Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
Highlights
Banana is one of the most consumed and commercially important fruit crops
Our results showed that 83.6%, 93.2% and 91.9%
We present the first set of functional simple sequence repeats (SSRs) markers (FRSMs) developed for Musa spp. together with a freely searchable database
Summary
Banana is one of the most consumed and commercially important fruit crops. Approximately 90%. Many of these banana SSR markers are not publicly available, and their chromosomal location, degree of polymorphism and functional characteristics have not been estimated which has limited the application of banana SSR markers in genotyping, association studies and fine mapping of important agronomic traits in banana breeding Due to these limitations, there is a need for a well-curated SSR marker database based on information from in-silico data mining, including the genomic or chromosomic positions of SSRs, functional association and gene affinity, together with information based on experimental validation of SSRs, such as polymorphisms, transferability and allelic variations. The availability of these genome assemblies facilitates the extraction of geneic regions and the development and in-silico mapping of SSR markers Transcriptome sequences are another valuable resource for identifying transcription factor (TF)-encoding gene products and TF-functional domains that are useful for developing functionally relevant molecular markers. In view of the above, the present study was conducted to (i) develop functionally relevant novel SSR markers from Musa transcript sequences and identify their loci, (ii) assess the cross-taxon transferability of developed markers, (iii) estimate the usefulness of functionally relevant Musa SSR markers for comparative mapping, (iv) evaluate the potential of these SSR markers for large-scale genotyping applications in Musa spp., (v) apply the SSRs in genetic diversity and population structure analysis of Musa germplasm and (vi) develop a searchable freely accessible SSR marker database
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