Dataset Information

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development.

ABSTRACT: Broomcorn millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, which is well-adapted to extreme environments such as drought, heat, and salinity with an efficient C4 carbon fixation. Discovery and identification of genes involved in these processes will provide valuable information to improve the crop for meeting the challenge of global climate change. However, the lack of genetic resources and genomic information make gene discovery and molecular mechanism studies very difficult. Here, we sequenced and assembled the transcriptome of broomcorn millet using Illumina sequencing technology. After sequencing, a total of 45,406,730 and 51,160,820 clean paired-end reads were obtained for two genotypes Yumi No. 2 and Yumi No. 3. These reads were mixed and then assembled into 113,643 unigenes, with the length ranging from 351 to 15,691 bp, of which 62,543 contings could be assigned to 315 gene ontology (GO) categories. Cluster of orthologous groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses assigned could map 15,514 unigenes into 202 KEGG pathways and 51,020 unigenes to 25 COG categories, respectively. Furthermore, 35,216 simple sequence repeats (SSRs) were identified in 27,055 unigene sequences, of which trinucleotides were the most abundant repeat unit, accounting for 66.72% of SSRs. In addition, 292 differentially expressed genes were identified between the two genotypes, which were significantly enriched in 88 GO terms and 12 KEGG pathways. Finally, the expression patterns of four selected transcripts were validated through quantitative reverse transcription polymerase chain reaction analysis. Our study for the first time sequenced and assembled the transcriptome of broomcorn millet, which not only provided a rich sequence resource for gene discovery and marker development in this important crop, but will also facilitate the further investigation of the molecular mechanism of its favored agronomic traits and beyond.

SUBMITTER: Yue H

PROVIDER: S-EPMC4955294 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development.

Yue Hong H Wang Le L Liu Hui H Yue Wenjie W Du Xianghong X Song Weining W Nie Xiaojun X

Frontiers in plant science 20160721

Broomcorn millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, which is well-adapted to extreme environments such as drought, heat, and salinity with an efficient C4 carbon fixation. Discovery and identification of genes involved in these processes will provide valuable information to improve the crop for meeting the challenge of global climate change. However, the lack of genetic resources and genomic information make gene discovery and molecular mechanism studies very ...[more]

PMID: 27493657

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Project description:Waxy varieties of the tetraploid cereal broomcorn millet (Panicum miliaceum L.) have endosperm starch granules lacking detectable amylose. This study investigated the basis of this phenotype using molecular and biochemical methods. Iodine staining of starch granules in 72 plants from 38 landrace accessions found 58 nonwaxy and 14 waxy phenotype plants. All waxy types were in plants from Chinese and Korean accessions, a distribution similar to that of the waxy phenotype in other cereals. Granule-bound starch synthase I (GBSSI) protein was present in the endosperm of both nonwaxy and waxy individuals, but waxy types had little or no granule-bound starch synthase activity compared with the wild types. Sequencing of the GBSSI (Waxy) gene showed that this gene is present in two different forms (L and S) in P. miliaceum, which probably represent homeologues derived from two distinct diploid ancestors. Protein products of both these forms are present in starch granules. We identified three polymorphisms in the exon sequence coding for mature GBSSI peptides. A 15-bp deletion has occurred in the S type GBSSI, resulting in the loss of five amino acids from glucosyl transferase domain 1 (GTD1). The second GBSSI type (L) shows two sequence polymorphisms. One is the insertion of an adenine residue that causes a reading frameshift, and the second causes a cysteine-tyrosine amino acid polymorphism. These mutations appear to have occurred in parallel from the ancestral allele, resulting in three GBSSI-L alleles in total. Five of the six possible genotype combinations of the S and L alleles were observed. The deletion in the GBSSI-S gene causes loss of protein activity, and there was 100% correspondence between this deletion and the waxy phenotype. The frameshift mutation in the L gene results in the loss of L-type protein from starch granules. The L isoform with the tyrosine residue is present in starch granules but is nonfunctional. This loss of function may result from the substitution of tyrosine for cysteine, although it could not be determined whether the cysteine isoform of L represents the functional type. This is the first characterization of mutations that occur in combination in a functionally polyploid species to give a fully waxy phenotype.

Project description:Broomcorn millet (BM), one of the earliest domesticated cereal crops originating in northern China, can tolerate extreme conditions, such as drought and high temperatures, which are prevalent in saline-alkali, arid, and barren landscapes. However, its adaptive mechanism to alkali stress is yet to be comprehensively understood. In this study, 80 and 40 mM standard alkali stress concentrations were used to, respectively, evaluate the alkali tolerance at the germination and seedling stages of 296 BM genotypes. Principal component analysis (PCA), Pearson's correlation analysis, and F-value comprehensive analysis were performed on the germination parameters (germination potential, germination index, germination rate, vigor index, root length/weight, sprout length/weight, and alkali damage rate). Based on their respective F-values, the BM genotypes were divided into five categories ranging from highly alkali resistant to alkali sensitive. To study the response of seedlings to alkaline stress, we investigated the phenotypic parameters (plant height, green leaf area, biomass, and root structure) of 111 genotypes from the above five categories. Combining the parameters of alkali tolerance at the germination and seedling stages, these 111 genotypes were further subdivided into three groups with different alkali tolerances. Variations in physiological responses of the different alkali-tolerant genotypes were further investigated for antioxidant enzyme activity, soluble substances, malondialdehyde (MDA) content, electrolyte leakage rate, and leaf structure. Compared with alkali-sensitive genotypes, alkali-tolerant genotypes had high antioxidant enzyme activity and soluble osmolyte content, low MDA content and electrolyte leakage rate, and a more complete stomata structure. Taken together, this study provides a comprehensive and reliable method for evaluating alkali tolerance and will contribute to the improvement and restoration of saline-alkaline soils by BM.

Dataset Information

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development.

Publications

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development.

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