Endogenous hormone secretion proteins along with stress and defense proteins play predominant role in banana embryogenesis. This study reveals the underlying molecular mechanism during transition from vegetative to embryogenic state. Banana (Musa spp.) is well known globally as a food fruit crop for millions. The requirement of quality planting material of banana is enormous. Although mass multiplication through tissue culture is in vogue, high-throughput techniques like somatic embryogenesis (SE) as a mass multiplication tool needs to be improved. Apart from clonal propagation, SE has extensive applications in genetic improvement and mutation. SE in banana is completely genome-dependent and most of the commercial cultivars exhibit recalcitrance. Thus, understanding the molecular basis of embryogenesis in Musa will help to develop strategies for mass production of quality planting material. In this study, differentially expressed proteins between embryogenic calli (EC) and non-embryogenic calli (NEC) with respect to the explant, immature male flower buds (IMFB), of cv. Grand Naine (AAA) were determined using two-dimensional gel electrophoresis (2DE). The 2DE results were validated through qRT-PCR. In total, 65 proteins were identified: 42 were highly expressed and 23 were less expressed in EC compared to NEC and IMFB. qRT-PCR analysis of five candidate proteins, upregulated in EC, were well correlated with expression at transcript level. Further analysis of proteins showed that embryogenesis in banana is associated with the control of oxidative stress. The regulation of ROS scavenging system and protection of protein structure occurred in the presence of heat shock proteins. Alongside, high accumulation of stress-related cationic peroxidase and plant growth hormone-related proteins like indole-3-pyruvate monooxygenase and adenylate isopentenyltransferase in EC revealed the association with the induction of SE.
In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes. Differential gene expression between two conditions (control and drought) showed that at least 2268 and 2963 statistically significant, functionally known, non-redundant differentially expressed genes (DEGs) from tolerant and sensitive libraries. Drought has up-regulated 991 and 1378 DEGs and down-regulated 1104 and 1585 DEGs respectively in tolerant and sensitive libraries. Among DEGs, 15.9% are coding for transcription factors (TFs) comprising 46 families and 9.5% of DEGs are constituted by protein kinases from 82 families. Most enriched DEGs are mainly involved in protein modifications, lipid metabolism, alkaloid biosynthesis, carbohydrate degradation, glycan metabolism, and biosynthesis of amino acid, cofactor, nucleotide-sugar, hormone, terpenoids and other secondary metabolites. Several, specific genotype-dependent gene expression pattern was observed for drought stress in both cultivars. A subset of 9 DEGs was confirmed using quantitative reverse transcription-PCR. These results will provide necessary information for developing drought-resilient banana plants.
Albeit extensive cultivation of bitter melon both as vegetable and medicine in many countries of Asia, Africa, and South America, no serious efforts have been made for genetic and breeding studies on this 'orphan' crop. In contrast to popular cucurbits, it lacks a genetic linkage map as required for genomic depiction and precise breeding. We report here on the construction of the first genetic linkage map of bitter melon using a set of 146 F2 progenies derived from an inter-botanical variety cross between Taiwan White, Momordica charantia var. charantia, and CBM12, M. charantia var. muricata. This map consists of 108 AFLP markers and five qualitative trait loci dispersed over 11 linkage groups spanning a total distance of 3060.7 cM. The five qualitative traits mapped include fruit color, fruit luster, fruit surface structure, stigma color, and seed color; all of which exhibited monogenic segregation except seed color which showed digenic (9:7) mode of inheritance. Besides, twelve quantitative trait loci (QTL) controlling five polygenic fruit traits including length, diameter, weight, number, and yield were detected on five linkage groups that individually explained 11.1 to 39.7% of the corresponding total phenotypic variance. This map will be useful in marker-assisted breeding of these fruit traits and future mapping of genes/QTLs controlling phytomedicines content exhibiting contrasting variation between the parents.
Long non-coding RNAs (LncRNAs) are one of the many layers of transcription in higher plants. LncRNAs are responsive to biotic and abiotic stresses and regulate genes. In our study, we have identified 905 novel lncRNAs from 8471 drought-responsive, novel transcripts of RNASeq reads from two banana cultivars, a drought-tolerant cv. 'Saba' (ABB) and -susceptible cv. 'Grand Naine' (AAA). Of these 905 lncRNAs, 75 (8.3 %) transcripts were natural antisense RNAs (NATs) and 2 transcripts identified as precursors of microRNA-miR156 and miR166. Among the 905 identified lncRNAs, 216, 150 and 279, 164 lncRNAs were induced and reduced to drought stress, respectively, in tolerant and susceptible in comparison to their equivalent controls. The remaining 22 lncRNA of tolerant cultivars was not regulated by drought stress. Of the 882 drought-responsive lncRNAs, 44 new lncRNAs were identified as induced. Musa lncRNAs were unevenly distributed in 11 chromosomes of Musa acuminata and no lncRNAs were found in chromosome-9 of drought-tolerant cultivar. The average lengths of lncRNAs were 683 nucleotides (nt). Drought-responsive differential expression of lncRNAs was found between ?8.11585-and -4.04311-fold. Around 7.9 % of the identified lncRNAs were decoys of 85 conserved microRNAs. These findings will lay a basic platform for effective strategic planning of developing drought-resilient crop varieties.
The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a defense pathway. Overall, this preliminary study in Musa provides the basis for understanding the evolution and regulatory mechanism of MusaWRKY during nematode stress.
Expressed sequence tags (ESTs) databases of 11 Musa complementary DNA libraries were retrieved from National Center of Biotechnology Information and used for mining simple sequence repeats (SSRs). Out of 21,056 unique ESTs, SSR regions were found only in 5,158 ESTs. Among these SSR containing ESTs, the occurrence of trinucleotide repeats are the most abundant followed by mono-, di-, tetra-, hexa-, and pentanucleotides. Moreover, this study showed that the rate of class II SSRs (<20 nucleotides) was higher than the class I SSRs (<20 nucleotides), and proportion of class I and II SSRs as abundant for tri-repeats. As a representative sample, primers were synthesized for 24 ESTs, carrying >12 nucleotides of SSR region, and tested among the various genomic group of Musa accessions. The result showed that 88 % of primers were functional primers, and 43 % are showing polymorphism among the Musa accessions. Transferability studies of Musa EST-SSRs among the genera of the order Zingiberales exhibited 100 and 58 % transferability in Musaceae and Zingiberaceae, respectively. The sequence comparison of SSR regions among the different Musa accessions confirmed that polymorphism is mainly due to the variation in repeat length. High percentage of cross-species, cross-genera, and cross-family transferability also suggested that these Musa EST-SSR markers will be a valuable resource for the comparative mapping by developing COS markers, in evolutionary studies and in improvement of the members of Zingiberaceae and Musaceae.
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