Pangenome-scale analysis of the PYL gene family reveals evolutionary conservation, regulatory diversification and salt-responsive haplotypes in Brassica napus.

Authors

Xin Liu, Yongxin Nie, Xuyang Chen, Xingge Ding, Tingting Chen, Yuanlin Zhao, Xin Zhao, Yue Yan, Minghu Zhang, Meng Liu

Published in

Frontiers in plant science. Volume 17. Pages 1870359. Epub Jun 08, 2026.

Abstract

Abscisic acid (ABA) signaling is a central determinant of plant stress adaptation, yet the evolutionary and functional diversity of its receptor family remains poorly understood at the pangenome scale in polyploid crops. We analyzed the PYL ABA receptor family across eight high-quality Brassica napus genomes and identified 405 genes, revealing a predominantly conserved core repertoire together with a limited but dynamic dispensable fraction. Although BnPYLs retained a highly conserved phylogenetic framework, gene gain and loss varied among clades, and structural diversification was concentrated in non-core members. Promoter and transposable-element analyses indicated that regulatory-region variation may have contributed to family diversification, with the presence of putative MYB/MYC, ABA- jasmonate, and light-responsive cis-elements and widespread transposable-element accumulation in flanking regions. Copy number, structural variation and duplication analyses showed that the family was shaped primarily by ancient whole-genome duplication, followed by localized copy-number changes and asymmetric structural remodeling between subgenomes. Despite this genomic plasticity, BnPYLs remained under pervasive purifying selection and displayed strong syntenic conservation across accessions. Expression profiling uncovered substantial transcriptional divergence, including widespread root-preferential expression and selective induction of specific BnPYLs under salt stress. Four salt-responsive genes were validated by qRT-PCR, and haplotype analysis further showed that natural allelic variation at these loci is associated with yield performance under saline-alkaline conditions. These findings establish a pangenome framework for understanding the evolutionary stability and functional diversification of ABA receptors in rapeseed, and provide candidate allelic resources for future functional validation and breeding improvement of stress resilience and yield stability.

PMID:
42339382
Bibliographic data and abstract were imported from PubMed on 24 Jun 2026.

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