Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

Abstract

The genus Gossypium is comprised of 50 diverse cotton species representing eight different genomes (A through G and K), however, phylogenetic relationship using various DNA marker types such as RAPD and SSRs was determined on limited number of cotton species. In this report, we have demonstrated the application of genomic SSRs (gSSRs) and EST-SSRs, and after combining both the data sets, for resolving the phylogenies of 36 cotton species including seven races. Out of the 100 primer pairs surveyed (50 for gSSRs and 50 for ESTSSRs), 75 produced scorable amplification products in all species. Out of these, 73 were found to be polymorphic and amplified 135 alleles ranging from 1 to 5 alleles per SSR marker (average 2.87 alleles per marker). The gSSRs amplified higher number of alleles (72) compared to the EST-SSRs (63). In total 22 highly informative SSRs with PIC values C0.5 were identified. Genomic SSRs containing di-while EST-SSRs containing tri-nucleotide repeats exhibited high polymorphism compared to the other nucleotide repeats containing gSSRs/EST-SSRs. Number of tandem repeats and polymorphism were positively correlated. Neither the type of chromosome nor the location of the SSRs showed association with the polymorphism. Gossypium herbaceum var. africanum (Watt) Hutch. ex and Ghose and Gossypium robinsonii F. Muell. were found the most genetically diverse, while among races of Gossypium hirsutum L. ''yucatanense'' and G. hirsutum ''punctatum'' were found genetically diverse. Of the three data sets, clustering analysis based on EST-SSRs and combined data sets, revealed parallel results reported in earlier studies. This study further confirmed that Gossypium darwinii Watt has close relationship with Gossypium barbadense L. Moreover, Gossypium raimondii Ulbr. and G. herbaceum/Gossypium arboreum L. are close living relatives of the ancestor allotetraploid species. Our studies suggest that for resolving phylogenetic relationship among the various plant species EST-SSRs could be a better choice. This information can be instrumental in transferring novel alleles or loci from the wild species into the cultivated cotton species which would set a stage for cultivating genetically diverse cultivars-a way to achieve sustainable cotton production in changing climate.

Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee

“…eSSRs are preferred as anchor markers in comparative mapping studies due to their high transferability rate among related species unlike microsatellites from non-transcribed DNAs (Cavagnaro et al 2010). However, due to high selection pressure, eSSRs are less polymorphic compared to gSSRs (Tabbasam et al 2014).…”

Development of a Core Set of SSR Markers for Cultivar Identification and Seed Purity Tests in Oriental Melon (Cucumis melo L. var. makuwa)

“…The EST-SSR markers are developed using coding sequences that are more conserved than noncoding sequences. Since the genomic SSR markers are often derived from noncoding genomic sequences, higher levels of polymorphism are expected in genomic SSR markers than EST-SSR markers (Guo et al, 2007;Hu et al, 2011;Mujaju et al, 2013;Tabbasam et al, 2013). However, both EST-SSR and genomic SSR markers used in this study showed comparable ranges for the PIC values.…”

“…The three sets of SSR markers generated different dendrograms. This discrepancy was previously reported in other crop species and could be due to different genomic regions covered by both the markers and the variation in number of markers (Tabbasam et al, 2013;Parthiban et al, 2018). In addition, the EST-SSR markers are derived from expressed sequences compared to genomic sequences that are spread throughout the genome.…”

Genetic monitoring of introgressed alleles from Gossypium arboreum L. into G. hirsutum L. using SSR markers: a potential approach for bringing new alleles under cultivation

“…It is worth mentioning that all these markers have been derived from EST-SSRs and SSRs of G. hirsutum, and are successfully amplified in both the cotton species. Transferability between different species has also been demonstrated in several crop species (Kuleung et al, 2004;Saha et al, 2004) and also in the genus Gossypium (Tabbasam et al, 2014).…”

“…In cotton, availability of DNA markers (functional or structural) with high allelic variability which are transferable to other cotton species is important for undertaking genetic analysis. For example such markers can help in conducting QTL mapping, comparative mapping, gene-flow and allelic profile studies in cotton (Tabbasam et al, 2014). In this study, each of the alleles amplified by JESPR-156 and MGHES-15 in G. arboreum was introgressed in one of the BC4F2 plants showing the low introgression rate of donor genome in succeeding backcross populations.…”