Screening of qPCR Reference Genes in Quinoa Under Cold, Heat, and Drought Gradient Stress

Screening of qPCR Reference Genes in Quinoa Under Cold, Heat, and Drought Gradient Stress

Quinoa (<i>Chenopodium quinoa</i>), a stress-tolerant pseudocereal ideal for studying abiotic stress responses, was used to systematically identify optimal reference genes for qPCR normalization under gradient stresses: low temperatures (LT group: −2 °C to −10 °C), heat (HT group: 39° C...

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Bibliographic Details
Main Authors: Qiuwei Lu, Xueying Wang, Suxuan Dong, Jinghan Fu, Yiqing Lin, Ying Zhang, Bo Zhao, Fuye Guo
Format: Article
Language:English
Published: MDPI AG 2025-08-01
Series:Plants
Subjects:
<i>Chenopodium quinoa</i>
RT-qPCR
reference genes
low-temperature stress
heat stress
drought stress
Online Access:https://www.mdpi.com/2223-7747/14/15/2434
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Summary:Quinoa (<i>Chenopodium quinoa</i>), a stress-tolerant pseudocereal ideal for studying abiotic stress responses, was used to systematically identify optimal reference genes for qPCR normalization under gradient stresses: low temperatures (LT group: −2 °C to −10 °C), heat (HT group: 39° C to 45 °C), and drought (DR group: 7 to 13 days). Through multi-algorithm evaluation (GeNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder) of eleven candidates, condition-specific optimal genes were established as <i>ACT16</i> (Actin), <i>SAL92</i> (IT4 phosphatase-associated protein), <i>SSU32</i> (Ssu72-like family protein), and <i>TSB05</i> (Tryptophan synthase beta-subunit 2) for the LT group; <i>ACT16</i> and <i>NRP13</i> (Asparagine-rich protein) for the HT group; and <i>ACT16</i>, <i>SKP27</i> (S-phase kinase), and <i>NRP13</i> for the DR group, with <i>ACT16</i>, <i>NRP13</i>, <i>WLIM96</i> (LIM domain-containing protein), <i>SSU32</i>, <i>SKP27</i>, <i>SAL92</i>, and <i>UBC22</i> (ubiquitin-conjugating enzyme E2) demonstrating cross-stress stability (global group). <i>DHDPS96</i> (dihydrodipicolinate synthase) and <i>EF03</i> (translation elongation factor) showed minimal stability. Validation using stress-responsive markers—<i>COR72</i> (LT), <i>HSP44</i> (HT), <i>COR413-PM</i> (LT), and <i>DREB12</i> (DR)—confirmed reliability; <i>COR72</i> and <i>COR413-PM</i> exhibited oscillatory cold response patterns, <i>HSP44</i> peaked at 43 °C before declining, and <i>DREB12</i> showed progressive drought-induced upregulation. Crucially, normalization with unstable genes (<i>DHDPS96</i> and <i>EF03</i>) distorted expression profiles. This work provides validated reference standards for quinoa transcriptomics under abiotic stresses.
ISSN:2223-7747

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