The first integrated phenotypic, genetic and molecular characterization of WUEL in octoploid strawberry is provided and candidate loci and pathways are identified, thereby establishing a foundation for improving WUEL-related traits.
Abstract
Water availability is a major constraint for intensive crops such as strawberry (Fragaria × ananassa), yet the genetic, physiological and molecular basis of water use efficiency remains poorly understood. Here, we evaluated a diverse collection of 132 accessions under well-watered (WW) and water-limited (WL) conditions (40% reduced irrigation) to dissect variation in leaf-level water use efficiency (WUEL), agronomic performance, and fruit quality. Substantial phenotypic variation was observed across 25 traits. Under WW conditions, lower stomatal density was associated with higher WUEL, yield, fruit weight, and firmness, suggesting a favorable carbon–water balance. Population structure analysis revealed that modern and exotic cultivars combine higher WUEL and agronomic performance with reduced stomatal density, suggesting an indirect selection during breeding. Genome-wide association studies detected 25 marker–trait associations for 11 traits, with all but one specific to water regime, highlighting a complex genetic architecture and important environmental effects. Transcriptomic analysis of accessions contrasting in stomatal density and WUEL identified 4837 differentially expressed genes and revealed two distinct strategies underlying water management: (1) an energy-conservative strategy characterized by reduced stomatal density and higher WUEL, enhanced ABA signaling and optimized photosynthetic electron transport; and (2) an energy-demanding strategy associated with higher stomatal density and lower WUEL, increased autophagy, activated stress-mitigating pathways and higher investment in secondary metabolism. Together, these results provide the first integrated phenotypic, genetic and molecular characterization of WUEL in octoploid strawberry and identify candidate loci and pathways, thereby establishing a foundation for improving WUEL-related traits.
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
Yield losses due to water-deficit (WD) conditions, especially during the reproductive stages of plant development, pose a significant threat to global canola (Brassica napus L.) production. Therefore, it is critical to investigate traits contributing to improved productivity under increased WD conditions. Here we present phenotypic, physiological and transcriptomic changes in response to WD across contrasting canola accessions exhibiting variation in drought resistance-related traits. WD significantly reduced shoot biomass, plant height, harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water-use efficiency and carbon isotope discrimination. WD caused 49 to 100% of the seed yield reduction: the minimum seed yield reduction (49.66%) was observed in a doubled-haploid (DH) line, 06-5101.137, while the maximum yield reduction (94.1 to 100%) occurred in the late-flowering DH lines (06.5101.088, 06-5101.306). Seed yield showed a positive correlation (r = 0.35 to 0.97) with shoot biomass, plant height, harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water use efficiency and carbon isotope discrimination. However, it showed negative correlations with days to flower, specific leaf weight, root length and root biomass (r = −0.08 to −0.80) across water treatments. The leaf transcriptome analysis of the two parental lines of DH population that exhibit variation for effective water use under well-watered and water-deficient conditions revealed different categories of differentially expressed genes (DEGs): WD-responsive DEGs in BC1329 parental line (1116) and BC9102 (1205) with 754 and 853 DEGs unique to BC1329 and BC9102, respectively, WD-responsive DEGs (906), genotype-dependent DEGs (8465) and genotype × treatment interaction DEGs (353). DEG annotations revealed that the WD-treatment-affected genes were involved in stress responses and growth and development. We further located 235 DEGs within the QTL regions underlying agronomic and physiological performance. Our study provides a conceptual framework for the morphological, physiological and molecular determinants involved in water-use efficiency. Seedlings’ traits with high heritability values, such as shoot biomass, leaf weight, leaf water content and Δ13C, serve as proxies for trait-based selection for improved seed yield under both water-limited and non-water-limited conditions.
