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Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize (Zea mays L.) and their implications in breeding programs

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Abstract

Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses.

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Data availability

All data generated or analysed during this study are included in supplementary files (Table S1, S2, and S3).

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  1. Seema Sheoran & Sandeep Kumar

    Present address: ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, 132001, India

Authors and Affiliations

  1. ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India

    Seema Sheoran, Mamta Gupta & Sujay Rakshit

  2. ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India

    Shweta Kumari

  3. ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462030, India

    Sandeep Kumar

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  1. Seema Sheoran
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  5. Sujay Rakshit
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Contributions

Seema Sheoran: Data compilation and analysis, interpretation of results, manuscript drafting. Mamta Gupta: Data formatting and analysis. Shweta Kumari: Meta-QTL analysis. Sandeep Kumar: QTL studies data compilation and candidate genes description identification. Sujay Rakshit: Planning, interpretation and editing of manuscript. All the authors reviewed the manuscript.

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Correspondence to Sujay Rakshit.

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Key message

A total of 32 meta-QTL conferring tolerances to different abiotic stresses in maize were identified from 244 initial major QTL detected in 33 published QTL mapping studies.

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Sheoran, S., Gupta, M., Kumari, S. et al. Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize (Zea mays L.) and their implications in breeding programs. Mol Breeding 42, 26 (2022). https://doi.org/10.1007/s11032-022-01294-9

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