Development and Universality Evaluation of EST-SSR Markers from GenBank in Jute

Yuan, Minhang; XiongWei, He; Xing, Lianxi; Fang, Pingping; Lin, Lihui; Tao, Aifen; JianTang, Xu; Qi, Jianmin

doi:10.3724/sp.j.1006.2014.01213

Cited by 11 publications

(8 citation statements)

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“…Among various molecular markers, SSRs have become established as a power tool for genetic diversity studies because SSRs have several desirable characteristics, such as high level of reproducibility, codominant nature and abundance [ 4 – 5 , 7 – 9 ]. Furthermore, SSR markers have high level of cross-species transferability for the two different jute species [ 2 , 10 ]. Therefore, to date SSR markers have been utilized on genetic diversity in jute [ 4 – 5 , 8 – 9 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp.) Evaluated by SSR Markers

Yuan

Tao

et al. 2015

PLoS ONE

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Population structure and relationship analysis is of great importance in the germplasm utilization and association mapping. Jute, comprised of white jute (C. capsularis L) and dark jute (C. olitorius L), is second to cotton in its commercial significance in the world. Here, we assessed the genetic structure and relationship in a panel of 159 jute accessions from 11 countries and regions using 63 SSRs. The structure analysis divided the 159 jute accessions from white and dark jute into Co and Cc group, further into Co1, Co2, Cc1 and Cc2 subgroups. Out of Cc1 subgroup, 81 accessions were from China and the remaining 10 accessions were from India (2), Japan (5), Thailand, Vietnam (2) and Pakistan (1). Out of Cc2 subgroup, 35 accessions were from China, and the remaining 3 accessions were from India, Pakistan and Thailand respectively. It can be inferred that the genetic background of these jute accessions was not always correlative with their geographical regions. Similar results were found in Co1 and Co2 subgroups. Analysis of molecular variance revealed 81% molecular variation between groups but it was low (19%) within subgroups, which further confirmed the genetic differentiation between the two groups. The genetic relationship analysis showed that the most diverse genotypes were Maliyeshengchangguo and Changguozhongyueyin in dark jute, BZ-2-2, Aidianyehuangma, Yangjuchiyuanguo, Zijinhuangma and Jute 179 in white jute, which could be used as the potential parents in breeding programs for jute improvement. These results would be very useful for association studies and breeding in jute.

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Section: Introductionmentioning

confidence: 99%

Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp.) Evaluated by SSR Markers

Yuan

Tao

et al. 2015

PLoS ONE

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“…Progeny of 104 F 2 individuals was taken to the F 8 generation through single‐seed descent and was employed in the construction of a genetic linkage map. A modified cetyltrimethylammonium bromide (CTAB) method (Saghai‐Maroof, Soliman, Jorgensen, & Allard, ; Zhang et al, ) was used to extract genomic DNA from the fresh leaves of young seedlings (30‐days old) for both parent lines and RILs. DNA quality and DNA quantity were determined using gel electrophoresis (1% agarose gel) and a UV absorbance assay using a UV‐Vis spectrophotometer (Bio Photometer Plus; Eppendorf AG), respectively.…”

Section: Methodsmentioning

confidence: 99%

“…PCR reaction conditions were set as follows: initial denaturation at 94°C for 5 min, 36 cycles at 94°C for 50 s (denaturation), annealing at 52–56°C for 1 min, extension at 72°C for 1 min and at 72°C for 7 min (final extension). Electrophoresis and nucleic acid staining were performed according to Zhang et al (). 173 InDel and 5,074 SLAF markers obtained from the previous studies (Tao et al, ; Zhang et al, ) were also tested for polymorphism between the parents of the intraspecific populations.…”

Section: Methodsmentioning

confidence: 99%

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Evaluation of newly developed SSR markers and identification of quantitative trait loci for bast fibre cellulose in white jute (Corchorus capsularis)

Niyitanga

Ibrahim

et al. 2019

Plant Breeding

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Cellulose is one of the main chemical component of bast fibre in jute. However, quantitative trait loci (QTL) for bast fibre cellulose content remains elusive. In this study, we identified 846 new SSR markers from 70,792 unigenes in the NCBI and validated them in a panel of 24 diverse jute accessions. Of 846 SSRs, 748 (88.41%) were successfully amplified, and 585 (69.14%) showed polymorphisms, implying that these are high‐quality SSRs. Furthermore, 585 SSRs along with 5,074 polymorphic SLAF (specific locus amplified fragment) and 173 InDel markers were used to reconstruct a high‐dense linkage map in a recombinant inbred population with 104 F8 lines. Totally, 835 markers were successfully mapped to a whole length of 604.5 cM with a mean distance of 2.84 cM between adjacent markers. Furthermore, five QTLs for bast fibre cellulose were identified. One major QTL (qBFC1‐1) was stable in 2 years and explained average phenotypic variance with 14.34%. These results may be useful for developing enhanced bast fibre quality in white jute through marker‐assisted selection (MAS) breeding.

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“…Generation and characterization of gene libraries is the priority for plant breeders because it is a fundamental platform in diverse aspects as genetic and physical mapping, molecular marker, new genes isolation and identification, and comparative genomics research (Talon and Gmitter, 2008;Zhang et al, 2011b;Zheng et al, 2011;Zhang et al, 2014). Expressed sequence tag (EST) projects provide a very useful and quick means of accessing gene sequence and expression information (Manickavelu et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Construction of a full-length cDNA library and analysis of expressed sequence tags in white jute (Corchorus capsularis L.)

Tao¹,

Li²,

Qi³

et al. 2015

Afr. J. Biotechnol.

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White jute (Corchorus capsularis L.) is recognized as an important industrial raw material fibre crop owing to its elite characters. However, little information is known about its molecular basis and genomics. In this study, a complementary DNA library of white jute was constructed and expressed sequence tags (ESTs) were characterized. The titers of original and amplified libraries were 2.32 × 10 7 and 1.07 × 10 9 pfu/mL, respectively. The recombinant frequency was 98.3% in the library. Most of the sequences ranged from 500 to 1500 bp with an average length of 750 bp. Results show 203 (73%) ESTs exhibited significant similarity with known or putative functional nucleotide sequences in the GenBank databases. Cluster analysis allowed the identification of 61 unique sequences. These genes were classified into six types by Gene Ontology (GO) annotation. The results also indicated that unigenes of C. capsularis have higher homology to Populus trichocarpa, Ricinus communis and Corchorus olitorius. This report will provide a valuable resource for the further investigations in the gene cloning, transcription or expression for white jute.

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Development and Universality Evaluation of EST-SSR Markers from GenBank in Jute

Cited by 11 publications

References 0 publications

Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp.) Evaluated by SSR Markers

Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp.) Evaluated by SSR Markers

Evaluation of newly developed SSR markers and identification of quantitative trait loci for bast fibre cellulose in white jute (Corchorus capsularis)

Construction of a full-length cDNA library and analysis of expressed sequence tags in white jute (Corchorus capsularis L.)

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