Genome-wide identification of the PYL gene family and functional validation of SiPYL3 in foxtail millet (Setaria italica)

Abstract

PYL (pyrabactin resistance-like) functions not only as a receptor but also as a crucial component in the ABA signaling pathway. Nevertheless, the functions of the SiPYL genes in foxtail millet remain largely unexplored. In this study, a comprehensive bioinformatics-based analysis of the PYL gene family in foxtail millet was conducted across the whole genome. As a result, ten SiPYL genes were identified and subsequently classified into three groups. Additionally, an in-depth investigation was carried out on the gene structure, conserved motifs, chromosomal localization, cis-acting elements, collinearity, and expression patterns of these SiPYL genes. The expression profiles of SiPYL family members under drought, salt, and ABA treatments suggested that they might adopt distinct strategies in response to adverse environmental conditions. Based on the qRT-PCR results, we found that the transcript levels of SiPYL3 were significantly upregulated under various abiotic stress conditions. Functional verification demonstrated that SiPYL3 might play a role in weakening drought resistance while positively modulating salt tolerance during the seedling stage. Furthermore, the overexpression of SiPYL3 leads to an increase in both the grain number and grain weight in rice. The outcomes of haplotype analysis indicated that SiPYL3^HAP4 exhibited a higher thousand grain weight compared with other SiPYL3 haplotypes. In conclusion, our results revealed the fundamental characteristics of the SiPYL gene family and laid a solid basis for the breeding of high-yield and stress-tolerant foxtail millet varieties.