Identification and characterization of PEBP family genes reveal CcFT8 a probable candidate for photoperiod insensitivity in C. cajan

Understanding the molecular mechanism underlying photoperiod sensitivity will play a crucial role in extending the cropping area of Cajanus cajan, a photoperiod sensitive major grain legume of India and Africa. In flowering plants, Flowering locus T (FT) gene is involved in the production of florigen molecule which is essential for induction of flowering, influenced largely by the duration of photoperiod. To understand the structural and regulatory nature of this gene, a genome-wide survey was carried out, revealing the presence of 13 PEBP (FT) family genes in C. cajan. Based on the gene expression profiling of 13 PEBP genes across the 30 tissues of C. cajan, CcFT6 and CcFT8 were found to be probable Flowering locus T genes responsible for the production of florigen as both of them showed expression in reproductive leaf. Expression analysis in photoperiod sensitive, MAL3 genotype revealed that CcFT6 is upregulated under SD. However, in photoperiod insensitive genotype (ICP20338) CcFT6 and CcFT8 were upregulated in SD and LD, respectively. Hence, in ICP20338 under SD, flowering induction occurs with the involvement of CcFT6 while under LD, flowering induction seems to be associated with the expression of CcFT8. CcFT6 was found to be expressed only under favourable photoperiodic condition (SD) in both MAL3 and ICP20338 and may be regulated through a photoperiod dependent pathway. The presence of additional florigen producing gene, CcFT8 in ICP20338 which has the ability to flower in a photoperiod independent manner under LD conditions might provide some clues on its photoperiod insensitive nature. This study will provide a detailed characterization of the genes involved in photoperiodic regulation of flowering in C. cajan

Identification and characterization of novel drought-responsive lncRNAs in stone apple (Aegle marmelos L.) through whole-transcriptome analysis

Stone apple (Aegle marmelos L.) is a subtropical fruit tree of the Rutaceae family, highly valued in traditional medicine across the Indian subcontinent. We conceived this study with the objective of developing a comprehensive transcriptome dataset, identifying SSRs for marker-assisted breeding, and delineating regulators of gene expression, with a specific emphasis on non-coding RNA (ncRNA), particularly related to drought stress. To achieve this, RNA-seq was conducted using RNA pooled from various tissues, including roots, leaves, inflorescence, and developing seeds from stone apple, and the clean reads were assembled into 40,886 unigenes. Subsequently, the unigenes were categorized into gene ontology categories encompassing biological processes, molecular functions, and cellular components. Within the unigenes, we identified a total of 9174 perfect simple sequence repeats (SSRs), 2167 transcription factors (TFs) distributed among 69 families, and 415 transcription regulators (TRs) across 27 families. Additionally, 19 microRNAs (miRNAs) from 12 families, 16,811 potential long noncoding RNAs (lncRNAs), and six functional endogenous target mimics (eTMs) were detected. Analysis of lncRNA-miRNA-mRNA interactions unveiled multiple regulatory nodes, elucidating lncRNA/miRNA-driven gene expression control in stone apple. The increased co-expression of selected drought-related lncRNAs and their cognate target mRNAs supported the aforementioned findings under drought conditions. Overall, this study significantly advances our understanding of stone apple genomics and lays a foundation for future omics-based studies, thereby facilitating the deployment of climate-resilient strategies in the species

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Not AvailableCluster bean (Cyamopsis tetragonoloba), also known as guar, is an important industrial crop owing to its high gum content in the endosperm. Availability of sufficient genomic resources, especially, DNA markers, greatly aids genetic improvement of a crop. In this study, we identified 1859 genomic SSRs, for the first time, from 1091 scaffolds representing 60% of the cluster bean genome. Further we validated 89 of these markers using 54 cultivated guar accessions and two wild relatives, Cyamopsis serrata and Cyamopsis senegalensis. Seven SSRs were monomorphic even with the wild relatives while 11 were polymorphic only between species with 72 being polymorphic within C. tetragonoloba accessions. Polymorphism information content of the markers ranged from 0.017 to 0.62 with an average of 0.19. Cross-transferability rates of 62% observed for the genomic SSRs suggested divergence between the cultivated and the wild species. Genomic SSRs mined in this study though showed a high proportion of dinucleotide repeats (48.5%), while tri-and tetranucleotide repeats were found to be more polymorphic. Genetic diversity analysis of the 56 accessions using the 82 polymorphic markers could differentiate the cultivated accessions of C. tetragonoloba into four major clusters, two of which had two sub-clusters while the wild accessions formed a separate cluster. Since chromosome-wide distribution of the SSRs is unknown and genetic linkage maps in guar is not available, we used the soybean genome as a reference and identified 29 genome-wide and unlinked SSRs markers. Population structure analysis (PSA) using these markers revealed six subpopulations, more or less similar to the major and sub-clusters identified by the neighbor joining analysis. Further PSA identified an entry from subpopulation 6 to have admixture with the wild relatives. Annotation of the validated genomic SSR containing sequences using green plant nr protein database revealed that 16 of them were genic in nature. This is the first report on genomic SSRs and their utilization in unraveling the genetic diversity in cluster bean.Not Availabl

