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

Abstract

BackgroundGermplasm 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.ResultsWe 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.ConclusionsWhole-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0663-6) contains supplementary material, which is available to authorized users.

Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication

“…Contrary to these expectations, our estimates of gene diversity in mango were lower than those from the only other comparable report. Sherman et al (2015) estimated gene diversity from transcriptome-derived single nucleotide polymorphism (SNP) markers in mango to have a median value of 0.28-0.43, roughly 1.5-2-fold higher than the average values calculated here. The explanation for this discrepancy is not immediately clear; however, more recent empirical work indicates that missing data may not inflate diversity indices in empirical datasets as much as was proposed initially (Hodel et al, 2017).…”

“…(), both of which used microsatellite markers, found Southeast Asian mango cultivars to be the most differentiated from other populations, whereas Sherman et al . () found population structure between Asian and Western mango cultivars using single nucleotide polymorphisms (SNPs).…”

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

“…These unigenes were used for BLASTX-algorithm based searches and annotations against the protein databases Nr, SwissPort, COG, KEGG, and GO. In total, 24,911 unigenes (34.62%) were annotated in sugar apple, which is much smaller than other fruit trees, such as pineapple (58.33%), mango (85%), and loquat (70.57%), and similar to the number annotated in manchurian walnut (39.92%) and “Bartlett” pears (32.8%) (Gong et al, 2015; Nham et al, 2015; Sherman et al, 2015; Hu et al, 2016; Liu and Fan, 2016). This indicated that the functions of a large portion of the genes of sugar apple have not yet been identified.…”

The Role of 1‐Methylcyclopropene in the regulation of ethylene biosynthesis and ethylene receptor gene expression in Mangifera indica L. (Mango Fruit)

“…Mango is a fruit with a great market value. However, the storage life of mango is short (Sherman et al, 2015). Although mangos are harvested in the mature-green stage, they ripen quickly and often decay while being traded (Lalel, Singh, & Tan, 2003).…”