Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome

Abstract

Background: Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers.

Results: We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background.

Conclusions: Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.

Fig. 1

Distribution of contig lengths and comparison with two published mango transcriptomes. The distribution of contig lengths from three assemblies was plotted: Leaf (a), Peel (b), and Pooled (c) of tissues. The distribution of consensus contig lengths is drawn as 100-bp long bins

Fig. 2

Comparison of mango gene ontology categories in three transcriptome assemblies. Contigs were annotated by running blast search against ‘nr’ database and then performing mapping to Slim-GO categories by Blast2GO. The distribution of contigs of the three ontologies, biological processes, molecular functions, and cellular components was plotted for transcripts that were included exclusively in the transcriptome from the pool (Pool only) of tissues (root, leaf, flower and fruit developmental stage 3; turquoise bars)

Fig. 3

SSR length and motif distribution. The number of mono- to hexanucleotide SSR motifs was counted (a). The nucleotide compositions of the most frequent motifs (di- and trinucleotide motifs) were determined for each type and are illustrated in a bar plot for dinucleotide (b) and trinucleotide motifs (c). Motifs that are reverse-complementary were plotted as stacked bars: “plus strand” (red) and “minus strand” (green)

Fig. 4

Dendrogram and genetic structure of 74 accessions in the Israeli mango germplasm collection. Genotyping of 74 mango accessions from the Israeli mango collection was performed with 239 SNPs. The genotyping results were used to classify the accessions into sub-populations and reveal their genetic structure. a Classification was performed by drawing a dendrogram based on 1- proportion of shared alleles (PSA) as a genetic distance. Only confident branches with bootstrap values ≥90 were assigned. The two major groups are notated as subpopulation 1 (SP1) and as subpopulation 2 (SP2). b Genetic structure was revealed by STRUCTURE program with K = 2 as found by simulation and ΔK likelihood method. The division of STRUCTURE’s Q-value bar plot into two (vertical blue line) corresponds to the two major significant clusters in the dendrogram. Note that the Y-axis (not plotted) scale is between 0 and 1 and represents proportion