Theoretical and Applied Genetics最新文献

Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is the most destructive foliar pathogen of oat. Almost 100 genes conferring resistance to Pca have been cataloged. However, only limited genes have been mapped, and the chromosomal location of most remains undetermined. The goals of this study were to detect the chromosomal locations of 13 cataloged Pc genes and one uncharacterized but highly effective resistance gene and to identify functions related to them. We used an A. sativa L. nested association mapping population comprising 14 biparental F_2:3 families, derived from crosses between a donor carrying Pca resistance and the Pca susceptible variety "Swan." A total of 2,356 F_2:3 lines were phenotyped for response to pathotypes of Pca, from which the final AsNAM population of 707 individuals were selected. Based on DArT-Seq genotype data 15,940 high-quality single nucleotide polymorphisms were identified. Using the IBD mixed model, eight resistance QTLs to Pca with varying phenotypic variance were identified. The locations of four previously mapped genes were confirmed (Pc38, chr7D; Pc45, chr2D; Pc46, chr3D; Pc50, chr3D), and two genes were mapped for the first time (Pc36, chr1C; Pc70, chr5D). Resistance QTLs from the highly resistant Ensiler variety were also identified for the first time. The results revealed that some families had a single dominant gene controlling resistance, while others had more complex resistance. Several genes were linked or allelic (Pc13, Pc46, and Pc50 on chr3D; Pc36 and Pc60 on chr 1C; Pc38 and Pc64 on chr 7D). A total of 31 putative genes belonging to eight protein families related with disease resistance were identified in detected QTL regions.

Key message: BS-D275, a new locus on chromosome arm 2DS, is genetically independent of WFZP-2D and controls branched spike architecture in common wheat (Triticum aestivum). Branched spikes enhance wheat yield potential by increasing grain number. We identified the locus BS-D275 for spike branching in the winter wheat line Dong 275 and mapped it to chromosome arm 2DS using a recombinant inbred line (RIL) population derived from the cross of Dong 275 (branched spikes) × Zhongmai 175 (standard spikes). Across multiple field trials, spike branching and awn length segregated as polygenic, unlinked traits. Bulk segregant RNA-seq (BSR-Seq) of leaf and inflorescence samples, integrated with molecular markers, delimited BS-D275 to a 1.52-cM interval spanning 829 kb (84.03-84.86 Mb) in the Chinese Spring telomere-to-telomere reference genome. Diagnostic markers and sequence comparison positioned BS-D275 11 Mb distal to the spike-branching locus WFZP-2D (73.09 Mb), confirming their independence. The interval contains 10 inflorescence-specific candidate genes. CSIAAS2DG0371200/TraesCS2D02G133500, encoding a GTPase-activating protein, carries a Dong 275-specific 4-bp frameshift and is highly expressed in spikes, making it the most likely candidate for BS-D275. Parallel BSR-Seq of awned versus tip-awned bulks mapped the awn suppressor to the B1 locus (CSIAAS5AG1310200/TraesCS5A02G542800) on chromosome arm 5AL, demonstrating that awn development and spike branching are under separate genetic control. WFZP-2D represses awn development while BS-D275 does not, which provides evidence that BS-D275 is most likely a novel regulator of spike branching. Diagnostic markers for BS-D275 will accelerate marker-assisted selection for high-yielding, branched-spike wheat.

