Analysis of natural variation in SlGRF10 in over 1,000 tomato accessions revealed that increased single-nucleotide polymorphism diversity in SlGRF10 is associated with lower fruit weight, which suggests that putative impaired activity contributes to reduced fruit weight, while breeding-induced reduction of genetic variation may have promoted increased fruit weight.
Abstract
Abstract Fruit weight is a key determinant of yield in high-value vegetable crops such as tomato. Despite extensive research, the molecular mechanisms underlying this complex trait remain largely elusive, with only a few genes cloned to date based on quantitative trait loci (QTL). Here, we analyzed 2 populations and reanalyzed 3 previously published populations and identified 945 QTL associated with agro-morphological traits, including both previously reported and unidentified loci. We focused on SlGRF10 (GROWTH-REGULATING FACTOR 10) underlying a fruit weight QTL, fw1.2. Loss of SlGRF10 reduced fruit weight by decreasing cell size, without affecting cell number. Analysis of natural variation in SlGRF10 in over 1,000 tomato accessions revealed that increased single-nucleotide polymorphism diversity in SlGRF10 is associated with lower fruit weight. This suggests that putative impaired activity contributes to reduced fruit weight, while breeding-induced reduction of genetic variation may have promoted increased fruit weight. Transcriptome profiling of SlGRF10 knockout lines 7 and 20 days postanthesis identified several differentially expressed genes involved in cell cycle progression. Our findings not only confirm the role of SlGRF10 in regulating tomato fruit weight but also highlight a set of candidate genes associated with key morpho-physiological traits. With fw11.3, named as CELL SIZE REGULATOR, being the only QTL related to cell size determination in tomato fruits so far, SlGRF10 offers a valuable target for precision breeding and enhances our understanding of fruit weight in tomato and related fruit-bearing species.
INTRODUCTION
Seed weight and nutritional composition (protein and oil content) are critical agronomic traits that collectively determine the yield and quality in soybean. However, the genetic architecture and regulatory mechanisms governing these traits remain poorly understood.
OBJECTIVES
This study aimed to identify the key genes and molecular mechanisms governing 100-seed weight and nutritional quality in soybean, providing a theoretical framework for the dual-enhancement of seed weight and protein content.
METHODS
A genome-wide association study (GWAS) was conducted using 1,702 diverse soybean cultivars to identify candidate loci associated with seed weight. Functional characterization was conducted through CRISPR-mediated knockout and overexpression analyses. Population genomic analyses were further performed to elucidate the evolutionary history and selection signals of the candidate gene.
RESULTS
We identified GmSW6 (Seed Weight 6), encoding a 2-oxoglutarate Fe(II)-dependent dioxygenase (2OGD), as a master regulator of 100-seed weight. Knockout of GmSW6 markedly enhanced seed weight and protein content while simultaneously reducing oil content. Mechanistically, we demonstrated that the transcription factor GmSW13 directly activates GmSW6 expression. This GmSW13-GmSW6 module, in turn, upregulates GmOLEO1 to coordinately modulate both seed weight and quality. Population genomic analysis revealed that the elite allele, GmSW6G, is significantly associated with increased seed weight and has undergone intense positive selection during soybean domestication and modern improvement.
CONCLUSION
Our findings elucidate a hierarchical genetic pathway governing soybean seed development and provide potent molecular targets for simultaneous improvement of seed weight and protein content in future 'designer' varieties.
Hao Zhang, Tianli Ge, Shiyu Guo et al.· Journal of Advanced Research· 0 citations
Fruit shape is a pivotal agronomic trait in tomato that significantly influences market classification and commercial value, yet the transcriptional regulation underlying its development are not fully elucidated. In this study, we identify WRKY-S as a critical regulator of fruit shape through its function in early fruit development. Expression analysis revealed that WRKY-S is highly expressed during early fruit stages. CRISPR/Cas9-mediated knockout of WRKY-S produced rounded fruits with reduced cell number along the proximal-distal axis, while overexpression resulted in irregular fruit shapes. Furthermore, WRKY-S can directly target the known fruit shape regulator gene FS8.1 to repress its expression. Notably, wrky-s mutants also exhibited increased inflorescence branching, higher fruit numbers, and improved yield without compromising fruit weight. Our findings establish WRKY-S as a novel transcriptional factor that modifies fruit shape and improves yield-related traits, providing new insights for tomato breeding.
Chunying Feng, Xinshuang Zhang, Ruoyu Yang et al.· Horticulture Research· 0 citations
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.
Mario Ruiz-Velázquez, Cristina Castillejo, J. F. Sánchez-Sevilla et al.· Horticulture Research· 0 citations
Fruit size is a key determinant of apple fruit quality and market value and is strongly influenced by phytohormone-regulated cell proliferation and expansion during early fruit development. Cytokinin oxidase/dehydrogenase (CKX) enzymes regulate cytokinin homeostasis by irreversibly degrading active cytokinins, but the contribution of natural variation in CKX genes to fruit size remains poorly understood. Here, we identified MdCKX6 as a candidate regulator of fruit growth in apple (Malus domestica). MdCKX6 exhibited pronounced allele-specific expression during fruit development in the cultivar 'Royal Gala'. Sequence analysis identified a promoter SNP associated with differential promoter activity and allele-specific expression. Genotyping of diverse apple cultivars and wild Malus accessions revealed a significant association between MdCKX6 promoter genotype and fruit size. Cultivars carrying low-expression alleles produced larger fruits, whereas high-expression alleles were associated with smaller fruits. To investigate gene function, MdCKX6 was overexpressed in tomato, resulting in reduced fruit size. Histological analyses of the transgenic tomato fruit revealed smaller pericarp cells. Transcriptome analysis of transgenic fruits revealed widespread changes in genes associated with cell-cycle regulation, cell wall modification, hormone-related processes, and transcriptional regulation. Together, these results identify MdCKX6 as a potential negative regulator of apple fruit growth and reveal an association between cis-regulatory variants, gene expression, and fruit size. This study provides new insights into the role of cytokinin metabolism in fruit development and highlights regulatory variation in MdCKX6 as a potential target for apple breeding.
M. Rahman, Hussain Ahmed, Zhe Zhou et al.· Plant Science· 0 citations
