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Arumuganathan and Earle (1991) estimated that the nuclear DNA content of mango is only 0.91 pg. Because of their high level of polymorphism, DNA markers have greater usefulness than protein markers. There have been several studies on the use of molecular markers for taxonomic purposes of mangoes.

RFLPS. A limited number of studies have used restriction fragment length polymorphism (RFLP) markers in mango. Eiadthong et al. (1999) used RFLPs developed from cpDNA to analyse phylogenetic relationships in 13 Mangifera species separating M. indica and M. sylvatica from the rest of species: M. caloneura, M. cochinchinensis, M. collina, M. flava, M. foetida, M. gedebe, M. griffithii, M. macrocarpa, M. oblongifolia, M. odorata and M. pentandra. Ravishankar et al. (2004) used cpDNA RFLPs together with random amplified polymorphic DNA (RAPD) markers to separate monoembryonic and polyembryonic Indian cultivars.

RAPDS. Ravishankar et al. (2000) used RAPD markers to show the close genetic relationship among Indian mango cultivars from the same geographic region, thereby demonstrating that they evolved locally by selection and vegetative propagation. Considerable genetic variation was observed among 50 Indian mango cultivars by Kumar et al. (2001). In a study involving several Indian cultivars with a high degree of morphological variation, Karihaloo et al. (2003), using 22 primers that yielded 314 polymorphic markers, demonstrated that there are two zones of mango diversity in India: a north-eastern and a south-western cluster with variation within and between these zones.

Although phenotypic variation exists within polyembryonic ‘Kensington Pride’, RAPD markers showed limited genetic variation, so that variation was ascribed to environmental effects (Bally et al., 1996). Similarly, RAPD markers showed that there was little genetic heterogeneity between and within six populations of ‘Hilacha’ mango (Díaz-Matallana et al., 2009). RAPD markers have also been used to differentiate zygotic from nucellar seedlings in polyembryonic cultivars (Cordeiro et al., 2006; Martinez et al., 2012).

Schnell et al. (1995) examined 25 mango accessions of the National Mango Germplasm Repository (Miami, Florida, USA) for RAPD genetic markers using 80 primers; combinations of six commercial primers differentiated the ‘Florida’ mango cultivars. Bompard and Schnell (1998) performed an UPGMA (unweighted pair group method with arithmetic mean) cluster analysis of subgenus Mangifera based upon the RAPD banding patterns recorded by Schnell and Knight (1992) and Schnell et al. (1995) and validated the current taxonomy based upon floral morphology. Forty mango cultivars in a Brazilian germplasm repository were characterized, and their geographic diversity was determined by RAPD markers by De Souza and Lima (2004). RAPD markers were also used to differentiate mango accessions according to their geographic origin, i.e. Florida, USA, Mexico, the Philippines and Reunion (López-Valenzuela et al., 1997). This study identified a marker for polyembryony (GenBank: AF061639), which has been shown to be determined by a single dominant gene (Aron et al., 1998; Ravishankar et al., 2004), and demonstrated that ‘Manila’, the most widely grown mango cultivar of Mexico, is identical to ‘Carabao’, the premier mango of the Philippines. Additional studies on fingerprinting and diversity have been carried out in different mango growing areas such as Brazil (Souza et al., 2011), Egypt (Mansour et al., 2014), Indonesia (Fitmawati and Purwoko, 2010), India (Roy and Chattopadhyay, 2011), Mauritius (Ramessur and Ranghoo-Sanmukhiya, 2011) and Pakistan (Ahmad et al., 2008).

Jayasankar and Litz (1998) utilized RAPDs to detect DNA markers that could be associated with in vitro selection of mango embryogenic cultures that were resistant to the phytotoxin(s) produced by C. gloeosporioides. They observed that distinct markers that were associated with in vitro selection occurred in ‘Carabao’ with eight primers and in ‘Hindi’ with five primers.

AFLP. Amplified fragment length polymorphism (AFLP) markers have been used for mango cultivar identification and in the study of phylogenetic relationships of cultivars and with other Mangifera species and for genetic mapping. AFLP analysis was used to differentiate mango accessions in different regions. Thus, Gálvez-López et al. (2009) distinguished 16 Mexican mango landraces with 269 polymorphic markers revealing high genetic similarity that clustered in two groups with significant genetic differentiation observed based on geographic origin; Santos et al. (2008) studied the genetic relationship of 105 local and foreign mango accessions in Brazil, and Gao et al. (2013) analysed 200 accessions in China. Eiadthong et al. (2000) analysed the phylogenetic relationships among 14 Mangifera species, showing that M. indica was closely related to M. sylvatica, M. laurina and M. oblongifolia. Genetic diversity among Mangifera landraces and other Mangifera species was also verified by Yamanaka et al. (2006); clustering analysis of data separated 35 accessions into four groups that corresponded to four species, M. indica, M. odorata, M. foetida and M. caesia. Several studies have also used AFLPs to construct genetic maps (Chunwongse et al., 2000; Kashkush et al., 2001; Fang et al., 2003; Yamanaka et al., 2006).

