Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

Corchorus capsularis (white jute) and C. olitorius (dark jute) are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR) loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60%) followed by dinucleotide repeats (37.6%). Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR) markers were successfully mapped to the existing single-nucleotide polymorphism (SNP) linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/) for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute

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Not AvailableIn jute (Corchorus spp.), phenylpropanoid biosynthesis pathway is associated with lignocellulosic bast fibre development and production of various phytochemicals. Development of phenylpropanoid-related genic markers is thus a key component of gene-specific precision molecular breeding in jute. We identified a total of 12,772 SSRs in 10,041 unigenes and designed genic SSR markers associated with phenylpropanoid biosynthesis from bast transcriptome of Corchorus capsularis cv. ‘JRC-212’. A total of 39 and 14 SSR markers were developed from key genes of phenylpropanoid biosynthesis and bast fibre formation, respectively. Further, we developed 457 SSR markers associated with different regulatory gene sequences. Of these, 137 markers were for transcription factors such as WRKY, MYB, MYBrelated, bHLH and zinc finger, which are key regulators and/or modulators of the biosynthesis of phenylpropanoids. Additionally, 600 SSR primer pairs were also designed for other unigenes containing SSR. Diversity analysis based on a set of 41 genic SSR markers in 35 genotypes revealed high polymorphism. The genic SSRs described here are expected to be useful for molecular breeding targeting fibre quality, phytochemical-related and stress tolerance traits in jute.Not Availabl

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Not AvailableEnzyme β-galactosidase (EC 3.2.1.23) is known to influence vascular differentiation during early vegetative growth of plants, but its role in hypocotyl development is not yet fully understood. We generated the hypocotyl transcriptome data of a hypocotyl-defect jute (Corchorus capsularis L.) mutant (52,393 unigenes) and its wildtype (WT) cv. JRC-212 (44,720 unigenes) by paired-end RNA-seq and identified 11 isoforms of β-galactosidase,using a combination of sequence annotation, domain identification and structural-homology modeling. Phylogenetic analysis classified the jute β-galactosidases into six subfamilies of glycoside hydrolase-35 family, which are closely related to homologs from Malvaceous species. We also report here the expression of a β- galactosidase of glycoside hydrolase-2 family that was earlier considered to be absent in higher plants. Comparative analysis of domain structure allowed us to propose a domain-centric evolution of the five classes of plant β-galactosidases. Further, we observed 1.8–12.2-fold higher expression of nine β-galactosidase isoforms in the mutant hypocotyl, which was characterized by slower growth, undulated shape and deformed cell wall. In vitro and in vivo β-galactosidase activities were also higher in the mutant hypocotyl. Phenotypic analysis supported a significant (P≤0.01) positive correlation between enzyme activity and undulated hypocotyl. Taken together, our study identifies the complete set of β-galactosidases expressed in the jute hypocotyl, and provides compelling evidence that they may be involved in cell wall degradation during hypocotyl development.Not Availabl

Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in jute (Corchorus olitorius L.)

<p>We performed individual-based restriction site-associated DNA (RAD) sequencing to discover single-nucleotide polymorphisms (SNPs) across a diverse set of 225 fibre-type lines in jute (<i>Corchorus olitorius </i>L., Malvaceae s. l.) <i></i>and identified a set of 1115 polymorphic RAD-SNP markers (SNP containing RADseq loci), each supporting a single SNP with >0.05 minor allele frequency (MAF). Based on multilocus RAD-SNP genotypes of 221 lines (four lines were excluded due to >50 % missing genotypes) with a call rate of >0.95, we examined the geographic patterns of genetic diversity across nine predefined populations, viz. AFR1 (Kenya and Sudan), AFR2 (Tanzania), CI (central India), EI (east India), NI (north India), SI (south India), NPPK (Nepal and Pakistan), ESEA (China, Myanmar, Indonesia and Thailand) and RoW (Australia, Brazil, Germany and Russia) and determined their genetic relatedness by assessing the <i>F</i>_ST, AMOVA, <i>N</i>_mand PCA at the population level. Using five assignment tests with different statistical bases (<i>k</i>-means clustering, STRUCTURE, sNMF, DAPC and frequency-based assignment test), the most exhaustive yet to our knowledge, we inferred how these geographic populations are structured. We further applied subpopulation-based <i>F</i>_ST- (LOSITAN and BayeScan) and <i>G</i>_ST-outlier (HacDivSel) tests and an individual-based global approach (PCAdapt) based on principal component analysis (PCA) to detect putative RAD-SNP loci under selection. Instead of BLAST alone, we employed a serial approach based on BLAST, Blast2GO mapping, protein domain annotation (DoMosaics) and REViGO semantic analysis to identify candidate genes and retrieve the overrepresented gene ontology (GO) terms associated with the outlier RAD-SNP loci putatively involved in local adaptation.</p><p> </p><p> </p><p><br></p

Genomics for augmenting bast fibre yield and quality improvement in jute

<p>Jute (<i>Corchorus capsularis </i>L. and <i>C. olitorius</i> L., Malvaceae s. l.) is an important ligno-cellulosic bast fibre crop (2n = 2<i>x</i> = 14), with diversified industrial uses of textiles. We initiated genomics research in jute, with an objective to implement genomics-assisted breeding approaches for bast fibre yield and quality improvement. Here, we present a few important genomic resources and tools made available for jute over the past few years.</p

Development and validation of SSR and InDel markers in jute (Corchorus olitorius L.) using next-generation sequencing

We used next-generation sequencing based on Illumina NextSeq (Illumina, San Diego, CA), with 2 x 150 bp chemistry, to assemble <i>de novo</i> the whole genome shotgun (WGS) sequence of <i>Corchorus olitorius</i> cv. Sudan Green and identified genomic SSR and InDel markers. Of 13,814 SSRs identified, the number of di-, tri- and tetra-nucleotide repeat classes were 10,078, 2,388 and 1,348, respectively. Although a total of 5,471 InDels were detected at various positions, we could only identify 44 InDel markers based on stringent parameters. A total of 1,000 SSR (956) and InDel (44) markers were successfully validated in <i>Corchorus</i> spp

The draft genome of Corchorus olitorius cv. JRO-524 (Navin)

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000)