Theoretical and Applied Genetics最新文献

Key message: Rapid cycling genomic selection is a highly efficient tool for pre-breeding of maize landraces for complex traits, especially in combination with multi-trait selection and model retraining. The introduction of landrace-derived material into modern breeding programs can only succeed if it performs satisfactorily for yield and other key agronomic traits. In this study, we explored the prospects of rapid cycling genomic selection in maize (Zea mays L.) to accelerate pre-breeding of landraces in comparison with recurrent phenotypic selection. We performed three cycles of genomic selection for testcross performance. The selection criterion was based on directional selection for biomass yield and stabilizing selection for plant height and flowering time. The prediction model was trained on testcrosses of 419 doubled-haploid (DH) lines derived from two European landraces. To estimate selection response and prediction accuracies, DH lines from all cycles (N = 204, C0-C3) were evaluated together with seven commercial hybrids in seven environments. Selection narrowed the yield gap to the commercial hybrids significantly with an increase in dry matter yield of about 10% in comparison with the reference population (C0). Despite stabilizing selection for plant height and flowering time, both traits showed a correlated response with biomass yield pointing to the importance of optimizing multi-trait selection, especially in landraces. Prediction accuracies were intermediate to high in the training population and decreased in the following cycles. Retraining the prediction model increased the prediction accuracy for all traits. Our results support the hypothesis that pre-breeding can be accelerated significantly by rapid cycling genomic selection and give valuable insights into key factors determining its success.

Key message: The natural variation of TaDHN4D1, co-targeted by TaNAC4 and TaWRKY19, influences salt stress tolerance in wheat. Salt stress is a significant abiotic stressor that negatively affects wheat production. In this study, we elucidated the role of wheat TaDHN4D1 in response to salt stress. Our results indicated that the overexpression of TaDHN4D1 alters sodium (Na⁺) balance under salt stress and significantly enhances the ability of wheat to eliminate reactive oxygen species (ROS), thereby improving its salt tolerance. Furthermore, we discovered that TaNAC4 binds to the promoter of TaDHN4D1, positively regulating its expression. We also examined the expression levels of TaDHN4D1 across various wheat germplasms and found that the expression level of TaDHN4D1 in the wheat landrace BD2 (TaDHN4D1^BD2) was significantly higher than in other wheat varieties. Additionally, we identified sequence variations in the promoter of TaDHN4D1^BD2, including an additional W-box, which is recognized by TaWRKY19. This interaction suggests that TaNAC4 and TaWRKY19 cotarget the TaDHN4D1^BD2 promoter, regulating the expression of TaDHN4D1^BD2. Finally, we designed specific primers for TaDHN4D1^BD2 and, through molecular marker-assisted selection, developed salt-tolerant wheat materials containing TaDHN4D1^BD2. In conclusion, this study identifies a novel mechanism involved in the regulation of salt tolerance in wheat, providing valuable insights for the cultivation and breeding of salt-tolerant wheat.

Key message: QTL mapping and GWAS detected resistance QTL to Aphanomyces euteiches in faba bean, lentil, and Medicago truncatula. Weak genomic conservation between resistance QTL was identified between these legumes and pea. Aphanomyces root rot, caused by Aphanomyces euteiches, is a damaging disease affecting various legume species. Quantitative trait loci (QTL) for partial resistance have been mainly identified in pea, and to a lesser extent in lentil and Medicago truncatula. This study aimed to identify novel resistance loci from available lentil and faba bean populations, and examine genomic conservation of resistance QTL across legume host species. QTL mapping in the Pop2 faba bean recombinant inbred line (RIL) population and genome-wide association study (GWAS) in the AGILE lentil diversity panel were performed for resistance to A. euteiches under controlled conditions, using genotyping data previously reported. A previous QTL mapping in the LR3 M. truncatula RIL population was updated using 1,536 new SNPs (single-nucleotide polymorphisms). Synteny between resistance QTL to A. euteiches was analyzed based on gene orthology in QTL regions projected onto genomes, using the OrthoLegKB graph database. Four loci, including a major-effect QTL on chromosome 3, Ae-Vf3.1, were associated with resistance in faba bean. In lentil, six minor-effect GWAS-SNPs and two favorable haplotypes at Ae-Lc1.1 and Ae-Lc2.1 loci were identified. Updated analyses in M. truncatula narrowed to 8 Kb the interval of the major-effect locus AER1 and revealed three candidate genes. No synteny between major-effect QTL, detected in this study or previously reported in the literature, was identified across grain legume genomes. These results pave the way for translational genomics approaches facilitating resistance gene discovery and for resistance QTL deployment strategies in legume rotations to preserve their durability.

