Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species

Abstract

Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database. Of the 14 cotton SSR loci tested, 13 (92.86 %) amplified in G. arboreum and 71.43 % exhibited cross-genera transferability. Nine out of 11 jute SSRs (81.81 %) showed cross-transferability across genera. SSRs from both the species exhibited high polymorphism and resolving power in other species. The correlation between transferability of cotton and jute SSRs were highly significant (r = 0.813). The difference in transferability among species was also significant for both the marker groups. High transferability was observed at genus, tribe and subfamily level. At tribe level, transferability of jute SSRs (41.04 %) was higher than that of cotton SSRs (33.74 %). The tribe Byttnerieae exhibited highest SSR transferability (48.7 %). The high level of cross-genera transferability (>50 %) in ten species of Malvaceae, where no SSR resource is available, calls for large scale transferability testing from the enriched SSR databases of cotton and jute.

Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopumMart.) in Benin

“…In flowering plant, the efficiency of cross-species transfer of SSR markers is highly variable among taxa, especially when important differences in genome complexity exist between the marker source and the target [64]. Nevertheless, this method has been used successfully for accelerating the analysis of genetic diversity in many plant species, including palms [13,68–70] In the present study, we find that the transferability rate of microsatellite markers developed in other palms genera to the African fan palm, i.e. their ability to successfully amplify genomic DNA from the latter species, is very low.…”

“…As a result, they are markers of choice for the assessment of polymorphism among species, genetic structure within populations, phylogeny reconstruction, genetic mapping, evolutionary analysis, and molecular breeding [11–14]. However, the steps leading to the development of functional SSR markers, namely the initial identification of microsatellite loci, primer selection and assessment of amplification/polymorphism detection, require some prior knowledge of the genome of the target species and may prove to be expensive and time-consuming [13,15]. In order to overcome this difficulty, approaches relying on the transfer of SSR markers between species or genera have therefore been implemented.…”

Validation and Transferability of Simple Sequence Repeats (Ssr’s) From Some Species of Acacia Genus to Acacia Nilotica L.

“…Rest 17 primers were selected from other species of genus Acacia. Transferability of genomic resources from one species to another depends on upon the phylogenetic relationship between different species [48]. Genus Acacia is presently divided into three main subgenera: Acacia, Aculiferum and Phyllodinae (syn.…”

Development and validation of microsatellite markers for Karnal bunt (Tilletia indica) and loose smut (Ustilago segetum tritici) of wheat from related fungal species

“…Lack of high-quality genome sequences restricts usage of SSRs for the molecular characterization of both loose smut and Karnal bunt pathotypes. Previous studies have shown the SSR marker crosstransferability to closely related species and related genera (Peakall, Gilmore, Keys, Morgante, & Rafalski, 1998;Satya, Paswan, Ghosh, Majumdar, & Ali, 2016). Despite transfer rates of SSRs between genera of up to 10% in eudicots (Barbara et al 2007), a possible high transferability between distant genera has also been observed in some species (Gutierrez et al 2005;Rai et al 2013).…”