Search Results (185)

In this study, we dissect the genetic effects of two major rice heading date genes, Heading date 1 (Hd1) and Grain number, plant height, and heading date 7 (Ghd7), in the regulation of six photosynthesis-related traits: the chlorophyll a/b contents, net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), and transpiration rate (Tr). Using two sets of near-isogenic lines (Z43 and Z44) derived from a Zhenshan97/Milyang46 cross, functional Hd1 increased the chlorophyll contents but decreased the photosynthesis-related parameters; however, functional Ghd7 consistently inhibited all six traits. More importantly, there is a significant epistatic interaction between them: Hd1 only enhances the photosynthetic capacity under the non-functional background of ghd7 but intensifies its photosynthesis inhibition under the functional background of Ghd7. Transcriptome analysis showed that functional Ghd7 mainly down-regulated the expression of genes related to photosynthesis and chloroplast development, and the inhibitory effect was significantly enhanced in the presence of functional Hd1. GO enrichment analysis further confirmed that the chlorophyll synthesis, photosystem assembly, and electron transfer pathways were downregulated in the bifunctional allele combination. Although Hd1 promotes chlorophyll accumulation, it reduces the actual photosynthetic efficiency, indicating that it has different regulatory paths for chlorophyll synthesis and photosynthetic function. Both physiological and molecular evidence showed that the Hd1-Ghd7 module coordinated the regulation of the heading date and photosynthetic capacity, forming a trade-off relationship between “early heading–high photosynthesis” and “late heading–low photosynthesis”. This study reveals the pleiotropy of genes at the heading stage and provides a theoretical basis for the optimization of the source–sink balance in high-yield rice breeding. Full article

Wheat (Triticum aestivum L.) is one of the most cultivated crops in the world, but production is often affected by drought. The wheat chromosome 4A contains several quantitative trait loci (QTL) associated with drought tolerance and yield-related traits, making it a valuable target for genetic improvement. In this study, we developed near-isogenic lines (NILs) carrying qDT.4A.1, a major QTL for yield using a fast generation cycling system (FGCS) and characterized these NILs for grain yield and thousand-grain weight (TGW) under drought stress and control conditions. We identified a single nucleotide polymorphism (SNP) marker Kukri_c27037_112, which showed a consistent genotype–phenotype associations across two NIL pairs. This marker is linked to four candidate genes encoding a RING-finger E3 ubiquitin ligase, a receptor kinase, and a protein kinase family protein involved in drought stress response and pathways. In silico expression analyses revealed upregulation of these genes in grain tissue under drought conditions, supporting their potential role in grain development and yield formation during drought stress conditions. The identified SNP marker and its associated candidate genes are potential resources in marker-assisted selection and fine mapping pending further validation and functional studies. Our results provide valuable genomic resources, laying the foundation for the development of drought-tolerant wheat varieties and highlighting chromosome 4A as a key region governing drought tolerance. Full article

Fruit quality in melon (Cucumis melo L.) is determined by complex traits such as texture and aroma, which are shaped by both genetic factors and environmental conditions. In this study, we applied an integrated physiology–metabolomics–transcriptomics approach to examine the genetic and seasonal regulation of these traits in the near-isogenic line SC10-2, carrying a defined introgression on linkage group X (LG X), in comparison with its recurrent parent ‘Piel de Sapo’ (PS). Fruit firmness, juiciness, respiration, ethylene production, and volatile organic compounds (VOCs) were evaluated over postharvest ripening across two growing seasons. SC10-2 consistently exhibited firmer flesh, reduced juiciness, and distinct VOC profiles relative to PS, although the magnitude of these differences varied between seasons. Transcriptomic analysis identified 2954 differentially expressed genes genome-wide, including 909 genes located within the LG X introgression, among which candidate genes such as CmTrpD, CmHK4-like, and CmNAC18 showed expression patterns associated with texture- and aroma-related traits. Seasonal comparisons indicated that VOC composition was particularly sensitive to environmental variation, underscoring the contribution of genotype × season interactions to fruit quality expression. Together, these results refine the phenotypic and molecular characterization of the LG X introgression in SC10-2 and provide testable candidate genes and hypotheses for understanding the genetic basis of melon texture and aroma under the studied conditions. Full article

