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The genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet: an integrative meta-analysis approach

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Abstract

Drought stress is one of the most significant limiting factors limiting crop productions. Foxtail millet (Setaria italica) is among the most drought-tolerant crop plants, with a high degree of collinearity with other staple cereals. The present study used a meta-analysis approach to identify genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet. A meta-analysis employing all 448 collected original quantitative trait loci (QTL) identified 41 meta-QTL (MQTL) on the nine foxtail millet chromosomes. The confidence interval (CI) of the identified MQTL was determined to be 0.31–14.47 cM (5.23 cM average), which was 3.5 times narrower than the mean CI of the original QTL. Based on the available RNA-seq and microarray data, 1631 differentially expressed genes (DEGs) were detected in 41 MQTL. Furthermore, through synteny analysis, 8, 4, and 2 ortho-MQTL were recognized within co-linear regions of foxtail millet with rice (Oryza sativa), barley (Hordeum vulgare), and maize (Zea mays), respectively. To detect the most significant genome regions involved in the genetic control of drought tolerance and yield maintenance in foxtail millet, 10 MQTL with physical intervals of less than 1 Mb and seven hotspot regions with a high QTL-overview index were identified. Several candidate genes involved in foxtail millet sensing and signaling, transcription regulation, ROS inhibition, and adaptation to abiotic stress were detected by seeking drought-responsive genes in MQTL regions with a CI < 1 Mb. We hope that the achieved results would aid in developing new high-yielding drought-tolerant genotypes.

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Funding

This study was supported by Agricultural Biotechnology Research Institute of Iran (ABRII) (Grant No.: 12-05-05-017-96062-980197) and Biotechnology Development Council of the Islamic Republic of Iran (Grant No.: 980801).

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Authors and Affiliations

  1. Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran

    Fatemeh Loni & Ahmad Ismaili

  2. Molecular Physiology Department, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran

    Babak Nakhoda

  3. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran

    Hadi Darzi Ramandi

  4. Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran

    Zahra-Sadat Shobbar

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  1. Fatemeh Loni
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Contributions

FL and HDR performed the meta-analysis, drafted the manuscript and drew the graphs. FL analyzed the microarray data. The project was conceived, coordinated and supervised by Z-SS, who also revised the manuscript. The final manuscript was checked by AI and BN. All the authors reviewed and approved the final version of the manuscript.

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Correspondence to Ahmad Ismaili or Zahra-Sadat Shobbar.

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Communicated by Ben Zhang.

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Loni, F., Ismaili, A., Nakhoda, B. et al. The genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet: an integrative meta-analysis approach. Plant Growth Regul 101, 169–185 (2023). https://doi.org/10.1007/s10725-023-01010-3

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