Insertion of a TRIM-like sequence in MdFLS2-1 promoter is associated with its allele-specific expression in response to Alternaria alternata in apple

Zhaolin Liang; Kai Liu; Chunyang Jiang; An Yang; Jiadi Yan; Xiaolei Han; Caixia Zhang; Peihua Cong; Liyi Zhang

doi:10.3389/fpls.2022.1090621

Insertion of a TRIM-like sequence in MdFLS2-1 promoter is associated with its allele-specific expression in response to Alternaria alternata in apple

Front Plant Sci. 2022 Dec 29:13:1090621. doi: 10.3389/fpls.2022.1090621. eCollection 2022.

Authors

Zhaolin Liang^{1

2}, Kai Liu^{1

2}, Chunyang Jiang^{1

2}, An Yang^{1

2}, Jiadi Yan^{1

2}, Xiaolei Han^{1

2}, Caixia Zhang^{1

2}, Peihua Cong^{1

2}, Liyi Zhang^{1

2}

Affiliations

¹ Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China.
² Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China.

Abstract

Alternaria blotch disease, caused by Alternaria alternata apple pathotype (AAAP), is one of the major fungal diseases in apple. Early field observations revealed, the anther-derived homozygote Hanfu line (HFTH1) was highly susceptible to AAAP, whereas Hanfu (HF) exhibited resistance to AAAP. To understand the molecular mechanisms underlying the difference in sensitivity of HF and HFTH1 to AAAP, we performed allele-specific expression (ASE) analysis and comparative transcriptomic analysis before and after AAAP inoculation. We reported an important immune gene, namely, MdFLS2, which displayed strong ASE in HF with much lower expression levels of HFTH1-derived alleles. Transient overexpression of the dominant allele of MdFLS2-1 from HF in GL-3 apple leaves could enhance resistance to AAAP and induce expression of genes related to salicylic acid pathway. In addition, MdFLS2-1 was identified with an insertion of an 85-bp terminal-repeat retrotransposon in miniature (TRIM) element-like sequence in the upstream region of the nonreference allele. In contrast, only one terminal direct repeat (TDR) from TRIM-like sequence was present in the upstream region of the HFTH1-derived allele MdFLS2-2. Furthermore, the results of luciferase and β-glucuronidase reporter assays demonstrated that the intact TRIM-like sequence has enhancer activity. This suggested that insertion of the TRIM-like sequence regulates the expression level of the allele of MdFLS2, in turn, affecting the sensitivity of HF and HFTH1 to AAAP.

Keywords: MdFLS2; TRIM element; allele-specific expression; alternaria alternata apple pathotype; malus domestica borkh..