Theoretical and Applied Genetics最新文献

Drought stress is a major global challenge in crop production. The occurrence of drought during seed germination directly affects crop establishment and final yield. In this work, we performed whole-genome resequencing of 414 mungbean (Vigna radiata (L.) R. Wilczek) germplasms and identified 4,875,142 high-quality single-nucleotide polymorphisms (SNPs). Two seed germination traits of the mungbean panel under drought stress across two environments were evaluated via a genome-wide association study (GWAS), and the results revealed a significant quantitative trait locus (QTL). Additionally, kompetitive allele-specific PCR (KASP) markers that can identify the germination characteristics of mungbean seeds under drought stress were developed and verified. Moreover, among the nine candidate genes near this site, the expression levels of different haplotypes of VrERF088 differed. Interestingly, the only ABA-responsive element in the VrERF088 promoter was mutated. The results demonstrated that VrABI5 activates the transcriptional activity of the Hap1 promoter by binding to the ABRE motif. The overexpression of VrERF088 in Arabidopsis thaliana significantly reduced the germination rate of plants under drought stress by increasing the expression of the ABA response genes AtPM6 and AtLEA4 and reducing the expression of the germination-related genes AtEXPAs, resulting in hypersensitivity to ABA. Our results indicate that mutation of the ABRE motif in the VrERF088 promoter results in a relatively high germination rate under drought stress.

Key message: Identification of TaAGL6-B1 as the candidate gene underlying the B locus reveals its role as a key regulator of awn suppression in wheat2. A nonsynonymous substitution causes ectopic expression of TaAGL6-B1 in lemmas, repressing TaDL and inhibiting awn elongation. These findings elucidate the genetic network controlling awn development and provide molecular insight for wheat breeding. Awns are photosynthetically active structures that extend from the lemma and enhance grain filling and drought tolerance in wheat (Triticum aestivum L.), where their development is regulated by three major loci: B1 (Tipped1), B2 (Tipped2), and Hd (Hooded). The aim of this study was to identify the gene encoding the B2 locus, whose molecular identity remains elusive despite its central role in awn suppression. Fine mapping and association analyses identified TaAGL6-B1, an AGAMOUS-LIKE 6 transcription factor gene homologous to rice OsMADS6, as the most likely candidate gene. A non-synonymous substitution in the conserved K-box domain was strongly associated with awn phenotype. Cultivars carrying this amino acid substitution exhibit ectopic expression of TaAGL6-B1 in the lemma, the tissue from which they originate. Furthermore, we identified a cultivar that harbours an amino acid change and exhibits ectopic expression of TaAGL6-B1, yet retains long awns. Genomic sequencing of the TaAGL6-B1 allele in this cultivar revealed an 869-bp insertion in exon 8, resulting in a frameshift mutation that leads to loss of gene function. Additionally, the expression level of TaDL, a wheat orthologue of DROOPING LEAF (DL), which promotes awn elongation in rice, was elevated in long-awned cultivars and closely correlated with awn phenotype. Given that OsMADS6 represses DL in rice, ectopic expression of TaAGL6-B1 in lemmas could inhibit awn elongation by repressing TaDL. These findings strongly support TaAGL6-B1 as a B2 candidate gene and provide novel insights into the genetic network regulating awn development in wheat.