Adato et al. (1995) performed a genetic analysis of the progeny of a controlled ‘Tommy Atkins’ × ‘Keitt’ cross and demonstrated that each cultivar and rootstock selection could be identified by a distinct minisatellite, i.e. variable number of tandem repeats (VNTR) markers. Santos and Neto (2011) used AFLPs in combination with microsatellites to test the outcrossing rate in ‘Haden’ and ‘Tommy Atkins’.

SSRS. Simple sequence repeats (SSR) markers have been developed from microsatellite-enriched mango genomic DNA libraries and are accessible in GenBank with about 200 loci developed so far (Duval et al., 2005; Honsho et al., 2005; Schnell et al., 2005; Viruel et al., 2005; Ravishankar et al., 2011, 2015a; Chiang et al., 2012; Surapaneni et al., 2013; Tsai, 2014). Schnell et al. (2005) developed 25 SSR markers that fingerprinted mango accessions in the mango germplasm collections of south Florida, USA. Olano et al. (2005) and Schnell et al. (2006) determined that Florida mango selections are more closely derived from Indian (monoembryonic) than South-east Asian (polyembryonic) accessions. Only four Indian accessions and the West Indian ‘Turpentine’ (polyembryonic) likely contributed to the first Florida mango selections. Viruel et al. (2005) showed that three SSR markers could distinguish 28 cultivars. Honsho et al. (2005) demonstrated that 29 mango cultivars, among 36 mango cultivars tested, showed distinct patterns with six SSR markers, whereas seven cultivars could not be identified because of genotype similarities. Dillon et al. (2013) used SSR markers to assess the genetic diversity in 254 M. indica and related species accessions within the Australian mango genebank. Ravishankar et al. (2015a) sequenced genomic DNA from ‘Alphonso’ identifying 106,049 microsatellite repeats of which 90 were tested in 64 mango cultivars and four Mangifera species (M. andamanica, M. camptosperma, M. odorata and M. griffithii). The availability of SSRs has allowed their widespread use for characterization and genetic diversity studies in different mango-growing areas; those include Australia (Dillon et al., 2013), Brazil (Dos Santos Ribeiro et al., 2012), the Caribbean (Duval et al., 2009), India (Singh and Bhat, 2009; Begum et al., 2012; Surapaneni et al., 2013; Vasugi et al., 2013; Ravishankar et al., 2015b; Bajpai et al., 2016), Iran (Shamili et al., 2012), Kenya (Sennhenn et al., 2014; Gitahi et al., 2016), Myanmar (Hirano et al., 2010), Pakistan (Azmat et al., 2016) and Taiwan (Chiang et al., 2012; Tsai et al., 2013). SSR markers have also been used to analyse outcrossing rates (Perez et al., 2015, 2016).

SSRs developed in mango have been successfully transferred to other Mangifera species. Thus, Ravishankar et al. (2011) used SSRs developed in M. indica in M. odorata, M. andamanica, M. zeylanica, M. camptosperma and M. griffithii and Ravishankar et al. (2015a) in M. andamanica, M. camptosperma, M. odorata and M. griffithii.

Microsatellites developed from expressed sequence tags (EST-SSRs) correspond to coding DNA. Dillon et al. (2014) developed 24,840 ESTs from different tissues of ‘Kensington Pride’ and ‘Irwin’ from which 25 EST-SSRs were obtained which were transferable to other Mangifera species (M. caesia, M. foetida, M. laurina or M. odorata). Luo et al. (2015) developed 93 EST-SSR from seven mango cultivars from China.

INTER-SIMPLE SEQUENCE REPEAT (ISSR). Genetic diversity among 70 mango cultivars was analysed by Pandit et al. (2007) using 33 ISSR markers. Although Indian and non-Indian selections were found to be genetically different, cultivars of North and South India were not divergent. Twelve different cultivar-specific bands were identified for six cultivars. ISSRs were reported to be useful for identifying polymorphisms among Indian (Singh et al., 2009) and Australian (González et al., 2002) cultivars.

INTERNAL TRANSCRIBED SPACER (ITS). Yonemori et al. (2002) utilized conserved primers to amplify the transcribed spacer (ITS) region of nuclear ribosomal DNA of 14 Mangifera species. These ITS sequences demonstrated that a close relationship existed among M. indica, M. laurina and M. sylvatica, and all are related to M. oblongifolia, whereas other Mangifera species appear to be distantly related to these species.