Salinity is a major abiotic stress limiting rice production worldwide. This study aims to elucidate the effects of heading date on salt tolerance in rice. Five near-isogenic lines (NILs) developed from the SL2038/Koshihikari backcross population were grown with or without salt stress. SL2038 is a salt-tolerant line with delayed heading (~18 days) compared to the salt-sensitive background Koshihikari. The results showed that late-heading NILs produced significantly higher plant dry weight, panicle weight, percentage of filled grains, and grain weight (p < 0.05) under long-term salt stress. In Koshihikari, which exhibited delayed heading due to long-day treatment, the percentage of white heads was low, and panicle and grain weights were significantly higher under salt stress. Experiments with different sowing times indicated that late heading, such as sowing in June, resulted in higher grain weights. This is the first report to assess the impact of heading date on agronomic and yield-related traits under salt stress. In conclusion, even with a prolonged salt treatment period, heading during periods of low temperature and solar radiation results in higher grain weight under salt stress. This is proposed as one of the strategies for salt escape. These findings can be used to improve rice yield and implement crop management in salt-affected regions. Full article

Grain weight, a highly heritable yield component, is a primary breeding target for enhancing wheat productivity. Unraveling the molecular dynamics underlying grain development is essential for identifying key regulators controlling this trait. In this study, we employed an integrated multi-omics approach to analyze transcriptomic and proteomic profiles in developing grains using pairwise near-isogenic lines with contrasting grain weight across four grain developmental stages. Our analysis revealed that early grain development, particularly at 7 days post-anthesis, serves as a critical window during which differential regulation of genes and proteins involved in carbohydrate biosynthesis and metabolic pathways establishes the final grain weight. By combining weighted gene co-expression network analysis (WGCNA) and K-means clustering, we identified a grain weight-associated module and pinpointed four high-confidence candidate genes. Among these, TaYAK1-2D, which encodes a YAK family protein kinase, was functionally validated as a positive regulator of grain weight through mutational analysis. Sequence analysis revealed two major natural haplotypes of TaYAK1-2D, with TaYAK1-2D-Hap2 being significantly associated with higher grain weight across multiple environments. Our findings not only delineate a crucial metabolic window governing grain weight but also provide both a novel genetic target and a practical haplotype marker for molecular breeding aimed at yield improvement in wheat. Full article

Postharvest fungal pathogens, such as Botrytis cinerea, Alternaria alternata and Fusarium culmorum, pose major challenges for pepper (Capsicum annuum) storage and shelf-life. To explore the basis of induced resistance, near isogenic lines (NILs) differing in pigmentation (green vs. purple fruits and their red ripe counterparts) were artificially inoculated and evaluated for disease severity by phenotyping and by qPCR, and metabolite composition by spectroscopy and by HPLC. Infection severity was strongly dependent on whether purple or green NILs were infected and on ripening stage: economically ripe fruits were most susceptible to B. cinerea, whereas biologically ripe fruits displayed higher infection rates with A. alternata. In the case of B. cinerea infection, detailed HPLC analysis revealed that chlorogenic acid and p-coumaric acid were identified as infection-responsive metabolites after analyzing the metabolite changes upon infection. Total anthocyanin content and delphinidin derivatives measured decreased upon infection; however, this effect was not significant in correlation with the infection severity, indicating that B. cinerea infection in low, moderate or severe amounts will lead to the degradation of these compounds. Overall, our findings indicate that anthocyanin accumulation alone did not confer resistance to B. cinerea in pepper, whereas specific hydroxycinnamic acids emerged as infection-responsive markers. Full article

