Dataset Information

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis.

ABSTRACT: A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.

SUBMITTER: Ramakrishnan M

PROVIDER: S-EPMC5562303 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis.

Ramakrishnan M M Ceasar S Antony SA Vinod K K KK Duraipandiyan V V Ajeesh Krishna T P TP Upadhyaya Hari D HD Al-Dhabi N A NA Ignacimuthu S S

PloS one 20170818 8

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under P ...[more]

PMID: 28820887

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Project description:Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

Project description:Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal resistant and high yielding varieties of finger millet.

Dataset Information

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis.

Publications

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis.

Similar Datasets

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