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DEVELOPMENT AND CHARACTERIZATION OF EST-SSR MARKERS FROM DE NOVO TRANSCRIPTOME SEQUENCING DATA IN RUBBER TREE (HEVEA BRASILIENSIS)
Dejun Li - ไม่ระบุหน่วยงาน
ชื่อเรื่อง (EN): DEVELOPMENT AND CHARACTERIZATION OF EST-SSR MARKERS FROM DE NOVO TRANSCRIPTOME SEQUENCING DATA IN RUBBER TREE (HEVEA BRASILIENSIS)
ผู้แต่ง / หัวหน้าโครงการ (EN): Dejun Li
บทคัดย่อ (EN): Rubber tree (Hevea brasiliensis Muell. Arg.) is a perennial tropical tree native to the Amazonian rainforest, but is widely cultivated in Southeast Asia including Indonesia, Thailand and Malaysia. In the world, rubber tree is the only species cultivated commercially for natural rubber. As an important industrial material, natural rubber cannot be replaced by synthetic alternatives due to its unique properties. Molecular marker is very useful in various fields of molecular biology, such as DNA fingerprinting, marker-assisted selection, genetic mapping, etc. In recent years, some progress has been made in developing and utilizing molecular markers in rubber tree, but the category and number of molecular marker can’t keep up with the molecular biological development of rubber tree. In this research, the data from de novo transcriptome sequencing of rubber tree bark was utilized to develop EST-SSR markers (EST-SSRs) and analyze the characterizations of EST-SSRs. All the 22,756 unigenes obtained by SOAPdenovo program were used to predict potential microsatellites which were defined as di- to nona-nucleotide SSR with a minimum of three repetitions. Using the Simple Sequence Repeat Identification Tool (http://www.gramene.org/db/markers/ssrtool), a total of 39,257 potential EST-SSRs were found in 16,208 unigenes. Among the 16,208 unigenes, 6549 and 9659 unigenes contained one and more than one EST-SSRs, respectively. The number of potential EST-SSRs per unigenes was from 1 to 25 with an average of 2.42. In addition, the characterizations of the potential 39,257 EST-SSRs were also analyzed in this study. In total, the average length containing one EST-SSR was about 281.39bp. Among the 39,257 EST-SSRs, the di-nucleotide repeat motifs were the most abundant types (27,877, 71.01%), followed by tri- (10,490, 26.72 %), tetra- (430, 1.10%), penta- (203, 0.52%) and hexa-nucleotide (239, 0.61%) repeat motifs. Di- to nona-nucleotide motifs were further analyzed for the number of repeat units. The number of repeat units of potential EST-SSRs mostly distributed was 3, which accounting for 84.84%, followed by 4 (10.51%), 5 (2.23%) and 6 (0.84%). 98 potential EST-SSRs contained more than 14 repeat units, and all the repeats were di-nucleotide repeat. Within the potential EST-SSRs, 429 motif types were identified, of which, di-, tri-, tetra- and penta-nucleotide repeat had 6, 30, 99 and 88 types, respectively. As for the abundance of nucleotide repeats, the AG/TC di-nucleotide repeat was the most abundant motif detected in our EST-SSRs (8,569, 21.83%), followed by the motif CT/GA (7,320, 18.65%), AT/TA (4,981, 12.69%), AC/TG (3,071, 7.82%), CA/GT (2,681, 6.83%) and CG/GC (1,255, 3.20%). The six types of nucleotide repeats mentioned above represented about 71.01%, whereas the remaining 423 types of nucleotide repeats only accounted for 28.99%. In order to testify the validity of EST-SSRs, 40 pairs of EST-SSR primers were designed using Primer Premier 6.0 (PREMIER Biosoft International, Palo Alto CA). Among the 40 primer pairs, 39 were successful in PCR amplification in rubber tree. The remaining 1 primers failed to generate PCR products at various annealing temperatures and Mg2+ concentrations and would be excluded from further analysis. Of the 39 working primer pairs, 36 PCR products showed specific amplification. 30 PCR products were as sizes as they expected, and the other six generated larger PCR products than expected, suggesting that there may be an intron within the amplifying regions. 3 PCR products indicated more than one bands, and all of them contained one band which size is as they expected, which might result from the primer design or the high heterozygosity of rubber tree germplasm.
บทคัดย่อ: ไม่พบข้อมูลจากหน่วยงานต้นทาง
ภาษา (EN): en
เผยแพร่โดย (EN): การยางแห่งประเทศไทย
คำสำคัญ (EN): molecular marker
เจ้าของลิขสิทธิ์ (EN): การยางแห่งประเทศไทย
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Dejun Li. "DEVELOPMENT AND CHARACTERIZATION OF EST-SSR MARKERS FROM DE NOVO TRANSCRIPTOME SEQUENCING DATA IN RUBBER TREE (HEVEA BRASILIENSIS)". ไม่ระบุหน่วยงาน. ม.ป.ป.

Dejun Li. "DEVELOPMENT AND CHARACTERIZATION OF EST-SSR MARKERS FROM DE NOVO TRANSCRIPTOME SEQUENCING DATA IN RUBBER TREE (HEVEA BRASILIENSIS)". ไม่ระบุหน่วยงาน. ม.ป.ป.. Print.



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DEVELOPMENT AND CHARACTERIZATION OF EST-SSR MARKERS FROM DE NOVO TRANSCRIPTOME SEQUENCING DATA IN RUBBER TREE (HEVEA BRASILIENSIS)
Dejun Li
การยางแห่งประเทศไทย
ไม่ระบุวันที่เผยแพร่
Recent advances on biotechnology in rubber tree การพัฒนาเครื่องหมายโมเลกุล EST-SSR เพื่อการปรับปรุงพันธุ์ยางพารา De novo transcriptome sequencing of abiotic stress responsive transcripts of Hevea brasiliensis Differential expression of some ASR gene isoforms in the latex and bark of rubber tree. Effects of Ethrel stimulation. CURRENT CHALLENGESS FOR DE NOVO HEVEA BRASILIENSIS GENOME SEQUENCING Is impeded root growth related to the occurrence of rubber tree Trunk Phloem Necrosis (TPN)? Preliminary results from NE Thailand Components of Inorganic Phosphates in Rhizosphere of Rubber Tree (Hevea brasiliensis) Transcriptome Analyses Reveal Molecular Mechanism Underlying Tapping Panel Dryness of Rubber Tree (Hevea brasiliensis) DEVELOPMENT OF DWARF CLONES OF HEVEA BRASILIENSIS Process-based environmental models tree transpiration: A case study of rubber tree (Hevea brasiliensis)
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