To identify key genes involved in drought stress response among Chinese cabbage materials with different drought resistance, a pair of waxy near-isogenic lines (NILs) of Chinese cabbage were used as materials, and a 10% polyethylene glycol (PEG) 6000 solution was employed to simulate drought stress. A comparative analysis of phenotypes, physiology, and transcriptomes under drought stress was conducted in this study. Compared with the non-waxy material T065-2, the waxy material T065-1 exhibited 5068, 5512, 5210, and 5875 significantly differentially expressed genes (DEGs) at 0, 6, 12, and 24 h under drought stress, respectively. These DEGs were primarily enriched in “response to oxygen levels” and “secondary metabolite biosynthesis” biological processes and “biosynthesis of secondary metabolites” and “glucosinolate biosynthesis” pathways. Combined with gene function annotation, 26 genes related to the abscisic acid (ABA) signaling pathway (e.g., PYL2, PYL6, SnRK2.5, and SnRK2.10), 63 genes associated with wax synthesis and transport (e.g., MAH1, CER3a, ABCG25, and LTPG1), and 84 transcription factor genes (e.g., ERF, WRKY, and MYB) were identified, all of which showed significant differential expression in the waxy NILs of Chinese cabbage, potentially participating in drought stress response. The reliability of the transcriptomic analysis was validated using qRT-PCR. These findings provide a crucial theoretical foundation for exploring drought-resistant molecular markers and editing targets in Chinese cabbage, significantly accelerating the breeding of superior drought-resistant varieties. Full article

Arsenic (As) contamination in rice poses a serious risk to food safety and human health. Genetic dissection of As-related quantitative trait loci (QTLs) provides a sustainable strategy for breeding low-As cultivars. In this study, we aimed to improve the detection of minor-effect QTLs for total As accumulation by optimizing both environmental and genetic factors. A recombinant inbred line (RIL) population derived from the cross between Yuzhenxiang (YZX, indica) and YBK (Javanica) was used for initial QTL mapping, and a single locus, qAs1, was identified on chromosome1. To enhance As uptake and phenotypic differentiation, we conducted QTL validation and fine mapping under high-As and continuously flooded conditions using near-isogenic lines (NILs) to minimize background genetic interference. The effect of qAs1 was consistently validated across generations, and the locus was refined to a 159.5 kb genomic interval. Transcriptome analysis revealed three differentially expressed genes (LOC_Os01g52110, LOC_Os01g52214, and LOC_Os01g52260) involved in redox regulation and detoxification. These findings demonstrate the effectiveness of NIL-based fine mapping under optimized environmental conditions and provide promising targets for the genetic improvement of low-As rice cultivars. Full article

The regulatory mechanism of brassinolide (BR) signaling in cucurbitaceae crops remains incompletely understood. Previous research demonstrated that the rice genes GW5 and GW5L modulate seed morphology via the BR pathway. However, the conservation of their orthologs in watermelon and their evolutionary trajectory are yet to be elucidated. In this study utilizing the watermelon 97103v2 genome, we identified 15 GW5-LIKE genes. Through structure, phylogenetic tree construction, collinearity, promoter and spatiotemporal expression analysis, we determined that ClGL1 to ClGL3 are the most closely related to GW5 and GW5L. Subsequently, two crucial materials were acquired: the inbred line Jing L6M harboring the homozygous mutant Clgl1, and the near-isogenic line Changhong, a Jing L6M backcross containing the wild-type allele ClGL1. Apart from the disparity in fruit morphology, a clear difference in seed shape was observed between the two. Furthermore, exogenous BR treatment demonstrated that ClGL1 positively regulated the BR signal, aligning with the positive impact of GW5 and GW5L. In conclusion, ClGL1 modulates the morphology of watermelon fruit and seed by enhancing BR signaling, which provides a key gene and theoretical basis for BR signaling evolution and molecular design breeding in Cucurbitaceae. Full article

