Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L

Pan-genomic evolutionary analysis of MsPR10 gene family reveals MsPR10.SC10 plays a positive role in alfalfa salt tolerance

The PR10 gene family plays a critical role in plant stress responses. Phylogenetic analysis across species indicated that the PR10 gene first appeared during plant terrestrialization and underwent significant expansion. And, PR10 is conserved in leguminous plants, yet its genomic architecture and functional mechanisms in alfalfa (Medicago sativa L.) remains unclear. In this study, a pan-genomic analysis of 28 alfalfa accessions identified a total of 1657 MsPR10 genes, with tandem duplication accounting for the majority of gene expansion (61.19%). These MsPR10 genes were clustered into 81 Orthologous Gene Groups (OGGs) based on conservative levels, ranging from core to cloud genes. Significant expansion of PR10 genes in Zhongmu No.1 alfalfa (ZMNO) was associated with elevated transposon activity and selective pressure. Transcriptomic analysis indicated MsPR10.SC10 may be a key gene in alfalfa salt-tolerance. Transgenic alfalfa plants overexpressing MsPR10.SC10 were generated by Agrobacterium-mediated transformation. Detailed physiological tests suggested overexpression of MsPR10.SC10 enhanced salt tolerance of alfalfa by maintaining ion homeostasis (reducing Na+/K+ ratio), boosting antioxidant capacity by increasing SOD/ POD activity and reducing H2O2/ MDA accumulation, and regulates the expression of salt stress responsive genes. This study reveals the pan-genomic architecture of the PR10 gene family members in alfalfa, and provides valuable candidate gene for breeding of salt tolerant alfalfa cultivar and may also other crops.

Integrated genome-wide and expression analysis of YABBY genes in Triticum aestivum under PEG-induced osmotic, cold and combined stress.

Integrated Genomic, Transcriptomic and Metabolomic Analyses Identify Key Genetic Determinants and Regulatory Networks for Salinity Tolerance in Macrobrachium rosenbergii

Collectively, the NY strain achieves strong salinity tolerance by integrating genetic variation, transcriptional reprogramming and metabolic remodeling, synergistically maintaining ion homeostasis, osmotic balance and energy supply.

From QTL to candidate genes: a data-driven approach to unravel the genetic architecture of yellow rust resistance in central European wheat

A new approach to identify environment-specific quantitative trait loci (QTL) using GWAS and the validated resistance gene Yr27 was identified as sole candidate gene for one QTL region of particular relevance for Central European wheat.

Integrated BSA-seq and RNA-seq analyses reveal CmRABE1c as a negative regulator of drought tolerance and enable the development of a promoter SNP marker in Chinese chestnut

Drought stress severely limits both yield and nut quality of Chinese chestnut (Castanea mollissima Blume), an economically and ecologically important woody grain species native to China. However, the genetic basis of drought tolerance in Chinese chestnut remains a research gap. Our study fills this gap by identifying novel drought-responsive genes, which represents the first comprehensive molecular characterization of drought adaptation in this species. To dissect the genetic basis of drought tolerance and develop functional markers, we investigated 316 F1 seedlings derived from the cross between the drought-tolerant ‘Yanlong’ cultivar and the drought-sensitive ‘Shuofeng’. Bulked segregant analysis coupled with next-generation sequencing (BSA-seq) identified 80 drought-associated quantitative trait loci (QTLs) across 12 chromosomes. Integration of BSA−seq, RNA-seq, and parental resequencing resulted in the identification of a core candidate gene, CmRABE1c, encoding a ras-related protein. CmRABE1c overexpression in tobacco and poplar confirmed its negative regulatory role in drought tolerance. Notably, a GG-to-AA substitution at -312/-313 bp in the CmRABE1c promoter disrupted the GT1-motif and was significantly associated with drought tolerance across 60 chestnut accessions. Furthermore, transgenic tobacco and poplar assays proved this SNP may be diagnostic by showing that the AA allele confers superior drought tolerance compared to the GG allele. This diagnostic marker likely can be directly applied in marker-assisted selection (MAS) to screen and develop drought-tolerant chestnut cultivars, thereby accelerating breeding efficiency. In summary, this study provides valuable genetic resources and a robust functional SNP marker for drought resistance breeding in Chinese chestnut.

Integrating multiomic resources and gene expression studies to identify candidates for engineering climate-resilient Brassica

Climate-related stresses, including drought, salinity, temperature extremes (cold and heat), and waterlogging, substantially constrain Brassica napus productivity, particularly when they occur during reproductive development or as compound stresses. Because B. napus is an allotetraploid species, stress-resilience traits are shaped by polygenic inheritance, gene redundancy, and subgenome-specific regulation. This review integrates QTL mapping, GWAS, transcriptomic evidence, and functional studies to prioritize candidate genes and pathway-level modules associated with climate-resilience. Drought and salinity candidates converge on ABA signaling, osmotic adjustment, proline biosynthesis, aquaporin-mediated water transport, and ion-homeostasis pathways, including SOS and NHX-related components. Temperature resilience is associated with CBF/DREB-mediated cold acclimation and HSF-HSP-DREB2A-linked proteostasis under heat stress. Waterlogging tolerance is linked to hypoxia and ethylene signaling, redox protection, and CIPK15/SnRK1-related energy regulation. We distinguish positional candidates from expression-supported and experimentally validated genes and discuss how these targets can be used in MAS, genomic selection, allele pyramiding, and genome editing. Current evidence supports pathway-level convergence, but causal validation of individual B. napus gene copies and evaluation of yield trade-offs remain major priorities.