Deciphering genetic diversity phylogeny and assembly of Allium species through micro satellite markers on nuclear DNA

Abstract

The genus Allium is the most diverse, with cultivated crops such as onion, garlic, bunching onion, chives, leeks, and shallots, and several wild and semi-domesticated Allium species utilized as minor vegetables. These minor species are the genetic resources for various abiotic and biotic stresses. To employ underutilized species in breeding programmes, the magnitude of the genetic background of cultivated and semi-domesticated alliums, the phylogeny and diversity of the population must be known. In this study, nineteen SSR markers were employed to study the divergence and population structure of 95 Allium accessions which includes species, varieties, and interspecific hybrids, yielded 92 polymorphic loci, averaging 4.84 loci per SSR. PIC values range between 0.24 (ACM 018) and 0.98 (ACM 099). The cross transferability of ACM markers among Allium species ranges from 1.33 to 10.53 per cent, which is relatively low. The genotypes investigated were clustered into four primary clusters A, B, C, and D with 13 sub clusters I-XIII, conferring to the clustering results. The population structure investigations also found that K is a peak at value 4, implying that the population is predominantly segregated into four distinct groups, which associates the clustering pattern. The employed SSR markers adeptly unravel the complexities of diversity within alliums, holding promise for refining future breeding programs targeting elite progenies.

Keywords: Allium; Diversity; Molecular markers; Population structure; SSR; Wild species.

Fig. 1

Allium species maintained at National Active Germplasm Site for onion, garlic and allies, India a) Allium altaicum CGN14769, b) Allium angulosum EC32846, c) Allium cepa var. aggregatum, d) Allium chinense MMK130, e) Allium fistulosum EC461748, f) Allium hookeri NG3255, g) Allium macranthum NMK3227, h) Allium przewalskianum MMK110, i) Allium schoenoprasum NR6 NGB5969, j) Allium tuberosum MKG84 and l) Allium cepa var. Bhima Red.

Fig. 2

Genetic diversity of Allium species produced by SSR markers in MEGA11 software through Unweighted Pair Group Method with Average (UPGMA) based on the dissimilarity matrix developed from jaccard's similarity matrix generated through NTSYS-pc Version 2.02i.

Fig. 3

Structure results, comparison of ΔK values for Allium using SSR; the maximum value of ΔK at K = 4 was considered to be the appropriate number of populations.

Fig. 4

Bayesian grouping of the population represented by using a barplot (1–7: Allium altaicum, Allium angulosum and Allium cepa var aggregatum. 8–12: Allium chinensis. 13-27: Allium fistulosum. 28–32: Allium fragrans and Allium hookeri. 32–47: Allium macranthum. 48–54: Allium przewalskianum.55-56: Allium schoenoprasum. 57-78: Allium tuberosum. 79–81: Allium fistulosum × Allium cepa. 82–83: Allium sativum. 84-95: Allium cepa). *Same colours indicate the sharing of genome counterparts. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)