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Not AvailableCluster bean (Cyamopsis tetragonoloba), also known as guar, is an important industrial crop owing to its high gum content in the endosperm. Availability of sufficient genomic resources, especially, DNA markers, greatly aids genetic improvement of a crop. In this study, we identified 1859 genomic SSRs, for the first time, from 1091 scaffolds representing 60% of the cluster bean genome. Further we validated 89 of these markers using 54 cultivated guar accessions and two wild relatives, Cyamopsis serrata and Cyamopsis senegalensis. Seven SSRs were monomorphic even with the wild relatives while 11 were polymorphic only between species with 72 being polymorphic within C. tetragonoloba accessions. Polymorphism information content of the Markers ranged from 0.017 to 0.62 with an average of 0.19. Cross-Transferability rates of 62% observed for the genomic SSRs suggested Divergence between the cultivated and the wild species. Genomic SRs Mined in this study though showed a high proportion of dinucleotide repeats (48.5%), while tri- and tetranucleotide repeats were found to be more polymorphic. Genetic diversity analysis of the 56 accessions using the 82 polymorphic markers could differentiate the cultivated accessions of C. tetragonoloba into four major clusters, two of which had two sub-clusters while the wild accessions formed a separate cluster. Since chromosome-wide distribution of the SSRs is unknown and genetic linkage maps in guar is not available, we used the soybean genome as a reference and identified 29 genome-wide and unlinked SSRs markers. Population structure analysis (PSA) using these markers revealed six subpopulations, more or less similar to the major and sub-clusters identified by the neighbor joining analysis. Further PSA identified an entry from subpopulation 6 to have admixture with the wild relatives. Annotation of the validated genomic SSR containing sequences using green plant nr protein database revealed that 16 of them were genic in nature. This is the first report on genomic SSRs and their utilization in unraveling the genetic diversity in cluster bean.Not Availabl

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Not AvailableJack (Artocarpus heterophyllus) is a multipurpose fruit-tree species with minimal genomic resources. The study reports developing comprehensive transcriptome data containing 80,411 unigenes with an N50 value of 1265 bp. We predicted 64,215 CDSs from the unigenes and annotated and functionally categorized them into the biological process (23,230), molecular function (27,149), and cellular components (17,284). From 80,411 unigenes, we discovered 16,853 perfect SSRs with 192 distinct repeat motif types reiterating 4 to 22 times. Besides, we identified 2741 TFs from 69 TF families, 53 miRNAs from 19 conserved miRNA families, 25,953 potential lncRNAs, and placed three functional eTMs in different lncRNA-miRNA pairs. The regulatory networks involving genes, TFs, and miRNAs identified several regulatory and regulated nodes providing insight into miRNAs' gene associations and transcription factor-mediated regulation. The comparison of expression patterns of some selected miRNAs vis-à-vis their corresponding target genes showed an inverse relationship indicating the possible miRNA-mediated regulation of the genes.Not Availabl

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Not AvailableJack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.Not Availabl

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Not AvailableJack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.Not Availabl

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Not AvailableBrassica juncea is an economically important oilseed crop worldwide. It has limited genomic resources at present. We generated 47,962,057 expressed sequence reads which were assembled into 45,280 unigenes. A total of 4108 SSR loci (≥10 bp) were identified in these unigenes. Trinucleotide was the most frequent repeat unit (59.91 %) followed by di- (38.66 %), tetra - (0.71 %), hexa - (0.49 %) and pentanucleotide repeats (0.24 %). Primers were designed for 2863 SSR loci among which 460 were selected for primer synthesis. A total of 339 loci amplified successfully of which 134 (39.5 %) exhibited polymorphism among six B. juncea genotypes with PIC values ranging from 0.18 to 0.81. Further, 25 polymorphic SSRs were used for analysis of genetic variability in 25 genotypes of Brassicas and their wild relatives. Two to five alleles with PIC values 0.22–0.66 were detected at these loci. The dendrogram grouped the genotypes according to their known pedigree/systematic position.Not Availabl