Using principal component analysis and rna-seq to identify candidate genes that control salt tolerance in garlic (Allium sativum l.)

Xiangjun Zhou, Yanxia Dou, Xiaoxia Huang, Gang Li, Hongrui Zhang, Dagang Jiang, Jinping Fan, Jorge Alberto Condori-Apfata, Xiaoqin Liu, Sandro Jhonatan Condori Pacsi, Roxana M. Bardales, Mayela Elizabeth Mayta Anco, Herbert Omar Lazo Rodríguez, Herbert Angel Delgado Salazar, Maria Valderrama Valencia, Cankui Zhang

Research output: Contribution to journalArticlepeer-review


To examine physiological responses of garlic to salinity, 17-day-old seedlings of eight soft-neck accessions were treated with 200 mM NaCl for seven days in a hydroponic system. Several morphological and physiological traits were measured at the end of the treatment, including shoot height, shoot fresh weight, shoot dry weight, root length, root fresh weight, root dry weight, photosynthesis rate, and concentrations of Na+ and K+ in leaves. The principal component analysis showed that shoot dry weight and K+/Na+ ratio contribute the most to salt tolerance among the garlic accessions. As a result, salt-tolerant and sensitive accessions were grouped based on these two parameters. Furthermore, to investigate the molecular mechanisms in garlic in response to salinity, the transcriptomes of leaves and roots between salt-tolerant and salt-sensitive garlic accessions were compared. Approximately 1.5 billion read pairs were obtained from 24 libraries generated from the leaves and roots of the salt-tolerant and salt-sensitive garlic accessions. A total of 47,509 genes were identified by mapping the cleaned reads to the garlic reference genome. Statistical analysis indicated that 1282 and 1068 genes were upregulated solely in the tolerant leaves and roots, whereas 1505 and 1203 genes were downregulated exclusively in the tolerant leaves and roots after NaCl treatment, respectively. Functional categorization of these genes revealed their involvement in a variety of biological processes. Several genes important for carotenoid biosynthesis, auxin signaling, and K+ transport were strongly altered in roots by NaCl treatment and could be candidate genes for garlic salt tolerance improvement.

Original languageEnglish
Article number691
Issue number4
StatePublished - Apr 2021

Bibliographical note

Funding Information:
Funding: This work was supported by Nexus Crops CRISPR and Phenomics: Individual and Institutional Capacity Building for Crop Science at Universidad Nacional de San Agustin (UNSA), Peru and the USDA National Institute of Food and Agriculture (Hatch project 1007567).

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • Garlic
  • Principal component analysis
  • RNA-seq
  • Salt stress
  • Transcriptome


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