Using Principal Component Analysis and RNA-Seq to Identify Candidate Genes That Control Salt Tolerance in Garlic (Allium sativum L.)

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

doi:10.3390/agronomy11040691

Xiangjun Zhou, Gang Li + Show 14 more

Open Access

https://doi.org/10.3390/agronomy11040691

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Abstract

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.

Highlights

Na+ and K+ concentrations among these garlic accessions ranged from 14.00–28.19 mg/g DW and 29.34–46.05 mg/g DW, reAgronomy 2021, 11, 691 spectively (Table 1), indicating differences among the garlic accessions in the uptake and exclusion of Na+ and K+
At the end of the treatment, nine traits were measured in garlic seedlings under non-salinity (Hoagland solution) and salinity (Hoagland solution with 200 mM NaCl), including shoot height (SH), shoot fresh weight (SFW), shoot dry weight (SDW), root length (RL), root fresh weight (RFW), root dry weight (RDW), photosynthesis rate, as well as Na+ and K+ concentrations in leaves (Table 1)
An average of around 29.7%, 46.9%, 29.8%, 42.4%, 40.7%, 36%, and 77.7% reduction was found for SH, SFW, SDW, RL, RFW, RDW, and photosynthesis rate, respectively

Summary

Introduction

ABA plays a crucial role in salt tolerance in many plant species by regulating stomatal closure, root growth, and stressresponsive gene expression. Sucrose non-fermenting-1-related protein kinases (SnRK2.2, SnRK2.3, and SnRK2.6), the central components in the ABA signaling pathway, are activated following the perception of ABA and regulate ion transport, reactive oxygen species (ROS) production, and gene expression by phosphorylating different targets [17,18]. Another well-studied signaling cascade involved in salt stress responses is the salt overly sensitive (SOS) pathway. Despite common characteristics in adaptation and tolerance of plants to salinity, the dominant mechanism by which plants survive salinity stress could be different from species to species

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