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ABSTRACT:
PROVIDER: PRJEB25899 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We perfomed a high-resolution genetic map and QTL analysis of growth-related traits in 144 progenies of Hevea brasiliensis. The reference genome sequence was used to discover high-quality and nonredundant SNPs, which helped to obtain a higher-resolution genetic map with 18 linkage groups. Additionally, this project provided a better undestanding of QTL associated with growth and drought.
2018-10-11 | PRJEB25899 | EVA
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis
2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress
Project description:Ramie is an important industrial fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood. Herein, a high-density genetic map with 1085 markers spanning 2,118.8 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in eight, six, six, three, and ten QTLs for SD, SL, BW, BD and FY traits, respectively. These 33 QTLs were mapped into 11 genomic regions, thus forming 11 QTL clusters; there were 11 QTLs identified their beneficial alleles from the wild species BNT. Interestingly, all QTLs in Cluster 8 and Cluster 10 displayed overdominance, indicating that these two regions were likely heterotic loci. In addition, there were five fiber yield-related genes identified to undergo positive selection in previous study, and they were found to locate into the genomic region near to the QTLs of this study. The genetic dissection for FY and its related traits improved our understanding to the genetic basis of these traits, as well to their domestication in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.
2019-01-31 | GSE125891 | GEO
Project description:We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (RY8-79 and PR107). The output of sequenced data showed that more than 26 million sequence reads with average length of 90nt were generated in both clones. Totally 51829 unigenes (mean size = 640 bp) were assembled through transcriptome de novo assembly, which represent more than 16-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 6726 different expression unigenes (3018 up and 3708 down) were detected as PR107 versus RY8-79. Functional analysis showed mass of categories were reprogrammed between two clones, which relate latex generation and expelling difference between them. As a comparative transcriptome analysis, the results obtained here will greatly expand our understanding of physiological differences among varieties in molecular level and will contribute t The transcriptome of latex in Hevea brasiliensis
2015-03-29 | E-GEOD-59981 | biostudies-arrayexpress
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information.
2011-09-01 | GSE26514 | GEO
Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.
2022-06-23 | GSE186533 | GEO