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Key message: Designing genomic selection to capture the additive and epistatic effects. Genomic selection (GS) offers great potential to accelerate long-term genetic gain, but strategic decisions such as progeny size and number of crosses remain poorly established, particularly under contrasting resource scenarios. We conducted stochastic simulations of rice breeding programs over 50 years (10 cycles) using progeny sizes of 25, 50, 100, and 200 individuals, under both theoretical (unlimited resources) and practical (budget-constrained to 4000 F₂ individuals) contexts, and considering three levels of epistasis (absent, moderate, high). In theoretical scenarios, larger progenies consistently achieved higher gains. After 50 years, progenies of 200 individuals reached cumulative responses to selection of 2.39 (1.96% yr^-1) with no epistasis, 3.20 (2.60% yr^-1) under moderate epistasis, and 3.48 (3.34% yr^-1) under high epistasis. These schemes also maximized prediction accuracy and efficiently converted additive and epistatic variance into genetic gain. Conversely, under budget constraints, smaller progenies combined with more crosses outperformed larger ones. Progenies of 25 and 50 individuals achieved the greatest responses-up to 2.58 (2.07% yr^-1) without epistasis, 3.36 (2.76% yr^-1) under moderate epistasis, and 2.72 (2.45% yr^-1) under high epistasis-while maintaining higher genetic diversity across cycles. Our results demonstrate that in resource-unlimited conditions, larger progenies (200 individuals) maximize the capture of additive and epistatic effects, whereas in budget-constrained programs, smaller progenies (25-50 individuals) coupled with more crosses provide the most efficient strategy. These findings provide practical guidelines for breeders to design GS schemes that reconcile high long-term genetic gain with operational feasibility, highlighting the decisive role of epistasis in shaping gain trajectories.

Wheat stripe rust is a fungal disease that decreases wheat yield and quality. In this study, 300 winter wheat cultivars (lines) from different regions were infected with stripe rust and analyzed in terms of disease severity and infection type at the seedling and adult-plant stages. Additionally, a genome-wide association study was performed using the wheat 90 K SNP chip. Sixteen accessions exhibited all-stage resistance to the prevalent Pst races CYR32 and CYR34. Moreover, the enriched compressed mixed linear model detected 261 marker-trait associations at the seedling and adult-plant stages; these markers were located on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3D, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. By combining this finding with a linkage disequilibrium decay distance of 1.72 Mb, 20 and 12 quantitative trait loci related to stripe rust resistance at the seedling and adult-plant stages, respectively, were identified; these QTLs explained 0.01%-20.85% of the phenotypic variation. Comparative analysis with known Yr genes or quantitative trait loci (QTLs) revealed 11 potentially novel seedling-stage resistance loci and 7 novel adult-plant resistance loci. Three of these loci were on chromosomes 2A, 3A, and 3D, which explained 16.49%-20.85%, 7.41%-19.27%, and 8.78%-18.56% of the phenotypic variation, respectively. Additionally, haplotype analysis showed that Hap2 significantly improved stripe rust resistance. Additionally, functional Kompetitive allele-specific PCR markers were developed and validated for SNP loci Kukri_c2289_635. Hence, this study provides a theoretical basis, parental materials, and molecular markers that may be useful for breeding disease-resistant wheat cultivars.

Key message: Leaf and panicle blast resistances were moderately correlated and controlled by several genes, including Pi2/Pi9 and Pi33. GWAS-based marker weighting increased GBLUP predictive ability by up to 37% across two rice populations. Breeding for blast resistance remains a high priority in rice (Oryza sativa L.) improvement, yet the genetic complexity of leaf blast (BL) and panicle blast (PB) continues to challenge prediction accuracy in genomic selection (GS). Traditional GS approaches, such as genomic best linear unbiased prediction (GBLUP), assume equal contribution from all markers, potentially limiting the capture of key resistance loci. Recent advances integrating genome-wide association studies (GWAS) into GS offer new opportunities to weight markers based on their biological relevance. In this study, we dissected the genetic architecture of BL and PB resistance in two diverse rice populations and evaluated the performance of three weighted GBLUP models that incorporate marker information from GWAS. Marker weighting strategies included F_ST-based weighting (F_ST-w), squared additive effects (AE-w), and - log₁₀(p)-based weighting (- log₁₀(p)-w). We identified significant marker-trait associations (MTAs), including key loci near the Pi2/Pi9 cluster and Pi33 gene regions on chromosomes 6 and 8. A moderate genetic correlation (0.43-0.44) between BL and PB severity suggests partially shared genetic control. Across traits and populations, AE-w and - log₁₀(p)-w models improved predictive ability by 4-37% (0.03-0.23) and reduced normalized root mean square error by 3.8-35.3% relative to the unweighted GBLUP. These results demonstrate the value of integrating GWAS into GS (GS + GWAS) and highlight marker weighting as a practical strategy to enhance prediction accuracy for complex traits like blast resistance, ultimately accelerating genetic gains in rice breeding programs.

