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QTL and candidate gene analyses of rootstock-mediated mandarin fruit yield and quality traits under contrasting iron availabilities

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Abstract

The most sustainable approach to overcome iron deficiency in fruit crops is breeding for rootstocks with a higher capability to acquire iron (Fe) from the soil. The objective of this study was quantitative trait loci (QTL) and candidate gene analyses of rootstock-mediated low-Fe tolerance in terms of fruit yield and quality traits, including Fe fruit content, in a satsuma mandarin-grafted rootstock population derived from a cross between Citrus reshni (Cleopatra mandarin) and Poncirus trifoliata, under sufficient and low-Fe fertilization (15.3 vs 5.2 μM Fe, respectively). Iron reduction to one-third significantly decreased satsuma leaf chlorophyll concentration, fruit iron concentration, and the fruit/leaf iron proportion. Thirty-four QTLs were detected for 46 heritable traits. Eighteen of them were also found significant when testing each parental genome separately. Seven QTLs contributed to the fruit concentrations of Cu, Fe, K, Na, and S. QTLs involved in rootstock mediated tolerance to Fe deficiency and fruit quality traits distributed into five genomic regions whose gene contents (assuming collinearity with the C. clementina genome) were investigated for overrepresented molecular functions and biological processes, and putative functional candidates. Among them, a metal-NA-transporter YSL3 (Ciclev 10019170m), four phytochelatin synthases, an iron-chelate-transporter ATPase, and four basic/helix-loop helix genes coding for likely relevant transcription factors in Fe homeostasis under Fe deficiency were found as follows: bHLH3 (Ciclev10019816m), bHLH137.1 (Ciclev10031873m), bHLH123 (Ciclev10008228m), and ILR3 (Ciclev10009354m). Genes within three QTL regions supported a genetic connection between rootstock-mediated tolerance to Fe deficiency and biotic stresses in citrus.

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Data availability

The SSR primer sequences are available upon request, for scientific purposes only, from the corresponding author mjasins@ivia.es. The genetic linkage maps were submitted to the Citrus Genome Database (https://www.citrusgenomedb.org/). Other markers are described in Raga et al. (2016). The parents of the progeny are kept at the Citrus Germplasm Bank, and the accession references are: IVIA-385 (Cleopatra mandarin), IVIA-537 (Flying Dragon trifoliate orange) and IVIA-236 (Rich trifoliate orange). Genomic data on candidate genes are provided as electronic supplementary material EMS_6.

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Acknowledgments

We thank Mrs. Miryam Rojas at Servicio de Instrumentación Científica de la Estación Experimental del Zaidín (CSIC) for mineral analysis and Mr. José Cerdá for technical assistance.

Funding

This work was supported by grants from the Spanish Government (MJA) (AGL2014-56675-R, AGL2017-82452-C2-2-R),

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

    Maria J. Asins, M. Verónica Raga, Dolors Roca & Emilio A. Carbonell

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  1. Maria J. Asins
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  2. M. Verónica Raga
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  3. Dolors Roca
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Correspondence to Maria J. Asins.

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Asins, M.J., Raga, M.V., Roca, D. et al. QTL and candidate gene analyses of rootstock-mediated mandarin fruit yield and quality traits under contrasting iron availabilities. Tree Genetics & Genomes 16, 79 (2020). https://doi.org/10.1007/s11295-020-01472-w

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