Kernel row number (KRN) is a pivotal determinant for yield in maize breeding programs. However, the genetic basis underlying KRN remains largely elusive. To identify candidate genes regulating KRN, a population of 318 BC₄F₄ chromosomal segment substitution lines (CSSLs) was developed via backcrossing, with Baimaya (BMY) as the donor parent and B73 as the recurrent parent. Furthermore, a high-density genetic linkage map containing 2859 high-quality single-nucleotide polymorphism (SNP) markers was constructed for quantitative trait locus (QTL) mapping of KRN. Notably, 19 QTLs controlling KRN were detected across three environments and in the Best Linear Unbiased Prediction (BLUP) values; among these, a major-effect QTL (qKRN4.09-1) was consistently identified across all three environments and BLUP. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears from near-isogenic lines (NILs) uncovered a candidate gene, Zm00001eb205550. This gene exhibited significant downregulation in qKRN4.09-1^BMY, and two missense variants were detected between qKRN4.09-1^BMY and qKRN4.09-1^B73. Zm00001eb205550 exhibited preferential expression in developing ears. Moreover, the pyramiding of favorable alleles from the five stable QTLs significantly increased KRN in maize. These findings advance our genetic understanding of maize ear development and provide valuable genetic targets for improving KRN in maize breeding. Full article

Although heterosis plays a crucial role in enhancing crop yield and stress resistance, its underlying genetic mechanism remains not yet fully understood. Previous studies have shown that heterosis tends to increase with greater genetic distance in the absence of reproductive isolation barriers. However, whether variation in parental genome size alone can generate heterosis under near-isogenic backgrounds has not been thoroughly explored. Here, we used a rapeseed double haploid (DH) inducer line to generate progeny from the Pol CMS three-line hybrid Rongyou 18 (RY18). Although the progeny maintained the same ploidy level as the parents, their genome sizes showed notable variation (818.99–1024.88 Mb). To eliminate genetic distance effects, multiple DH progeny carrying restorer genes were crossed as paternal parents with the female parent 0068A of RY18, creating novel F₁ hybrids. Using RY18 as the control, we observed a marked reduction in the genetic distance between the newly induced restorer line and the female parent (0068A). Correlation analysis further revealed a significant negative correlation (r = −0.310 *) between the paternal genome size and heterosis for thousand-seed weight (TSW). Furthermore, the genomic expansion in hybrid offspring relative to the male parent showed that significant correlations were observed between paternal genome size and heterosis over the standard for both TSW (r = 0.300, p < 0.05) and plot yield (r = 0.326, p < 0.05). Resequencing of high-and low-yielding F₁ hybrids identified SNP sites, indicating that under an identical genetic background, heterosis for yield was more pronounced on chromosome A and chromosome C04. The doubled haploid (DH) induction line facilitates the generation of parental lines with distinct genome sizes, potentially providing a potential novel approach for studying heterosis research in Brassica napus. Full article

Clubroot disease, caused by Plasmodiophora brassicae, is a threat to Brassica crops; therefore, understanding of host-resistance is important for developing clubroot-resistant cultivars. Using multi-omics analysis of clubroot-resistant (CR) and -susceptible (CS) near-isogenic lines (NILs) of B. napus, carrying the resistance of turnip (B. rapa var. rapifera), we characterized the host resistance mechanisms. Through proteome analysis, we identified 6626 differentially abundant proteins (DAPs) (2353 in CR-NILs, 4273 in CS-NILs) (q < 0.05), of which 50 in CR- and 62 in CS-NILs were detected across the disease developmental stages. Notable proteins included those involved in reactive oxygen species scavenging (BnaA09T0647200WE)], cell-wall modifications (BnaA04T0244300WE) and glucosinolate biosynthesis (BnaA01T0266700WE) in the CR-NILs. Additionally, disease-resistance proteins like ENHANCED DISEASE RESISTANCE 2-like (BnaA03T0055600WE) and hairpin-induced family protein YLS9 (BnaA08T0237900WE) showed increased abundance in CR-NILs. In contrast, CS-NILs exhibited decreased abundance of defense-related proteins, including proteins containing CUPIN domain (BnaA09T0578800WE) and LACCASE (BnaA02T0019200WE). Integration of proteome data with transcriptome data revealed 33 genes in CR- and 32 in CS-NILs showing a consistent pattern, including the genes related to PLANT INVERTASE/PECTIN METHYLESTERASE INHIBITOR (BnaC04T0003100WE), KELCH MOTIF (BnaC02T0374800WE), LACCASE (BnaA02T0019200WE), and antioxidant-related transcripts [GLUTATHIONE S-TRANSFERASES (BnaA03T0280900WE) and 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE (BnaA09T0641500WE)]. Our findings offer valuable new targets for breeding clubroot-resistant B. napus. Full article