H. Raman, B. McVittie, Niharika Sharma et al.· International Journal of Mol...· 0 citations
Drought during reproductive development and grain filling is a major constraint to bread wheat productivity in rainfed environments. In the present study, we employed genome-wide association analysis in an untapped diversity panel of wheat genotypes relevant to natural dryland conditions. A total of 186 genotypes were evaluated for drought-related physiological, biomass, and architectural traits under terminal rainfed stress in Azerbaijan. Relative water content, plant height, fresh weight, dry weight, flag leaf length, and flag leaf width were assessed at the milk ripening stage. These data were subjected to genome-wide association analysis using 19,737 SNP markers to identify loci and epistatic interactions involved in the determination of these traits. The panel showed broad phenotypic variation and significant genotypic effects for all traits, with broad-sense heritability ranging from 0.991 for plant height to 0.385 for flag leaf width. GWAS identified a major locus for relative water content on chromosome 2D at SNP marker AX-86184518, which explained 11.94% of the genotypic variation. Candidate-gene analysis highlighted the proximal WEB-family-like gene TraesCS2D03G1001000 as the main candidate gene. Plant height showed strong additive loci, mainly on chromosomes 2A and 4A, whereas biomass and flag leaf traits showed suggestive additive loci and epistatic interactions. These findings provide candidate loci and interaction patterns in the genetic make-up of essential traits, which may facilitate indirect selection in breeding new varieties.
S. Rustamova, A. Jahangirov, U. Gurbanova et al.· bioRxiv· 0 citations
Chlorophyll is the primary pigment responsible for capturing light energy and driving photosynthetic conversion. As the key photosynthetic organ during grain filling, the flag leaf plays a critical role in carbon assimilation, consequently, its chlorophyll content (FLC) represents a promising target for enhancing wheat yield and ensuring food security. Dissecting the genetic basis underlying FLC and elucidating its relationships with other agronomic traits are essential for accelerating molecular breeding aiming at improving photosynthetic efficiency and yield in wheat varieties. In this study, a major and environmentally stable quantitative trait locus (QTL) for FLC was detected using a population of 197 recombinant inbred lines (RILs). This QTL, designated
QFLC.scwl-4B
, was consistently mapped to chromosome arm 4BS across multiple environments, explaining 9.36%–31.82% of the phenotypic variance (PVE). The effect of
QFLC.scwl-4B
was further validated in an additional RIL population under diverse environmental conditions. Correlation and effect analyses revealed that
QFLC.scwl-4B
exhibits pleiotropic, leading to increased FLC, spikelet number per spike (SNS), and flag leaf thickness (FLT), alongside reduced productive tiller number (PTN). Furthermore, a putative candidate gene for
QFLC.scwl-4B
,
TraesCS4B03G0098300
, was identified as an ortholog of gene in BBX family, which is known to repress chlorophyll degradation and senescence, and likely involved in chlorophyll synthesis. Further, the promoter region of
TraesCS4B03G0098300
harbors a single nucleotide polymorphism (G/C) between the two parents. Collectively, these findings provide valuable QTL resources and candidate gene targets for marker-assisted selection in breeding programs aiming at developing wheat varieties with high photosynthetic efficiency and yield.
Jia-Jun Liu, Na-Na Qin, De-Fu Wang et al.· Frontiers in Plant Science· 0 citations
Analysis of candidate genes associated with NUE in a diploid potato diversity panel by evaluating morphological, physiological, and biochemical variables under contrasting nitrogen levels suggested distinct adaptive strategies.
A. Jiménez-Medrano, Johana Carolina Soto-Sedano, S. Magnitskiy et al.· ACS Agricultural Science &am...· 0 citations
Transgenic evaluations confirmed that OsSLT1 acts as a positive regulator of salt tolerance at the seedling stage, and no significant changes in Na+ or K+ accumulation were observed in flag leaves under the tested salt-stress condition, suggesting that OsSLT1 may regulate salt tolerance through mechanisms beyond classical shoot ion accumulation.
Sheng-Chang Wang, Yan-Hong Zhang, Haifu Tu et al.· Molecular breeding· 0 citations
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