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QTL and candidate gene analyses of rootstock-mediated tomato fruit yield and quality traits under low iron stress

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Abstract

The use of iron-efficient rootstocks can be a sustainable way to enhance iron (Fe) fruit content in tomato. A hybrid tomato variety was grafted on a genotyped population of recombinant inbred lines derived from Solanum pimpinellifolium, and compared with self- and non-grafted controls under low iron (5.2 µM) growing conditions. Rootstock effects on total fruit yield, fruit [Fe] and yield Fe content (FeUEc) were the target traits; other minerals were also investigated by quantitative trait loci (QTL) and candidate gene analyses. The rootstock genotype affected fruit concentrations of Fe, Ca, Mg, Mn, Na, P, S, Si and Al. Most rootstocks increased FeUEc. Fruit and leaf [Fe] and FeUEc were genetically complex, involving epistatic interactions. Six and eight QTLs were detected for these traits, respectively, by multiple QTL mapping. Two kinds of relevant genes were found among candidates within QTLs for iron related traits: those coding for secretory proteins specific of the tomato xylem sap under iron deficiency, and others having a role in iron uptake such as TOMLHA1, FRO1, NRAMP2, FER and MYB72. Detected QTLs might reflect differences in the regulatory regions of those relevant genes, more than in their coding sequences.

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Acknowledgements

We thank Mrs. Miryam Rojas at Servicio de Instrumentación Científica de la Estación Experimental del Zaidín (CSIC) for mineral analysis, and Dr. Luis Galipienso (IVIA) for viral tests. This work was supported by grants from the Spanish Government (MJA) (AGL2014-56675-R, AGL2017-82452-C2-2-R), and Fondo Social Europeo de la Comunitat Valenciana (DT) (01/15-FSE-02).

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  1. Instituto Valenciano de Investigaciones Agrarias, Carretera de Moncada a Náquera Km 4.5, Apartado Oficial, 46113, Moncada, Valencia, Spain

    M. J. Asins, M. V. Raga, D. Torrent, D. Roca & E. A. Carbonell

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  1. M. J. Asins
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  2. M. V. Raga
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  3. D. Torrent
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Correspondence to M. J. Asins.

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Supplementary Fig.

 1-Course of the experiment; (A), general view of grafted tomato plants grown under commercial conditions but limiting Fe nutrition (March 2017); (B), fruit yield (May 2017); (C), a hand is holding a truss with bronze, deformed tomatoes. (PDF 353 kb)

Supplementary Fig.

 2-Relative (A) and absolute (B) mean concentrations of elements at the fruits (left) and leaves (right) of the commercial tomato variety grafted on the recombinant inbred lines. Y axes in B correspond to element concentration in ppm. (PDF 91 kb)

Supplementary Fig.

 3-Graphic representation of principal component analysis of variability found among grafted RILs under commercial, iron limiting conditions for vegetative, mineral, and fruit yield and quality traits. Three groups of elements are noted (encircled). (PDF 129 kb)

Supplementary Table

 4-Pearson coefficients between significantly correlated traits (p ≤ 0.05). (XLSX 18 kb)

Supplementary Table

 5-Summary list of candidate genes for major QTLs (See QTLs with SNP in bold and excluding those related to Fe traits at Table 2), some of them are segregating for frameshift Indels (Kevei et al. 2015) in parental genomes, E9 or L5, (Mut.). The Locus reference, its relative root expression (Exp.) in Heinz cultivar (Max: maximum, H: high, M: medium, VL: very low, L: low and N: no data), and the number of genes counted from the QTL peak (Ord.) are also shown. (XLSX 12 kb)

Supplementary Fig.

 6-LOD profiles of QTLs for Fe_L, Fe_F and FeUEc. QTL peaks detected for two traits at the same region are encircled. Genetic positions along the 12 chromosomes are shown under the X axis. (PDF 130 kb)

Supplementary Table

 7-Overrepresented Biological processes within QTLs detected for iron related traits by means of the PANTHER Classification System (http://www.pantherdb.org/) using the Fisher´s Exact with FDR multiple test correction. The suffix _All denotes all downloaded genes were considered, while _Seg corresponds to those genes segregating in the RIL population for frameshift mutations only. (XLSX 13 kb)

Supplementary Table

 8-List of genes within  %Cit_12, the QTL detected for citric acid fruit content in chromosome 12, some segregating for frameshift Indels (Kevei et al. 2015) in parental genomes, E9 or L5, (Mut.). The Locus reference, its relative root expression (Exp.) in Heinz cultivar (Max: maximum, H: high, M: medium, VL: very low, L: low and N: no data), and the number of genes counted from the QTL peak (Ord.) are also shown. (XLSX 23 kb)

Supplementary Table

 9-List of genes within QTLs detected for frequency of fruits with blossom end rot (pFNber), some segregating for frameshift Indels (Kevei et al. 2015) in parental genomes, E9 or L5, (Mut.). The Locus reference, its relative root expression (Exp.) in Heinz cultivar (Max: maximum, H: high, M: medium, VL: very low, L: low and N: no data), and the number of genes counted from the QTL peak (Ord.) are also shown. (XLSX 40 kb)

Supplementary Fig.

 10-Overrepresented molecular functions within blossom end rot QTLs by means of the PANTHER Classification System (http://www.pantherdb.org/) using the Fisher´s Exact with FDR multiple test correction. (PDF 171 kb)

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Asins, M.J., Raga, M.V., Torrent, D. et al. QTL and candidate gene analyses of rootstock-mediated tomato fruit yield and quality traits under low iron stress. Euphytica 216, 63 (2020). https://doi.org/10.1007/s10681-020-02599-6

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