Key message: A missense SNP G → A mutation in the z-type thioredoxin-coding gene CsTRX z (CsDVL) reveals its pivotal regulatory function in chloroplast development, chlorophyll homeostasis, and low-temperature-sensitive photosynthetic regulation, with direct implications for targeted genetic improvement in breeding programs. Thioredoxins (TRXs), pivotal redox regulators modulating protein function, are essential for plant stress adaptation, development, and growth. While extensively characterized in model species (e.g., Arabidopsis, rice), their roles in vegetable crops remain underexplored. Here, we report a missense SNP (G → A) in the z-type thioredoxin CsTRX z (CsDVL), identified via ethyl methanesulfonate (EMS) mutagenesis, as the causal variant underlying the Dominant Virescent Leaf phenotype in cucumber (Cucumis sativus). The mutant PSM004 exhibits transient yellow-green cotyledons at seedling emergence, reverting to wild-type pigmentation during later growth stages. Genetic and cytological analyses confirmed that the Dominant Virescent Leaf (DVL) locus perturbs chloroplast ultrastructure, chlorophyll biosynthesis, and photosynthetic efficiency. Positional cloning delimited DVL to a 75.9-Kb region on chromosome 6, with allelic diversity analysis pinpointing a G → A substitution in the fourth exon of CsTRX z as the causative mutation. Transcriptomic profiling revealed that this missense SNP reprograms expression of chloroplast-localized genes governing chlorophyll metabolism, redox homeostasis, carbohydrate flux, and photosynthetic machinery. Physiological assays further demonstrated thermosensitivity in PSM004, with low-temperature treatment (20 °C/15 °C) inducing reversible chlorosis in developing leaves. Our findings elucidate CsTRX z's conserved yet distinct role in chloroplast biogenesis beyond model systems and establish its utility as a genetic target for enhancing stress resilience and photosynthetic performance in cucumber breeding programs.

Key message: Substantial improvements in genomic prediction accuracy for rice gene bank accessions were achieved by incorporating SNPs of low call rate identified in a recently published rice pan-genome. Introduction of useful genetic variation to breeding populations is a key factor in achieving genetic gain in crop breeding. However, identifying donors from genetic diversity stored in gene banks requires extensive phenotyping, which is not feasible for many traits of interest. Genomic prediction (GP) of phenotypic values has been proposed to overcome this phenotyping bottleneck. A key challenge for GP is the identification of appropriate markers representative of genetic variation causal for phenotypes. Here we report on utilizing single nucleotide polymorphisms (SNPs) from the core and dispensable genomes of a rice pan-genome resource comprising 16 reference sequences. Using a published pan-genome graph, we identified SNPs within structural variations of the dispensable genome. In this SNP set, SNPs of low call rate (CR) were common. Presence-absence variation (PAV) of these SNPs was associated with subpopulation structure, indicating that SNP absence reflects on underlying sequence PAV rather than being solely due to technical errors in SNP detection. To incorporate these SNPs in GP models, we employed modified encoding, retaining information of PAV and nucleotide variation by one-hot encoding (OHE). Adding these to SNP matrices increased prediction accuracies of GP for some traits and subpopulations. Improvements could largely be attributed to the inclusion of PAV. Our results show that the traditional approach of applying strict CR filters to SNPs located in the dispensable genome disregards potentially valuable genetic information not in linkage with SNPs of high CR. The proposed strategy provides a straightforward way to enhance GP performance in rice gene bank accessions.

Pre-harvest sprouting (PHS) severely impacts white-grain wheat production. To uncover its genetic basis, we conducted a genome-wide association study (GWAS) across 273 wheat varieties and identified 41 quantitative trait loci (QTLs) for PHS resistance. Among these, a major and stable QTL on chromosome 6A, designated QTL15, was detected across all tested environments and accounted for up to 19.12% of the phenotypic variance. Integrated analysis of RNA-seq data and sequence variation within the QTL15 interval pinpointed TaIAA10-6A, an auxin-responsive Aux/IAA family gene, as the candidate. An elite haplotype, TaIAA10-6A-M, featuring an 18-bp deletion and a 21-bp substitution in its coding sequence, was strongly correlated with enhanced PHS resistance. Intriguingly, overexpressing TaIAA10-6A-M allele significantly increased PHS susceptibility, demonstrating that TaIAA10-6A encodes a dose-dependent PHS-promoting protein. Therefore, the TaIAA10-6A-M haplotype confers resistance by acting as a functionally attenuated allele that reduces PHS-promoting signal. A co-dominant CAPS marker, phs-TaIAA10-6A-M, was also developed and validated for its tight association with PHS resistance. Overall, this study not only elucidates a novel auxin-mediated regulatory mechanism for PHS in wheat but also provides a valuable gene resource for marker-assisted breeding of PHS-resistant white-grain wheat varieties.