Key message: Genetic analysis of wheat Distinctness, Uniformity, and Stability (DUS) characteristics identifies significant marker-trait associations for 15 DUS traits, including associations for 'seed: colouration with phenol' closely linked to Ppo-A1. Crop improvement via breeding underpins the yield gains required for future food security. Commercial development of new varieties is supported by the legal protection afforded by Plant Variety Rights, which for wheat is awarded via evaluation of 27 morphological 'characteristics' as part of Distinctness, Uniformity, and Stability (DUS) testing. While identification of molecular markers predictive for wheat DUS characteristics would be useful to aid processes such as variety identification and DUS test optimization, little is known about their genetic control. Here we assemble a panel of 412 European wheat varieties, along with corresponding DUS phenotypic data and genotype using the TaNG 43k genotyping array. The resulting 14,921 polymorphic genetic markers were distributed approximately evenly between the A (33%), B (38%), and D (29%) wheat sub-genomes. DUS characteristic heritability (h²) varied (mean = 0.44), ranging from 0.27 ('ear: glaucosity') to 1.00 ('ear: scurs or awns'). Subsequent genome-wide association study (GWAS) identified significant marker-trait associations for 15 of the 24 DUS characteristics analysed, resolved into 57 genetic loci. Of note, a highly significant association (- log₁₀P = 44.79) for 'seed: colouration with phenol' on chromosome 2A was just 0.37 Mb from the Ppo-A1 gene known to control discolouration in wheat food products. GWAS was less successful for DUS characteristics with low heritability (traits with h² below or above 0.5 had a mean of 1.2 and 5.3 GWAS hits, respectively), for which the use of molecular markers would be more suited to alternative approaches such as genomic prediction. Collectively, this work will inform marker-aided approaches for DUS-relevant applications.

Rice grain protein content is crucial for its quality and nutritional value, but the mechanisms of nitrogen transport to the grain remain poorly understood. This study demonstrates that the amino acid transporter OsAAP4 regulates protein accumulation in rice grains. OsAAP4 is expressed during grain filling, increasing at the mid-filling stage. Analysis of aap4 mutants in Zhonghua11 and Nipponbare backgrounds revealed significantly reduced grain yield and polished rice protein content compared to wild-type. Furthermore, mutant grains showed markedly lower nitrogen content at both filling and maturity stages. Analysis of amino acid concentrations revealed that the contents of most amino acids in the grains of the aap4 mutant were significantly lower than those in the wild type. Nitrogen content analysis indicated that the aap4 mutation had a minimal impact on plant nitrogen content, suggesting that the reduced grain protein content in the aap4 mutant was due to its loss of function within the grain. Yeast heterologous complementation experiments suggest that OsAAP4 may mediate the transmembrane transport of amino acids. Further investigation revealed that OsAAP4 can encode a plasma membrane localized protein and is expressed in the vascular bundles of grains during filling. Interestingly, overexpression of OsAAP4 simultaneously increased both rice yield and grain protein content. Transcriptomic analysis revealed that OsAAP4 may influence plant hormone signaling, protein formation on the ER, and various amino acid metabolic processes in grains. Collectively, these findings indicate that OsAAP4 might plays a crucial role in the translocation of amino acids into grains, thereby regulating grain protein content.