Key message: Widely used rootstock 'Carolina strongback' delays female flowering of scion(s). Two stable QTLs influencing female flowering time and fruiting time across the seasons and years were identified on chromosome 3. Inbred lines of Citrullus amarus, a wild relative of cultivated watermelon, are widely used as rootstocks to control soil-borne diseases for watermelon (Citrullus lanatus) production. The most commonly used watermelon rootstock, 'Carolina strongback' (Syngenta, Basel, Switzerland) flowers weeks later than commercial watermelon cultivars, which delays the onset of female flowering (DFF) of the scion, leading to an undesirable delay in fruit maturity and harvesting. Understanding the genetics of DFF in a C. amarus population will facilitate the development of rootstocks with the early flowering habits preferred for commercial production. A recombinant inbred line population (N = 129 lines) developed between C. amarus lines, USVL246-FR2 and USVL114, was evaluated in field trials in spring and fall of 2022 and 2023 for DFF and days to fruiting (DFT) after being transplanted into the field. The correlation between DFF and DFT is 0.92. Broad-sense heritability of DFF and DFT was 0.23 and 0.31, respectively. Two QTLs influencing both the DFF and DFT across the seasons and years were identified at 90.5 and 56.0 cM on chromosome 3 and together explained 39.7% variance of DFF. Two additional QTLs associated with DFF were season-specific with a spring and a fall QTL on chromosome 10 and on the proximal end of chromosome 3, respectively. Genes coding for putative proteins involved in inducing anthesis, activation and regulation of FT proteins were identified in the 1.5 LOD interval of the stable major QTLs on chromosome 3.

Leaf senescence is a turning point for grain development and closely related to yield and grain quality. Fine-tuning leaf senescence could be a vital strategy for yield improvement. However, our knowledge of the regulatory genes of leaf senescence is limited in wheat. In this study, we identified a methanesulfonate (EMS) mutant, wheat pale green 1 (wpg1), exhibiting obvious leaf chlorisis and premature senescence (PS) since the jointing stage. The chloroplast structure of the chlorisis leaf of wpg1 seemed intact, whereas its chlorophyll content was significantly decreased compared to the wild type (WT). The content of nitrogen (N), the core element for chlorophyll, was much lower in leaves of wpg1 than in WT. The spatio-temporal pattern analysis of nitrogen content further indicated accelerated N allocation from vegetation tissues to spike in wpg1, resulting in a significant decrease in nitrogen content in leaves, but a substantial increase in grains compared to WT. Genetic analysis showed that leaf chlorisis and PS is controlled by a single dominant locus, designated as Wheat Pale Green 1 (WPG1), which was further mapped to a physical interval of 34.69 M-41.19 M on chromosome 2A. Transcriptomic analysis revealed that expression of photosynthesis-related genes, and N absorption and transportation genes consistently decreased in wpg1, which revalidated the underlying relationship between N shortage and leaf chlorisis. The results presented here lays the basis for further dissecting the causal gene of WPG1 and the subsequent molecular mechanism underlying the regulation of leaf senescence, N allocation, and possibly the photosynthesis in wheat.

Key message: A major QTL, qEFT13.1, for flowering time in cultivated peanut, was fine-mapped to a 169-kb interval on chromosome 13, and AhFPA1, a homolog of AtFPA, was identified as the causal gene through functional validation. Flowering time serves as a key agronomic trait that significantly impacts yield, quality, and environmental adaptation in cultivated peanuts (Arachis hypogaea). Here, the fine-mapping of the locus and an investigation of its causal gene are presented. In this study, the early-flowering genotype Jihua 23 and the late-flowering genotype SN012 were selected to construct a genetic population for mapping key genes controlling flowering time. Based on phenotypic data from the F₂ and F_2:3 populations, a major-effect QTL, qEFT13.1, was identified on chromosome 13 using a combination of QTL-seq and conventional QTL analysis. A derived population consisting of 3,426 F_3:4 families was utilized for fine-mapping, narrowing down the qEFT13.1 locus to a 169-kb genomic interval, which harbored 20 genes. Integrated gene function annotation, candidate gene sequence analysis, and expression profiling suggested that AhFPA1, a homolog of the Arabidopsis autonomous flowering pathway gene AtFPA, is the candidate gene regulating flowering time in peanut. Overexpression of AhFPA1 in transgenic Arabidopsis revealed its function in accelerating flowering time. These results enhance our understanding of the genetic mechanisms governing early flowering in cultivated peanut, offering valuable insights for the breeding of early-maturing varieties.

Low-temperature stress poses a significant challenge to the growth and yield of rice seedlings. Although quantitative trait loci (QTLs) have been mapped and underlying genes for cold tolerance identified, breeding efforts remain constrained by the lack of precise molecular markers. In this study, we analyzed 529 accessions from the 3K Rice Genomic Diversity Panel to investigate genetic variations in OsCTS11, a known negative regulator of cold tolerance in rice seedlings. Linkage disequilibrium (LD) analysis identified three critical LD blocks (BLOCK1-3) within OsCTS11, each containing four distinct haplotypes. Association analysis revealed that Hap4 in BLOCK1, Hap3 in BLOCK2, and Hap4 in BLOCK3 significantly increased seedling survival rates to 65.38%, 58.41%, and 51.48%, respectively, predominantly in japonica subspecies. These beneficial haplotypes demonstrated adaptation to temperate zones (30°-40°N) and tropical highlands (800-1500 m elevation), consistent with the evolutionary progression of cold tolerance in japonica rice. The utility of KASP molecular markers based on SNP sites was validated through this study. Among 42 rice varieties screened, indica R676 and japonica Nangeng 5718, both possessing dominant haplotypes, exhibited higher survival rates compared to varieties lacking these haplotypes. Marker-assisted backcrossing facilitated the development of four novel cold-tolerant germplasms (YR05-YR08) incorporating advantageous OsCTS11 haplotypes. Notably, YR08 (Hap4 + Hap3 + Hap4) showed significantly improved seedling establishment under cold stress, illustrating the synergistic benefits of stacked haplotypes. This research underscores the potential of leveraging natural variation haplotypes to create precise molecular markers for identifying beneficial OsCTS11 haplotypes, providing a novel approach to exploiting negative regulatory genes in rice breeding programs.