Bentazon is an effective post-emergence herbicide in soybean. A loss of function of cytochrome P450 hydroxylase encoded by a recessive gene, bzn-1 (Glyma.16G149300), is known to confer high sensitivity to bentazon, while there is natural variation causing moderate sensitivity to bentazon that cannot be accounted for by bzn-1. Here, we identified another recessive gene, bzn-2, that confers the moderate sensitivity to bentazon. The candidate region of bzn-2 was narrowed down to 92 kb on chromosome 11 by positional cloning using recombinant inbred lines from a cross between bentazon-tolerant and moderately sensitive varieties. Sequence comparison of these varieties for 12 genes located in the candidate region revealed that the moderately sensitive variety had a single-base substitution that caused a stop codon in the coding region of Glyma.11G138300. This gene encodes GRAS SCL14 (GRAS: GIBBERELLIN ACID INSENSITIVE, REPRESSOR of GA1, and SCARECROW; SCL: SCARECROW-like 14), a class II TGA transcription factor. Screening of germplasms by an amplification-refractory mutation system (ARMS) marker clearly distinguished the accessions that are moderately sensitive to bentazon. Three independent EMS mutants of Glyma.11G138300 were moderately sensitive to bentazon, strongly supporting Glyma.11G138300 as the causal gene for bzn-2. The low expression of mutated Glyma.11G138300 reduced expression of Glyma.16G149300, encoding the P450, resulting in a moderately sensitive phenotype. To the best of our knowledge, this is the first report demonstrating that natural variation in the GRAS gene family confers herbicide tolerance. Our findings are useful for understanding the mechanism of detoxification and for selection of bentazon tolerance through breeding.

Key message: Nucleolar dominance is an essential phenomenon as the control mechanism of polyploidization. This study provided valuable insights into elucidating the regulatory mechanisms and timing of nucleolar dominance during wheat polyploidization. We performed expression analyses of nucleolar organizer regions (NORs) to elucidate the status and regulatory mechanism of nucleolar dominance in wheat on the basis of sequence differences in the external transcribed sequence (ETS) region of ribosomal DNAs (rDNAs). In hexaploid wheat, the B-genome ETS subtype was predominantly expressed. In contrast, the D-genome subtype was slightly expressed, and the A-genome subtype was not expressed. D-genome subtype expression increased in lines lacking the B-genome NOR, but A-genome subtype expression was not restored. These results suggested that the regulatory mechanisms of the B genome's dominance for the D and A genomes differed. In synthetic wheat, rDNA units derived from the D genome, which were highly expressed in the diploid parental species, were suppressed to the level of established hexaploid lines, indicating that nucleolar dominance in wheat was established relatively early after polyploidization. Analysis using partial deletion lines of the short arm of the chromosome 1B or 6B revealed that even after the loss of the NOR, as the degree of deletion of the short arm increased, the recovery of D-genome subtype expression increased. These results suggest that not only does the NOR region on the B genome regulate nucleolar dominance but also that there may be another regulatory region on the short arm of chromosomes 1B and 6B.

