High temperatures interfere with meiotic recombination and the subsequent progression of meiosis in plants, but few genes involved in meiotic thermotolerance have been characterized. Here, we characterize a maize (Zea mays) classic dominant male-sterile mutant Ms42, which has defects in pairing and synapsis of homologous chromosomes and DNA double-strand break (DSB) repair. Ms42 encodes a member of the heat shock protein family, HSP101, which accumulates in pollen mother cells. Analysis of the dominant Ms42 mutant and hsp101 null mutants reveals that HSP101 functions in RADIATION SENSITIVE 51 loading, DSB repair, and subsequent meiosis. Consistent with these functions, overexpression of Hsp101 in anthers results in robust microspores with enhanced heat tolerance. These results demonstrate that HSP101 mediates thermotolerance during microsporogenesis, shedding light on the genetic basis underlying the adaptation of male meiocytes to high temperatures.

The sugarcane genus Saccharum is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph–based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 homolog linked to tillering as a promising gene-editing target to boost cane yield. Additionally, the pangenome supports dosage-informed genome-wide association study, improving heritability estimates and identification of sugar or leaf-angle–associated loci, including SaIRX10 and SaBAK5 . Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.

Accessible chromatin regions (ACRs) encompass diverse cis-regulatory elements (CREs) crucial for gene regulation, but their variations from parents to hybrids and their contribution to heterosis remain poorly understood. Here, using MNase hypersensitivity sequencing (MH-seq) across the maize B73–Mo17 pan-genome, we analyze chromatin accessibility in inbreds and their hybrids. Approximately 81% of ACRs are syntenic in parents, while ~20% show parent-specific accessibility driven by motif divergence. Chromatin accessibility is more stably inherited than transcriptomic profiles, yet ~3.5% of ACRs exhibit non-additive inheritance in hybrid. Among these, transgressively up-regulated ACRs are evolutionarily constrained, enhanced for chromatin modifications and interactions, and localized within enhancers and CRE-clusters serving as regulatory hubs, regulating complex traits including photoperiod and metabolite levels. Overexpression of a candidate rhamnosyl transferase gene under hybrid chromatin context increases plant height, suggesting a potential contribution to heterosis. Our study provides an insightful perspective on the role of chromatin accessibility in driving heterosis.

Tripidium arundinaceum , a wild perennial grass with exceptional stress tolerance, has been tested in sugarcane breeding. Its complex polyploid genome has hindered understanding of its evolution and adaptive traits. Here, we present a high-quality, haplotype-resolved reference genome for autohexaploid T. arundinaceum Hainan92-105 (2 n = 6 x = 60). T. arundinaceum is likely originated from a diploid ancestor approximately 1.31 million years ago and contains abundant repetitive sequences from two major recent bursts of long terminal repeat retrotransposons following polyploidization. Phylogenetic analyses place Saccharum closer to Sorghum bicolor than to T. arundinaceum , indicating that the polyploidizations in these two lineages occurred independently. Population genomics analysis reveals southwestern China (Yunnan) as a diversity center for T. arundinaceum within China. Genotype–environment associations highlight temperature and precipitation as key local adaptation drivers mediated by stress-associated genes. This study provides a genomic resource for understanding polyploid evolution and climate adaptation in T. arundinaceum .