Key message: This study identified efficient marker combinations consisting of two significant SNPs associated with salt tolerance in cowpea, providing genomic insights and candidate frameworks for future validation and breeding applications. Salt stress is a major abiotic factor that severely reduces crop productivity, particularly in arid and semi-arid regions. Its effects are further exacerbated by climate change and the continuous buildup of salts in the soil. Although cowpea (Vigna unguiculata L.) is regarded as a promising crop in drought- and heat-prone areas, it remains especially susceptible to salt stress during its early developmental stages. To investigate the genetic foundation of salt tolerance, a genome-wide association study (GWAS) was carried out using 401 genetically diverse cowpea germplasms. This analysis integrated phenotypic assessments under 200 mM NaCl treatment at the early vegetative stage with 34,704 high-quality single-nucleotide polymorphisms (SNPs). Four morpho-physiological traits were chosen to assess responses to salt stress, including leaf scorch score (LSS), leaf chlorophyll content (LCC), and the contents of leaf sodium ions (LSI) and leaf chloride ions (LCI). GWAS identified several significant marker-trait associations, among which six SNPs with the highest statistical significance across the four traits were selected. Candidate genes associated with these SNPs were involved in ion transport, regulation of reactive oxygen species (ROS), and secondary metabolite biosynthesis, which are fundamental mechanisms in salt tolerance. Moreover, the combination of two SNPs, 2_52855 and 2_38343, proved to be the most effective marker for distinguishing salt-tolerant germplasms. Germplasms containing the GC genotype at this combination, meaning the G allele at the SNP 2_52855 and the C allele at the SNP 2_38343, consistently demonstrated enhanced salt tolerance. These findings enhance our understanding of the genetic architecture of salt stress response in cowpea and provide a foundation for identifying molecular markers that can be validated and applied in future breeding efforts.

Key message: Through the integration of GWAS and RNA-seq analysis, three candidate genes associated with unsaturated fatty acids were identified in soybean. Heterologous overexpression of these genes in Arabidopsis confirmed their functions in altering seed fatty acid profiles. As a major source of the world's vegetable oil, the nutritional value and storage stability of soybean oil are largely determined by the relative contents of unsaturated fatty acids (UFAs). However, the genetic regulations of UFAs in soybean remains incompletely understood. To elucidate the regulatory mechanisms governing UFAs in soybean seed, a panel of 312 soybean accessions was evaluated across five environments, and a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTLs) for UFA traits. A total of 52 stable QTLs were detected in at least two environments, including 20, 16 and 16 QTLs associated with oleic acid (OA), linoleic acid (LA) and linolenic acid (LNA), respectively. Of them, qOA10-4 and qLNA13-2 were consistently detected across four environments, while qOA13-2/qLA13-1 and qLA15-1/qLNA15-1 exhibited pleiotropic effects. Candidate gene analysis within 50 kb flanking regions of lead SNPs identified 189 genes, including 61, 56 and 93 genes for OA, LA and LNA, respectively. Integrated analysis of GWAS and transcriptome data revealed 41 candidate genes showing significant differential expression between the lines with divergent UFA profiles. Sequence comparison of three prioritized candidates, GmABH, GmCFE, and GmPI-PLC, identified a key non-synonymous SNP in the GmABH coding region and promoter variations in all three candidates. Heterologous overexpression in Arabidopsis confirmed that all three candidate genes significantly altered the UFA profiles of the Arabidopsis seeds. The QTLs and candidate genes identified in this study might be useful for the improvement of UFAs in soybean.

Seed oil content (SOC) of oilseed rape (Brassica napus L.) is an important agricultural trait that is controlled by a complex regulatory mechanism. In this study, we performed integrated analyses of Genome-Wide Association Studies (GWAS) and Target Induced Local Lesions in Genomes (TILLING) to explore genetic loci/mutant alleles associated with SOC in rapeseed. GWAS analysis of a diverse panel of 324 accessions identified 142 SOC-associated quantitative trait loci (QTLs). Of them, qSOC.C06.4 encompassed the HD-ZIP transcription factor BnaC.GL2.b, which may regulate oil accumulation predicted by haplotypes analysis. An EMS (ethylmethanesulfonate)-TILLING platform that consists of 4,734 M₂ plants was constructed to identify the mutants of BnaC.GL2.b in rapeseed. Five mutant alleles of BnaC.GL2.b were identified using TILLING, of which three missense mutants exhibited higher SOC than the controls (two nonsense mutants). In addition, we measured SOC of 9332 M₂ plants ranging from 22.06% to 51.00%, with the average of 38.19%. Together, we propose to use GWAS combined with TILLING to identify causal genes and mutant alleles for a quantitative trait in the polyploid rapeseed. Furthermore, our new rapeseed germplasm resources may be useful for mutation breeding.