Bacterial spot of the pepper (BSP) and the tomato (BST) caused by multiple Xanthomonas spp. remains a major constraint to production of both crops worldwide. The widespread breakdown of dominant resistance genes, such as Bs2, due to the emergence of virulent races, like Xanthomonas euvesicatoria P6, has underscored the need for more durable, non-race-specific resistance. The recessive genes, bs5; bs6; and bs8, have emerged as promising alternatives, conferring broad-spectrum resistance without triggering a hypersensitive response. In this study, we systematically evaluated the individual and combinatorial effects of these three recessive resistance genes against three Xanthomonas species, X. euvesicatoria (Xe), X. hortorum pv. gardneri (Xhg), and X. perforans (Xp). Using near-isogenic lines (NILs) developed in the susceptible Early Calwonder (ECW) background, we assessed the in planta bacterial population growth and symptom development across a panel of eight genotypes carrying different gene combinations. Our results demonstrate that bs5, particularly when combined with either bs6 or bs8, significantly reduces bacterial growth and disease severity across all three Xanthomonas species. The triple-stacked line (ECW568 (i.e., bs5, bs6, and bs8)) consistently displayed the strongest suppression of pathogen proliferation and symptom development. By contrast, bs6 and bs8, alone or in combination, were largely ineffective. In some cases, combining bs6 with bs8 was less effective than bs8 alone. These findings reinforce the central role of bs5 in conferring quantitative resistance and highlight the additive benefit of pyramiding recessive resistance genes. Furthermore, we have demonstrated that these recessive resistance genes are effective in limiting the ability of the emerging pathogen, X. perforans, to grow in planta, and thus are predicted to offer a high level of resistance in the field. Our work provides key insights for breeding durable, broad-spectrum resistance into commercial pepper cultivars and offers a framework for integrated disease management strategies in the face of rapidly evolving bacterial pathogens Full article

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL-Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL-Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL-Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL-Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers. Full article

To elucidate the genetic basis of thousand-kernel weight (TKW) related to fundamental traits such as kernel length (KL), kernel width (KW), and kernel diameter ratio (KDR) at the individual quantitative trait loci (QTL) level, both unconditional QTL analysis and conditional QTL analysis for TKW were analyzed using a recombinant inbred line (RIL) population, along with a simplified physical map. A total of 37 unconditional QTLs and 34 conditional QTLs were identified. Six QTLs exhibited independent effects from individual traits (KL, KW, or KDR), while 18 QTLs showed common influences from two or three of these traits simultaneously. Additionally, 26 pairs of epistatically interacting QTLs involving 16 loci were detected. Subsequently, fine mapping of the stable and major-effect QTL QTkw1B was carried out using the derived near-isogenic lines (NILs), ultimately locating it within the interval of 698.15–700.19 Mb on chromosome 1B of the KN9204 genome. The conditional QTL analysis and genetic effect analysis based on NILs both indicated that the increase in TKW was primarily contributed by kernel length. The QTL identified in the present study through the combination of conditional and unconditional QTL mapping could increase the understanding of the genetic interrelationships between TKW and kernel size traits at the individual QTL level and provide a theoretical basis for subsequent candidate gene mining. Full article