Dataset Information

Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.

ABSTRACT: The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.

SUBMITTER: Biswas MK

PROVIDER: S-EPMC4488140 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Amaranth (Amaranthus spp.) belonging to Amaranthaceae, is known as "the crop of the future" because of its incredible nutritional quality. Amaranthus spp. (> 70) have a huge diversity in terms of their plant morphology, production and nutritional quality; however, these species are not well characterized at molecular level due to unavailability of robust and reproducible molecular markers, which is essential for crop improvement programs. In the present study, 13,051 genome-wide microsatellite motifs were identified and subsequently utilized for marker development using A. hypochondriacus (L.) genome (JPXE01.1). Out of those, 1538 motifs were found with flanking sequences suitable for primer designing. Among designed primers, 225 were utilized for validation of which 119 (52.89%) primers were amplified. Cross-species transferability and evolutionary relatedness among ten species of Amaranthus (A. hypochondriacus, A. caudatus, A. retroflexus, A. cruentus, A. tricolor, A. lividus, A. hybridus, A. viridis, A. edulis, and A. dubius) were also studied using 45 microsatellite motifs. The maximum (86.67%) and minimum (28.89%) cross-species transferability were observed in A. caudatus and A. dubius, respectively, that indicated high variability present across the Amaranthus spp. Total 97 alleles were detected among 10 species of Amaranthus. The averages of major allele frequency, gene diversity, heterozygosity and PIC were 0.733, 0.347, 0.06, and 0.291, respectively. Nei's genetic dissimilarity coefficients ranged from 0.0625 (between A. tricolor and A. hybridus) to 0.7918 (between A. viridis and A. lividus). The phylogenetic tree grouped ten species into three major clusters. Genome-wide development of microsatellite markers and their transferability revealed relationships among amaranth species which ultimately can be useful for species identification, DNA fingerprinting, and QTLs/gene(s) identification.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-021-02930-5.

Project description:BackgroundAlthough banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores.ResultsThe study generated 846,762 high quality sequence reads, with an average length of 334 bp and totalling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases.Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82.ConclusionsA large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.

Dataset Information

Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets