Dark Jute Research Articles

Comparative transcriptomics discovers the genetic basis of contrasting waterlogging tolerance between two cultivated jute species

Farmers prefer dark jute (Corchorus olitorius var. O-9897) to white jute (Corchorus capsularis var. CVL-1) because dark jute produces more bast fiber and has greater fiber strength. Crossing incompatibility between these two jute species is the main genetic barrier to transfer waterlogging-tolerant capability from white jute to dark jute. So, to develop a waterlogging-tolerant dark jute variety, gene(s) of interest for certain morphological, anatomical, and physiological features must be transferred from white jute to dark jute without the use of traditional crossing techniques. Therefore, we investigated the comparative gene expressions of CVL-1 and O-9897 tap roots using RNA-Seq and qRT-PCR techniques as well as observed the morphological, histological and physiological behavior under waterlogging treatments. CVL-1 develops schizogenous aerenchyma for oxygen storage, as well as vascular tissues in its adventitious roots for moving water and nutrients from the water solution to the stem, which keeps its tap root less active and so saves more energy in its tap roots. O-9897, on the other hand, degrades its adventitious roots with lysigenous aerenchyma, which results in the formation of no vascular tissues. Thus, O-9897 solely uses its adventitious roots for oxygen storage, while its tap roots are used for water and nutrient transfer, resulting in constant energy depletion in O-9897 tap roots. Consequently, CVL-1 can maintain its normal growth and O-9897 diminishes its bast fiber yield with the lack of energy. The key genes involved in the biogenesis of energy and phytohormones have been more inducing in CVL-1 than O-9897. ATP-producing glycolytic enzyme, phosphoglycerate kinase (CCACVL1_10615) showed remarkable upregulation in CVL-1 while missing in O-9897, playing a vital role in CVL-1 waterlogging tolerance. Our findings reveal a novel mechanism of waterlogging tolerance in white jute, which can be applied to the development of waterlogging-tolerant dark jute varieties in the future.

Multi‐omics provides new insights into the domestication and improvement of dark jute ( Corchorus olitorius )

Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

Genome-wide identification and expression profiling of AP2/ERF superfamily genes under stress conditions in dark jute (Corchorus olitorius L.)

The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TF) in plants that play a vital role in regulating plant growth, development and stress response. A total of 119 CoAP2/ERF genes were identified from the dark jute genome, one of the most important bast fibre crops. Among these, 17 were AP2, 97 ERF, 4 RAV and 1 Soloist gene family. Phylogenetic analysis revealed that the AP2/ERF genes can be divided into 10 groups. These genes were distributed randomly across the linkage groups and found three tandem and eight segmental duplications which arose from ancient duplication events. Expression profiling of CoAP2/ERF genes was assessed using RNA-Seq data and qRT-PCR analysis in tissues during development and under biotic (Macrophomina phaseolina) and abiotic (waterlogging, salinity, drought) stresses. CoERF-21, CoERF-34 and CoERF-39 genes were significantly upregulated during waterlogging stress and CoDREB-11, CoDREB-14 and CoRAV-01 genes were upregulated under salinity and drought stress condition. Gene evolution analysis among the Malvaceae family showed dark jute were separated 14 and 22 Mya from cacao and cotton respectively and expression correlation analysis revealed the functions of superfamily genes were expanded and enhanced through gene duplication. These findings provide new insights into AP2/ERF gene evolution, divergence in dark jute and considered a valuable resource for further functional validation as well as for utilization in stress resistance variety development program.

Evaluation of dark jute SSR markers and morphological traits in genetic diversity assessment of jute mallow (Corchorus olitorius L.) cultivars

The jute mallow (C. olitorius L.) is an important nutritious green leafy vegetable in the tropical region of Africa. This study assesses the extent of genetic diversity and intra-specific relationships among 16 cultivated jute mallows of Nigeria (14), [Ghana (1) and Togo (1), used as checks, evaluating 16 dark jute SSR markers and 16 morphological traits (quantitative and qualitative). The study reveals moderate to high variation among the cultivars in the number of pods, pod yield and plant height traits. Based on the principal component (PC) analysis of the quantitative traits, the pod length, pod width, number of pods, pod yield and plant height are important traits composing PC1. On the other hand, the pod pedicel length and days of 50% flowering traits are highly correlated variables in PC2. Pod length, pod width, pod pedicel length and plant height account for the total diversity. Two main groups (I and II) and an outgroup are identified among the 16 cultivars based on the quantitative traits. among the cultivars, leaf shapes identified are ovate (38% of cultivars), lanceolate (6%), oblanceolate (25%) and palmately lobed (31%). Three markers which have monomorphic alleles are excluded and thirteen markers are used to analyse the genetic diversity. A total of 41 alleles are amplified using the 13 polymorphic markers with an average of 2.75 per locus. The mean polymorphism information content (PIC) value is 0.42, ranging from 0.06 to 0.73. The mean gene diversity or expected heterozygosity = 0.05 (from 0.06 to 0.76). The observed heterozygosity (Ho) ranges from 0.00 to 0.88, with a mean of 0.60. The mean genetic dissimilarity is 0.35. Thus, the SSR data indicate a moderate genetic dissimilarity within jute mallow under study. Clustering using the neighbour-joining dendrogram predicated on the SSR data separates the cultivars into three major groups in which the two cultivars from Ghana and Togo show distinctiveness from the cultivars from Nigeria. Principal coordinate analysis of SSR data is consistent with neighbour-joining groupings. The study based on a set of dark jute markers and morphological traits reveals that the extent of genetic diversity of cultivated jute mallow and could be used in germplasm evaluation. In addition to the knowledge of the high genetic variability observed in the number of pod and the yield of some of the studied cultivars, further efforts are needed to characterise the cultivar pods’ nutritive values for human health.

Development of Novel Small InDel Markers in Jute (Corchorus spp.)

Jute, including white and dark jute, is an agroeconomically important fiber crop worldwide. However, no practical information is available for expressed sequence tag-derived InDel (insertion and deletion) in jute to date. Previously, we de novo assembled 48,914 unigenes from white jute. In this study, 4815 InDels were called from these unigenes. The size <5 bp was the most abundant types (69.88%), and the AG-rich nucleotide InDels were the predominant. Subsequently, a sample of 173 InDels (TFCcID), located in genes encoding transcription factors, were selected to survey polymorphisms among 24 diverse accessions derived from a panel of 159 jute germplasm. Of these, 119(68.8%) successfully amplified and detected polymorphism, indicating that these InDels are of good quality. The 119 polymorphic InDels were successfully mapped to the existing contigs of jute variety CVL-1. Single marker analysis of these polymorphic TFCcIDs was conducted to associate specific markers to cellulose content of bast fiber. Five markers from TFCcIDs were identified to be significantly correlated to cellulose content of bast fiber. To our knowledge, it is the first successful development of InDel markers on a large scale in jute, which will accelerate related researches on genetic map construction and marker assisted selection of bast fiber quality.

Morphological, Histobiochemical and Molecular Characterisation of Low Lignin Phloem Fibre (llpf) Mutant of Dark Jute (Corchorus olitorius L.).

Lignin is a versatile plant metabolite challenging high-end industrial applications of several plant products including jute. Application of developmental mutant in regulation of lignification in jute may open up door for much awaited jute based diversified products. In the present study, a novel dark jute (Corchorus olitorius L.) mutant with low lignin (7.23%) in phloem fibre being compared to wild-type JRO 204 (13.7%) was identified and characterised. Unique morphological features including undulated stem, petiole and leaf vein distinguished the mutant in gamma ray irradiated mutant population. Histological and biochemical analysis revealed reduced lignification of phloem fibre cellsof the plant. RT-PCR analysis demonstrated temporal transcriptional regulation of CCoAMT1 gene in the mutant. The mutant was found an extremely useful model to study phloem fibre developmental biology in the crop besides acting as a donor genetic stock for low lignin containing jute fibre in dark jute improvement programme.

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.

Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp.).

Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively). The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.

Genetic linkage map construction for white jute (Corchorus capsularis L.) using SRAP, ISSR and RAPD markers

AbstractWhite jute (Corchorus capsularis) and dark jute (Corchorus olitorius) are two important cultivated crops that are used for natural fibre production. Some genetic maps have been developed for dark jute, but the genetic map information for white jute (C. capsularis) is limited. In this study, a linkage map comprising 44 sequence‐related amplified polymorphisms (SRAPs), 57 intersimple sequence repeats (ISSRs) and 18 randomly amplified polymorphic DNA (RAPD) covering 2185.7 cM with a mean density of 18.7 cM per locus was constructed in an F2 population consisting of 185 individuals derived from a cross between two diverse genotypes of ‘Xinxuan No. 1’ and ‘Qiongyueqing’ in white jute. These markers were evenly distributed in the linkage groups without any clustering. This genetic linkage map construction will facilitate the mapping of agronomic traits and marker‐assisted selection breeding in white jute.

Origins of white (Corchorus capsularis L.) and dark (C. olitorius L.) jute: a reevaluation based on nuclear and chloroplast microsatellites

Using a suite of morphological traits and neutral molecular markers, we have reevaluated the origins of the two cultivated jute species. The nine Corchorus species, which are restricted to both Africa and Asia, were phenotyped for bast fibre yield- and quality-linked traits, morpho-phenetically classified based on those traits’ similarities, genotyped by nuclear microsatellites and haplotyped by chloroplast microsatellites. The two cultivated jute species contain ~70% of the neutral genetic diversity present in their wild relatives. Phylogenetic analyses using 38 highly polymorphic nuclear microsatellites identified C. aestuans as the common ancestor to both the cultivated jute species. C. urticifolius is the nuclear progenitor of C. olitorius (dark jute), but no close nuclear progenitor of C. capsularis (white jute) could be identified. Although either C. aestuans or C. pseudo-olitorius or both appear to be the possible cytoplasmic progenitors of white jute, the matrilineal ancestry of dark jute remains obscure. However, the presence of a single, unique chloroplast haplotype in each of the two cultivated species indicates the involvement of other unknown wild relatives. Taken together with archaeobotanical evidence, our results suggest that dark jute had its origin in equatorial region of east Africa, but was domesticated in India. We could not support an Indo-Myanmar origin of white jute, and possibly it also originated in Africa, but was domesticated in Asia.

A secondary phloic (bast) fibre-shy (bfs) mutant of dark jute (Corchorus olitorius L.) develops lignified fibre cells but is defective in cambial activity

Bast fibre development in jute (Corchorus spp.) is a complex process that involves the differentiation of secondary phloic fibres (SPF) from the cambium followed by lignification of the fibre wall. We have identified a unique radiation-induced bast fibre-shy mutant of dark jute (C. olitorius L.), which is concurrently defective in the differentiation of SPF and secondary xylem (wood) but develops lignified fibre cells. It displays the most unusual phenotype with stunted growth and abnormal leaf shape, matures earlier, yields significantly less bast fibres and wood, and produces poorer quality fibres than its parental wild-type. Cambial activities in the mutant and the normal type were monitored by estimating the fibre content that entails the total number of fibre cell bundles (FCBs) in an entire transversal section. The results show that a multi-fold reduction of bast fibre yield in the mutant is related to development-specific loss of cambium function along the length of the stem from to top to bottom. Since lignification of the fibre wall in the mutant is not only normal but also developmentally uniform, cambium function may be unrelated to the lignification process during bast fibre development. Lignin does not influence bast fibre strength and fineness. The architecture of the mostly triangular FCB wedges, which is governed by a balanced growth between radially elongating FCBs and tangentially expanding ray cells due to development-specific activation of the fusiform and ray initials of the cambium, conditions fibre fineness. Our study shows that mutation could specifically impair the cambial activity by rendering those initials that differentiate the SPF and secondary xylem nonfunctional.