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. 2017 Aug 18;12(8):e0183261.
doi: 10.1371/journal.pone.0183261. eCollection 2017.

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

M Ramakrishnan  1 , S Antony Ceasar  1   2 , K K Vinod  3 , V Duraipandiyan  1   4 , T P Ajeesh Krishna  1 , Hari D Upadhyaya  5 , N A Al-Dhabi  4 , S Ignacimuthu  1   6
Affiliations

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

M Ramakrishnan et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Root hair responses in the selected low P responding finger millet genotypes showing low and high number of root hairs under Psuf (*) and Pdef (**) conditions respectively.
Fig 2
Fig 2. Venn diagram comparing the genotype list based on low P tolerance exhibited for traits SL, RL, RHD and RHL.
The graphical comparison was analyzed based on genotypes’ performance for SL, RL, RHD and RHL under Pdef. The SDW and RDW were not used for graphical comparison. The graphical comparison identified 12 (9.40%) genotypes as low P tolerants, which produced higher values for traits SL, RL, RHD and RHL.
Fig 3
Fig 3. Identification of optimum population structure using Evanno’s method.
The ΔK values showed the highest peak corresponding to K = 3.
Fig 4
Fig 4. Inferred ancestry coefficients of the genotypes forming the sub-populations, SP1, SP2 and SP3.
See this image and copyright information in PMC

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