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
This study provides valuable genetic resources and a robust functional SNP marker for drought resistance breeding in Chinese chestnut, and proves this SNP may be diagnostic by showing that the AA allele confers superior drought tolerance compared to the GG allele.
Abstract
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.
Overall, transcription factors from the DREB, NAC, MYB, and WRKY families are still considered the primary regulatory targets, but CRISPR/Cas-based gene editing is now able to provide precise, multiplex gene modifications in polyploid wheat.
Amit Kumar, Shivani, R. Chaudhary et al.· Progressive Agriculture· 0 citations
Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.
Avanish Rai, Emil Vatov, Alicja Wieteska Georgieva et al.· Journal of Experimental Bota...· 0 citations
Oat (
Avena sativa
L.) is an important cereal crop used for both food and forage production, but its productivity is severely constrained by drought stress. Although non-coding RNAs (ncRNAs) are increasingly recognized as key regulators of plant responses to abiotic stress, the coordinated regulatory roles of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) in oat drought adaptation remain poorly understood.
In this study, four oat cultivars with contrasting drought tolerance were evaluated at the seedling stage under controlled drought conditions using 21 morphological, physiological, and photosynthetic traits. Principal component analysis (PCA) was performed to calculate a comprehensive drought resistance index (
F
value), allowing an integrated assessment of drought tolerance among the cultivars. Zhongyan No.1 (Z1) exhibited the highest drought tolerance, followed by Baiyan No.7 (B7), Denmark 440 (D4), and Longyan No.3 (L3). Based on these results, leaves from Z1 plants exposed to drought for 6 days were selected for whole-transcriptome sequencing. Transcriptome analysis identified 10,446 differentially expressed mRNAs, 116 differentially expressed lncRNAs, and 13 differentially expressed miRNAs. Functional enrichment analyses revealed that these drought-responsive transcripts were significantly enriched in pathways related to photosynthetic carbon fixation, starch and sucrose metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolism, suggesting extensive transcriptional reprogramming of carbon metabolism in response to drought stress. Furthermore, an lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) network was constructed, identifying a drought-responsive regulatory module centered on miR156 and comprising two lncRNAs, one miRNA, and eleven target mRNAs.
By integrating physiological evaluation with whole-transcriptome profiling, this study provided a comprehensive overview of ncRNA-mediated drought responses in oat seedlings by integrating physiological evaluation with whole-transcriptome profiling. The predicted regulatory networks, particularly the miR156-centered ceRNA module, provided valuable candidate regulatory modules for future functional validation and molecular breeding aimed at improving drought tolerance in oat.
Background: Drought tolerance in wheat is a complex trait controlled by multiple regulatory networks, among which calcium-dependent protein kinases (CDPKs) act as important components linking stress perception with downstream cellular responses. However, the functional contribution of individual CDPK members to drought adaptation in wheat remains largely unclear. This study aimed to identify and functionally characterize drought-responsive CDPK genes associated with differential drought responses in wheat. Methods: Two wheat lines derived from the same breeding background exhibiting contrasting drought adaption, 23B1 and 23B39, were subjected to PEG6000-induced osmotic stress. Growth traits, osmotic adjustment-related metabolites, membrane damage indicators, and antioxidant enzyme activity were evaluated. Transcriptomic analysis was performed at early drought-response stages, followed by differential expression analysis, functional enrichment, CDPK family screening, and qRT-PCR validation. The role of TaCDPK22-5A was further investigated using barley stripe mosaic virus (BSMV)-mediated virus-induced gene silencing (VIGS). Results: The drought-responsive line 23B1 maintained stronger growth, accumulated higher levels of proline and soluble sugars, exhibited enhanced peroxidase activity, and showed reduced membrane lipid peroxidation compared with 23B39. Transcriptome analysis revealed extensive transcriptional reprogramming under drought stress, with differentially expressed genes mainly associated with metabolic adjustment, transport regulation, secondary metabolism, and stress-responsive pathways. Among the identified CDPK members, TaCDPK22-5A showed a strong drought-responsive expression pattern in the line exhibiting stronger drought tolerance (23B1). Virus-induced gene silencing of TaCDPK22-5A significantly impaired drought tolerance, resulting in reduced growth, biomass accumulation, and chlorophyll retention under drought conditions. Conclusions: These findings demonstrate that TaCDPK22-5A contributes positively to drought adaptation in wheat and highlight CDPK-mediated calcium signaling as an important regulatory component of drought responses. The identified gene provides a potential target for improving drought resilience in wheat breeding.
Bo Liu, Yu Li, Hui-Na Li et al.· Genes· 0 citations
Background: Drought is one of the major abiotic stresses that affect and limit cotton growth and production. However, transcriptome differences between drought-tolerant and drought-susceptible cotton lines remain largely unknown. Methods and Results: In this study, two upland cotton cultivars, the drought-tolerant XLZ80 and drought-sensitive XLZ61, were subjected to comparative phenotypic and transcriptomic analyses under drought stress. Phenotypic evaluation showed that XLZ80 exhibited only mild leaf wilting, whereas XLZ61 displayed severe wilting symptoms after drought stress. RNA-seq analysis revealed that differentially expressed genes in XLZ80 were specifically enriched in pathways related to phosphatidylinositol signaling, phenylalanine metabolism, MAPK signaling, and betaine biosynthesis, while DEGs in XLZ61 were primarily involved in basal metabolic processes. A total of 9302 core DEGs were identified across and between the cultivars and were grouped into eight dynamic expression clusters containing 841 transcription factors. Weighted gene co-expression network analysis further identified three key modules associated with drought tolerance. Twelve hub genes, including GH_D02G2153 (MADS-box) and GH_A05G1087 (bZIP), were identified as central regulators. qRT-PCR validation confirmed that these genes exhibited faster and stronger induction in the tolerant cultivar. In summary, this study deepens the transcriptional-level understanding of drought stress responses in cotton and provides valuable gene resources for breeding drought-resistant cultivars.
Gang Wang, Wan-Li Han, Zhi-Bin Zhang et al.· Genes· 0 citations
Drought threatens global crop yields, and common oat, a vital nutritional source for food and feed, is particularly constrained in the semi‑arid regions where it is widely cultivated. Here, we report two high-quality genome assemblies for drought-resilient (Borris37) and drought-sensitive (XymC06) oat accessions with distinct seedling survival rates and genome sizes of 10.92 Gb and 10.96 Gb, and construct comprehensive landscapes of insertion‑deletions (InDels) and structural variants (SVs). Integrating population-level genomic, transcriptomic and phenotypic (seedling survival rate), we demonstrate that InDels and SVs underpin divergent drought resilience and identify 52 candidate genes associated with drought resistance whose expression is significantly modulated by these variants. Borris37 accumulates 36 favorable alleles of these genes. An InDel in the AsNF-YB3 promoter enhances binding to AsARF1, upregulating AsNF‑YB3 under drought, and overexpression of AsNF‑YB3 reduces ROS accumulation. Our findings provide resources and targets for drought‑resistance breeding in oat, thereby supporting global food security. Drought severely constrains common oat production. By generating genome assemblies for oat accessions with contrasting drought tolerance, the authors identify genetic variants and candidate genes underlying drought resistance, including an NF-Y transcription factor and its putative upstream regulator.
Shu-Hui Wang, Dong-Qing Liu, Ying-Ying Li et al.· Nature Communications· 0 citations
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