Key message: A large effect and environmentally stable QTL was identified on LG2 that confers high levels of INSV resistance in lettuce cultivar Eruption. Impatiens necrotic spot virus (INSV) has recently emerged as a major threat to lettuce production in the Salinas Valley of California, the region which contributes over 60% of the US national supply. This thrips-transmitted virus can infect lettuce plants at any growth stage, causing premature death or a total loss of marketability. Both INSV and its thrips vector have broad host ranges, which complicate disease management. Utilizing genetic resistance is the most sustainable approach; however, complete immunity has not been identified and the genetic basis of resistance to INSV in lettuce remains poorly understood. This study aimed to identify quantitative trait loci (QTL) and elucidate the underlying mechanism of INSV resistance in 'Eruption,' a lettuce cultivar exhibiting highly stable partial resistance across environments. Using 162 F_6:8 recombinant inbred lines (RILs) developed from a cross between moderately susceptible 'Reine des Glaces' and 'Eruption,' and a genetic linkage map comprising 1598 single nucleotide polymorphism (SNP) markers, phenotypic data collected from field and greenhouse experiments consistently revealed a highly significant, major QTL on linkage group 2. This QTL exhibited partial dominance with additive effects, explaining up to 61% of the total phenotypic variation for INSV disease severity. Furthermore, INSV resistance was found to be highly heritable, with heritability estimates of up to 0.89, indicating strong genetic control. Results of this study are crucial for fine mapping and the development of marker-assisted selection assays to accelerate the breeding of more advanced INSV-resistant lettuce cultivars.

Key message: QSes-7AL is the first major QTL for sharp eyespot resistance identified on wheat chromosome 7AL. The putative candidate gene TaPrx1L-7A was identified and preliminarily validated through integrated multi-omics data and molecular biology approaches. Wheat sharp eyespot is a soilborne disease caused by the necrotrophic fungal pathogen Rhizoctonia cerealis and is a major threat to wheat yield and quality worldwide. In this study, a novel major quantitative trait locus (QTL) for sharp eyespot resistance, designated QSes-7AL, was identified on chromosome 7AL (496.041-499.622 Mb) though analysis of a recombinant inbred line (RIL) population derived from a cross between H63-4 and Yangmai 158, using bulked segregant analysis (BSA), the wheat 660K SNP array, simple sequence repeat (SSR) markers, and kompetitive allele-specific PCR (KASP) markers. A peroxidase-encoding gene, TaPrx1L-7A, was identified as the most likely candidate gene for QSes-7AL based on integrated multi-omics data, gene function annotation, and expression pattern analysis. In addition, the gene was further validated as a strong candidate for QSes-7AL through diagnostic molecular marker, barley stripe mosaic virus-induced gene silencing (BSMV-VIGS), analysis of defense-related gene expression, and measurement of physiological indicators. Overall, these findings provide new insights into the molecular mechanisms underlying wheat resistance to sharp eyespot and offer a theoretical foundation for breeding resistant wheat varieties.

Wheat is a vital global crop, essential for food security, but its production is threatened by soil-borne diseases like Fusarium graminearum. This pathogen infects wheat at all growth stages and produces harmful mycotoxins, severely compromising both yield and quality. Piriformospora indica, endophytic fungi of plant rhizosphere, can not only effectively promote growth and development, but also improve disease resistance in plants. Here, the mechanism of TaCPS1 gene expression induced by P. indica colonization to improve wheat resistance to F. graminearum has been investigated. Results showed that colonization of P. indica decreased infection of F. graminearum and correspondingly reduced deoxynivalenol (DON) content in wheat roots. Transcriptome sequence analysis demonstrated colonization of P. indica leads to a high expression of the synthase gene family of diterpenoid metabolites. TaCPS1 gene, a crucial gene in the synthesis of diterpenoid metabolites, responded promptly to the colonization of P. indica. Subsequently, 31 transcription factors were screened by yeast one-hybrid library screening and TaZF-HD5 was verified to be interacted with the promoter of TaCPS1. The findings indicate that plants overexpression TaCPS1 demonstrated heightened responsiveness to P. indica colonization and exhibited enhanced resistance to root rot. The increased phytocassane content in TaCPS1 overexpression lines implies that TaCPS1 plays positive role in phytoalexin biosynthesis. The upregulated expression of TaCPS1 in response to the colonization of P. indica, thereby increasing the content of phytocassane synthesis, is one of the reasons why P. indica mediates wheat disease resistance to F. graminearum.