A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)

Kundu, Avijit; Chakraborty, Avrajit; Mandal, Nur Alam; Das, Debajeet; Karmakar, P. G.; Singh, Nagendra; Sarkar, Debabrata

doi:10.1007/s11032-015-0249-x

Cited by 43 publications

(31 citation statements)

References 58 publications

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“…Whole-genome optical mapping was used to improve the assemblies, resulting increase in N50 of the scaffolds to 4.0 Mb for C. olitorius and 8.5 Mb for C. capsularis (Supplementary Information and Supplementary Tables 3-6). We anchored ∼60% of each assembly to seven genetic linkage groups using a set of 1,389 molecular markers from a consensus genetic linkage map [8][9][10][11][12] ( Supplementary Fig. 3 and Supplementary Table 7).…”

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confidence: 99%

Comparative genomics of two jute species and insight into fibre biogenesis

Islam¹,

Saito²,

Emdad³

et al. 2017

Nature Plants

108

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Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

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confidence: 99%

Comparative genomics of two jute species and insight into fibre biogenesis

Islam¹,

Saito²,

Emdad³

et al. 2017

Nature Plants

108

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“…For the construction of seven chromosome-scale pseudomolecules, we used ALLMAPS [11] to integrate the genome assembly with a RAD-SNP-based genetic map of C. olitorius [12].…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…JRO-524. The assembled genome was integrated with a RAD-SNP-based genetic map of C. olitorius [12] and anchored contigs were joined together with 50 Ns to generate the chromosome-scale pseudomolecules.ChromosomeNo. of RAD-SNP markers in genetic mapNo.…”

Section: Data Descriptionmentioning

confidence: 99%

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

et al. 2017

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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).

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“…The "Plant slim" option of the GO-Slim tool of Blast2GO was used for gene annotations, such as by biological process, molecular function, and cellular component. In order to map the eSSR markers on the existing Restriction-site Associated DNA (RAD) linkage map of jute [9], the SSRcontaining unigenes were searched with BLASTN against the 503 RAD marker sequences using an E-value cutoff of 1e-10. The top-hit unigene sequences searched with eSSR markers were manually checked for the position of the SSR repeat, followed by estimation ot their locations on the map by conversion of basepair to cM length using the genome-wide corrected cM/Mb recombination rate 1.058 [9].…”

Section: Annotation Of Unigenes Containing Ssrs and Anchoring To Rad mentioning

confidence: 99%

“…In order to map the eSSR markers on the existing Restriction-site Associated DNA (RAD) linkage map of jute [9], the SSRcontaining unigenes were searched with BLASTN against the 503 RAD marker sequences using an E-value cutoff of 1e-10. The top-hit unigene sequences searched with eSSR markers were manually checked for the position of the SSR repeat, followed by estimation ot their locations on the map by conversion of basepair to cM length using the genome-wide corrected cM/Mb recombination rate 1.058 [9]. Finally, the eSSR markers anchored to adjacent RAD markers on the linkage map were represented using the Graphical GenoTypes 2 (GGT2) software [20].…”

Section: Annotation Of Unigenes Containing Ssrs and Anchoring To Rad mentioning

confidence: 99%

Jute eSSR marker and database

Saha¹

2017

Preprint

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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.

show abstract

A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)

Cited by 43 publications

References 58 publications

Comparative genomics of two jute species and insight into fibre biogenesis

Comparative genomics of two jute species and insight into fibre biogenesis

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

Jute eSSR marker and database

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