in India.

Subject of Research: Cytogenetic variation and knowledge gaps among Allium species occurring in India

Article Title:  Allium cytogenetics: a critical review on the Indian taxa

Article References: Bhowmick, B. K., Sarkar, S., Roychowdhury, D., Patil, S. D., Lekhak, M. M., Ohri, D., Rama Rao, S., Yadav, S. R., Verma, R. C., Dhar, M. K., Raina, S. N., & Jha, S. (2023). Allium cytogenetics: a critical review on the Indian taxa. Comparative Cytogenetics, 17, 129-156. https://doi.org/10.3897/compcytogen.17.98903

Image Credits: AI Generated

DOI: 10.3897/CompCytogen.17.98903

Keywords: Allium, cytogenetics, Indian flora, chromosome counts, ploidy, genome size, karyotypes, ribosomal DNA, Himalayan plants, critical, review, Indian