Key message: ABM-BOx is a mission-critical transformation engine, built to fast-track genetic gains, boost climate resilience, and modernize outdated breeding programs into agile, data-driven, demand-responsive innovation platforms setting a global benchmark. Rice plays a central role in global food security as climate threats continue to rise. Fast-tracking genetic gains and developing climate-resilient, market-preferred varieties require a bold, system-wide transformation of rice breeding practices worldwide. Baseline diagnostics of more than 25 national rice breeding programs across the Global South revealed critical bottlenecks: obsolete breeding strategy and scheme, fragmented workflows, limited technology access, and poor integration of seed system. This highlights the urgent need of breeding modernization to tackle rising food security risks. We introduce Accelerated Breeding Modernization-Breeding and Operational Excellence (ABM-BOx), a globally scalable framework to transform rice breeding programs into modern, data-driven, impact-oriented systems. ABM-BOx operationalizes a paradigm shift by translating the breeder's equation into real-world impact through two synergistic engines: Breeding Excellence (BE) and Operational Excellence (OE). BE focuses on enhancing genetic gains through demand-driven breeding, strategic parental selection, recurrent population breeding, simulation-driven breeding scheme optimization, genomic selection, and predictive breeding. These strategies increase selection intensity, selection accuracy and shorten the breeding cycle. OE ensures speed, efficiency, and scalability through speed breeding-field based platforms, smart breeding-digital tools, breeding informatics-AI-powered decision tools, strategic costing-optimizing investments, and resilient seed systems. Additionally, Capacity Reinforcement and Functional Transformation-Accelerated Breeding Modernization (CRaFT-ABM) strengthens institutional capacity by focusing on talent, infrastructure, governance, and networks. More than a framework, ABM-BOx is a mission-critical transformation engine that drives innovation, speed, and impact to empower rice breeding efforts globally.

Genomic selection (GS) has emerged as a promising approach in plant breeding, especially for complex traits like grain yield that are influenced by many small-effect quantitative trait loci (QTLs). Choosing the optimal prediction model is important for GS. Using 4 years of field data from a diverse panel of spring wheat lines, the present study assessed the ability of seven statistical models to predict grain yield (YLD), total spikelet number per spike (tSNS), thousand kernel weight (TKW), plant height (PHT), and heading date (HD). The Reproducing Kernel Hilbert Spaces (RKHS) model was used as a basis for comparing predictive ability improvement of the other six models when major plant adaptation genes controlling flowering time, photoperiod response, plant height, and vernalization were treated as fixed effects. Incorporating fixed effects into the model substantially improved genomic predictive abilities, increasing them by 13.6% for YLD, 19.8% for tSNS, 7.2% for TKW, 22.5% for HD, and 11.8% for PHT. Thus, wheat breeders could apply this approach to GS in cultivar development and improvement. This finding could also be applied for GS in other cereal crops. To our knowledge, this is the first demonstration in spring wheat of integrating adaptive marker sets (FT/Ppd/Rht/Vrn) as fixed effects within an RKHS framework to improve genomic prediction across yield and four yield-related traits.

Key message: Amplicon sequencing and read-backed haplotyping enable cost-effective genomic prediction in potato, with SNPs and haplotags showing similar performance across 23 traits, supporting scalable breeding applications and competitive prediction ability with GBS. Genomic prediction (GP) supports plant breeding by accelerating genetic improvement; however, the high cost associated with dense genotyping platforms restricts their use in routine breeding. This study evaluates the efficacy of PotatoMASH, a cost-effective, low-density, amplicon-sequencing platform generating SNPs and short-read multi-allelic haplotypes (haplotags), for GP in potato. First, we compared the prediction ability (PA) achieved using 2,236 SNPs and 2,000-3,390 haplotags from 339 amplicon loci of PotatoMASH with previously reported PA values obtained from a high-density 43.6 k SNP GBS dataset. PA was only moderately reduced, by 14% for SNPs and 9% for haplotags, indicating that the platform offers a scalable alternative to GBS. We then applied it to a diploid panel for GP of 23 agronomic, quality, and morphological traits. Both marker types yielded medium to high PA (0.29-0.81) across the traits. Haplotags outperformed SNPs in 11 traits, while SNPs performed better in six, with no difference in the remaining six traits. We conclude that PotatoMASH, which facilitates the concurrent detection of both SNPs and haplotypes at a reduced cost, provides a versatile and economical genotyping solution suitable for integrated pipelines that combine marker-assisted selection (MAS) and GP in potato breeding.