Theoretical and Applied Genetics最新文献

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.

Key message: This study is the first to establish an association between Zm00001eb257890 and maize kernel ratio (KR), offering novel insights into the genetic mechanisms regulating KR. These findings enhance our understanding of the genetic architecture of KR and provide promising targets for molecular breeding strategies aimed at improving maize yield. Kernel Ratio (KR) is a crucial trait determining kernel yield and the efficiency of assimilate partitioning to maize kernels. To explore its genetic basis, a multi-parent population (MPP) was developed by crossing the temperate inbred line Ye107 with five tropical/temperate inbred lines, generating 678 F₉ recombinant inbred lines (RILs). Phenotypic evaluation of KR was conducted across three environments (21JH, 22YS, 23YS), and best linear unbiased prediction (BLUP) values were estimated for subsequent analysis. Genome-wide SNPs were identified through whole-genome resequencing (WGRS), followed by combined genome-wide association study (GWAS) and QTL mapping to identify key loci and candidate genes regulating KR. GWAS identified 99 SNPs significantly associated with KR, 34 of which were consistently detected across multiple environments, explaining 1.56% to 9.00% of the phenotypic variation (PVE). QTL mapping identified 35 QTLs, including two stable QTLs, qKR5-3 and qKR5-7, that were consistently detected across multiple environments. Co-localization analysis identified five SNPs overlapping six QTL intervals. Notably, a non-synonymous mutation (SNP5_222146671) was located in the exon of Zm00001eb257890, which encodes a serine/threonine protein kinase VPS15, showing high expression in maize ear primordia. qRT-PCR and gene structure analyses demonstrated that Zm00001eb257890 was upregulated in low-KR parents (Chang7-2, Shen137) due to a G/A mutation (V₁₃₂₂I). Critically, in transgressive segregants from three RIL populations, the expression of Zm00001eb257890 was consistently and significantly higher in low-KR lines than in high-KR lines, showing a significant negative correlation with KR values (r = -0.83 to -0.96), providing notable functional evidence for its regulatory role. Epistatic analysis further revealed a significant interaction between SNP5_222146671 and SNP4_15864100 (STAT = 8.13), highlighting the polygenic regulatory network underlying KR. Taken together, these data significantly suggest Zm00001eb257890 as a key candidate gene regulating maize KR and provide valuable genetic targets for improving maize yield.

Key message: A complete set of monosomic alien addition lines (AⁿAⁿCⁿCⁿ + B^j_1-8, 2n = 39) of B subgenome derived from Brassica juncea in B. napus enhancing the genetic stock of B. napus was developed and comprehensively analyzed. Monosomic alien addition lines (MAALs), in which an alien chromosome from a related species is introduced into the genome of the recipient plant, serve as valuable resources for crop genetic analysis and breeding. In this study, we developed a complete set of MAALs for the B subgenome of Brassica juncea (A^jA^jB^jB^j, 2n = 36) in the background of B. napus (AⁿAⁿCⁿCⁿ, 2n = 38) through continuous backcrossing from BC₁ to BC₄ using B. napus and an octoploid progenitor (AABBCCRR, 2n = 72). Eight distinct MAALs (AⁿAⁿCⁿCⁿ + B^j_1-8, 2n = 39), each carrying a different B subgenome chromosome added to the B. napus genome, were identified by PCR amplification of B chromosome-specific primers and fluorescence in situ hybridization (FISH). Morphologically, most MAALs show distinct differences from one another and exhibit varying degrees of phenotypic divergence compared to the parental B. napus, such as purple seedling leaves in AACC-B5 and a higher seed number per silique in AACC-B7. Moreover, extensive homoeologous exchange (HE) was detected in MAALs. Bivalent pairing involving the alien chromosome was observed in 20% (AACC-B6) to 42% (AACC-B2) of pollen mother cells (PMCs), and the pairing rates between the alien B chromosome and C genome chromosomes were significantly higher than those between the alien B and A genome chromosomes. Additionally, B chromosomes exhibited varying effects on A-C chromosome pairing in different addition lines, with pairing frequencies ranging from 0.73 (AACC-B8) to 1.68 (AACC-B1) for A-C chromosome associations. Transmission rates of the added B chromosomes via ovules were significantly higher than those via pollen, indicating preferential transmission through female gametes. This MAAL collection provides valuable genetic stock for analyzing B subgenome structure, establishes a foundation for studying gene interactions among the A, B, and C genomes, and offers novel germplasm resources for B. napus practical breeding.

Key message: Identification and provision of genetic loci, candidate genes, critical germplasms, and theoretical evidence for breeding VB6-rich wheat cultivars. As a key functional component in daily diets, vitamin B6 (VB6) is essential for human metabolism. The consumption of VB6-rich wheat is an effective way to cope with human VB6 deficiency. We employed high-performance liquid chromatography to measure the wheat grain VB6 content of 262 accessions from a Chinese wheat mini-core collection grown in three different environments. The effects of the accession type and eleven agronomic traits on the VB6 content were analysed, and the QTLs associated with VB6 were mapped. The average total content of VB6 was 228.7 μg/100 g, and six accessions contained high contents of VB6 (> 320 μg/100 g). The effects on the VB6 content ranked as follows: genotype > genotype × environment > environment. The concentrations of VB6 did not significantly differ among accession types, between spring and winter varieties, or between red and white grains. The pyridoxine of VB6 was positively correlated with grain length but negatively correlated with plant height. Total VB6 was positively correlated with heading date, maturity date, grain length, and lutein content but negatively correlated with plant height. None of these correlations are believed to impose serious constraints on the breeding of VB6-rich wheat. Genome-wide association analysis revealed 12 stable QTLs associated with VB6, some of which showed cumulative effects. QPL.3A was verified in one population of doubled haploid lines. Transcriptomic analysis revealed four candidate genes for VB6 biosynthesis. This study provides genetic resources and theoretical evidence that is potentially useful for the breeding of VB6-rich wheat cultivars.

Deep-sowing is an effective strategy to ensure uniform seedling emergence and yield under drought stress condition for plants, which mainly depends on the mesocotyl or hypocotyl elongation in the monocots or dicots plants. In view of this, the hypocotyl lengths of 500 soybean accessions were evaluated under the deep-sowing conditions in nine environments, and the genetic loci and functional genes were discovered by combining with the deep re-sequencing genotypes (20 ×). The results showed that a total of 2,007 SNPs/SVs on 19 chromosomes were identified to associate with the hypocotyl length, of which 1,165 SNPs/SVs (58.05%) located on chromosome 14, and 706 SNPs/SVs (35.18%) located on chromosome 5. Moreover, 630 consistent SNPs/SVs on chromosomes 14 and 90 consistent SNPs/SVs on chromosomes 5 were detected across more than five environments. Furtherly, two causal genes, GmHYL05 and GmHYL14, were screened out in the consistent loci. Transgenic analyses revealed that the overexpression of GmHYL05 significantly enhanced the hypocotyl elongation in Arabidopsis, while the CRISPR/Cas9-mediated knockout of GmHYL05 resulted in decreasing of hypocotyl length in soybean. Similarly, the overexpression of GmHYL14 promoted the hypocotyl growth in Arabidopsis, while the nonsense mutation of GmHYL14 reduced the hypocotyl elongation in soybean. The cytological experiments revealed that both GmHYL05 and GmHYL14 increased the cell lengths of soybean hypocotyl, while not influenced the cell numbers, indicating GmHYL05 and GmHYL14 could regulate the hypocotyl elongation via influencing the cell expansion.