Genome-Wide Identification of the PYL Gene Family in Chenopodium quinoa: From Genes to Protein 3D Structure Analysis

Abstract

The halophytic crop Chenopodium quinoa has a remarkable resistance to harsh growth conditions in suboptimal environments and marginal soils. Additionally, quinoa is a pseudocereal and produces seeds with outstanding nutritional value. Quinoa is an allotetraploid (2n = 4× = 36) with an estimated genome size of approximately 1.5 Gbp. In plants, the family of pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory components of ABA receptors (RCAR) play a vital role in the initial step of ABA signaling, leading to abiotic stress resistance. Here 20 CqPYL genes were identified using the genome-search method. Based on the phylogenetic analysis, these CqPYL genes were divided into three classes or subfamilies. These genes have different structures and intron numbers, even within the same subfamily. Analysis of conserved motifs showed the presence of the PYR_PYL_RCAR motif domain in each PYL protein sequence. Furthermore, the tissue-specific expression of CqPYLs was analyzed through public available RNA-seq data. CqPYL4a/b and CqPYL8c/d showed higher expression levels in seedlings. Finally, 3D structures of the CqPYL proteins were predicted by homology modeling and analyzed through topology inspection to speculate on putative new ABA receptor features. This study provides a theoretical basis for further functional study of PYL genes for stress-resistance breeding of quinoa and other crops.