Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress

Abstract

Aluminum (Al) toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. Barley belongs to a group of crops that are most sensitive to Al in low pH soils. We present the RNA-seq analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 μM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. In the short-term experiment, more genes were differentially expressed (DEGs) between root meristems grown at pH = 6.0 and pH = 4.0, than between those grown at pH = 4.0 with and without Al treatment. The genes upregulated by low pH were associated mainly with response to oxidative stress, cell wall organization, and iron ion binding. Among genes upregulated by Al, overrepresented were those related to response to stress condition and calcium ion binding. In the long-term experiment, the number of DEGs between hydroponics at pH = 4.0 and 6.0 were lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 days Al treatment caused massive changes in the transcriptome profile. Over 4,000 genes were upregulated and almost 2,000 genes were downregulated by long-term Al stress. These DEGs were related to stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants. Additionally, we phenotyped the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH = 6.0, pH = 4.0, and pH = 4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress factor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be noted that in acidic arable lands, plants are exposed simultaneously to both of these stresses. The presented transcriptome analysis may help to find potential targets for breeding barley plants that are more tolerant to such conditions.

A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al

“…These results suggest that the genetic architecture for Al 3+ resistance and low pH tolerance in B. napus is distinct and complex. Similar conclusions that tolerance to low pH and resistance to Al 3+ stress are controlled by distinct genomic regions have been made for rice bean (Vigna umbellate), Arabidopsis and barley (Fan et al 2015;Nakano et al 2020;Szurman-Zubrzycka et al 2021). Nakano et al (2020) extended their investigation in Arabidopsis by using reverse genetics to confirm that some genes from the genetic regions they identified did influence aluminium resistance.…”

Transcriptomics and metabolomics reveal effect of arbuscular mycorrhizal fungi on growth and development of apple plants

“…Acidic conditions are more favorable for apple root growth ( Kochian et al., 2015 ). Although it is common that AMF promotes the accumulation of organic acids in plant roots, not all plant roots are adapted to acidic conditions, such as tomato, rice and barley ( Liu et al., 2016 ; Cristina et al., 2020 ; Szurman-Zubrzycka et al., 2021 ). Hage-Ahmed et al.…”

The barley DIR gene family: An expanded gene family that is involved in stress responses

“…For low nitrogen treatment, the seedlings of two barley genotypes BI-04 and BI-45 were treated with low nitrogen nutrient solution (0.24 mM ammonium nitrate) when the fourth leaf appeared, and new shoots were sampled immediately (0 h) or 1h and 24 h after the beginning of the low nitrogen treatment (Bio-project: PRJNA400519) ( Chen et al, 2018 ). For aluminum and low pH stress treatment, the root meristem of barley seedlings were grown under the optimal pH (6.0) and low pH (4.0) and aluminum (10 mM bioavailable Al 3+ ions) water culture conditions in two independent, short-term (24 h) and long-term (7 days), experiments (Bio-project: PRJNA704034) ( Szurman-Zubrzycka et al, 2021 ). Clean reads were mapped to the barley reference genome using the Hisat2 v2.2.1 software ( Pertea et al, 2015 ), and the corresponding gene expression levels, measured as the fragments per kilobase of transcript per million fragments mapped reads (FPKM) value, were evaluated by StringTie v1.3.5 ( Pertea et al, 2015 ).…”