Assessing diversity and phylogeny of Indonesian breadfruit (Artocarpus spp.) using internal transcribed spacer (ITS) region and leaf morphology

Abstract

Background: Breadfruit (Artocarpus spp.) is the main genus of Moraceae with multipurpose benefits, both ecologically and economically important, e.g., food ingredients, building materials, traditional medicine, and natural insecticides. However, most endemic Artocarpus have been threatened due to natural disasters and habitat degradation. The objective of our study was to determine the genetic diversity and relationships of endemic Artocarpus from South Borneo, Indonesia, using an internal transcribed spacer (ITS) region and leaf morphology.

Results: Morphologically, endemic Artocarpus endemic to South Borneo, Indonesia, has a different leaf shape, i.e., narrow-obovate to broad-elliptic, from simple to deeply dissected. Following the ITS region, this germplasm has a moderate level of nucleotide diversity (0.069). The phylogenetic analysis revealed Artocarpus into four (4) main clades, where the nearest is shown by the 'Puyian' (Artocarpus rigidus) and 'Binturung' (Artocarpus odoratissimus) at a coefficient divergence of 0.027, whereas the furthest by 'Kulur' (A. camansi) and 'Tiwadak' (A. integer) at a coefficient of 0.132.

Conclusion: In brief, although an endemic Artocarpus of South Borneo, Indonesia, has a moderate level of nucleotide diversity, this germplasm also shows a unique phylogenetic relationship. Thus, this information is urgent in supporting the future Artocarpus breeding and preservation programs, mainly to save this germplasm from being threatened.

Keywords: Breadfruit (Artocarpus spp.); Breeding and preservation; Genetic diversity; Nuclear DNA; Phylogenetic relationship.

Fig. 1

The map of South Borneo, Indonesia, shows the sampling location and the number of samples collected each. For more information about those samples, see Table 1

Fig. 2

Leaf morphology of endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia, shows two different forms, i.e., narrow-obovate to broad-elliptic, from simple to shallowly dissected. The name of each sample is provided in Table 1

Fig. 3

Multiple sequence alignments, showing two mutational events, i.e., substitutions and indels, from ITS sequence of endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia

Fig. 4

Nucleotide substitution patterns of endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia

Fig. 5

The secondary structures of the breadfruit (Artocarpus spp.) ITS sequence endemic to South Borneo, Indonesia, shows different forms. In this case, ‘Anjani’ (A. hirsutus) and ‘Tarap’ (A. sericicarpus) have similar

Fig. 6

The phylogenetic tree shows the grouping of endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia, into four main clades. Values and letters (nucleotides) on nodes indicate the bootstrap analysis 1000 times and possible ancestors, respectively

Fig. 7

Grouping of endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia, into five main groups based on principal component analysis (PCA)

Fig. 8

The heatmap shows the relationship among endemic breadfruit (Artocarpus spp.) from South Borneo, Indonesia, based on the coefficient divergence value. In this case, the lower the coefficient value, the closer the genetic relationship would be