Theoretical and Applied Genetics最新文献

Key message: The tonoplast-localized transporter TaTPK1-5D, interacting with TaCIPK23-4D , enhances low K⁺ tolerance in wheat by promoting vacuolar K⁺ efflux, providing a key genetic target for improving K⁺-use efficiency in breeding. Bread wheat (Triticum aestivum L.) serves as a staple food for more than one-third of the global population, and potassium (K⁺) is critical for wheat yield and quality. However, the molecular mechanisms underlying wheat survival under low-K⁺ conditions remain poorly understood. In this study, a phenotypic screening of 712 wheat accessions identified a low-K⁺ sensitive genotype (H735) and a low-K⁺ tolerant genotype (H467, namely Zhengmai 136). Measurements of K⁺ concentration and non-invasive micro-test technology revealed that the differential tolerance between the two genotypes was not attributable to root K⁺ uptake capacity, but rather to a higher vacuolar K⁺ efflux rate in H467 compared to H735. Through transcriptomic-assisted differential expression and co-expression network analysis, a tonoplast-localized K⁺ efflux transporter, TaTPK1-5D, was identified as a key candidate underlying differential low-K⁺ tolerance in wheat. Functional disruption of TaTPK1-5D^H467, but not TaTPK2-3D^H467/2-4D^H467/3-5D^H467, significantly reduced both low-K⁺ tolerance and vacuolar K⁺ efflux in H467. High TaTPK1-5D expression was consistently observed in several other K⁺-efficient wheat accessions. Importantly, yeast two-hybrid screening, bimolecular fluorescence complementation, and pull-down assays demonstrated that TaTPK1-5D interacted with the protein kinase TaCIPK23-4D. Functional disruption of TaCIPK23-4D led to dramatic sensitivity to low-K⁺ stress. These findings establish TaTPK1-5D as a major vacuolar K⁺ efflux transporter facilitating subcellular K⁺ remobilization under low-K⁺ conditions.

Key message: Net-form net blotch (NFNB) is a devastating fungal disease for barley. Three potentially novel QTL for resistance and identified SNP markers can contribute to the global control efforts of NFNB. Pyrenophora teres f. teres, the fungus responsible for the barley disease, net-form net blotch (NFNB), leads to considerable yield and quality reductions. This research involved collecting phenotypic and genotypic data from a barley doubled haploid (DH) mapping population consisting of 277 lines, which were exposed to the highly virulent Ptt isolate GPS18. The DH lines were derived via anther culture from second-generation hybrids of a cross between the disease-resistant barley cultivar Avcı 2002 ("A") and the susceptible cultivar Bülbül 89 ("B"). Anther pretreatment with 1.0 M mannitol resulted in a statistically superior response compared to 0.7 M mannitol in the F₂ progeny of the A × B cross. The highest callus induction rate was 37.6% in the "Br_Ind" medium, and the highest green plant formation rate was 24.7% in the "PD_Reg" medium. The use of sequencing-based diversity array technology (DArT-seq) identified 9170 SNP markers, which facilitated the creation of a linkage map spanning 1682.97 cM, with an average density of 1.49 markers/cM. Quantitative trait loci (QTL) analysis identified three QTL associated with Ptt resistance located on chromosomes 3H, 4H, and 6H. All three can be considered novel with the 3H QTL mapping in between Rpt1 and QRptta3, the 4H QTL maps to a distinct region of Rpt7, and the 6H QTL maps in between the Qns-6H.3 and SFNB-6H-33.74 loci. The SNPs associated with disease resistance identified within these QTL offer a foundation for developing DNA-based tests for resistance.

Cultivated peanut (Arachis hypogaea, AABB genome) is an allotetraploid species that likely originated from hybridization between the two wild diploid species A. duranensis (AA) and A. ipaensis (BB). Chromosome identification and genomic evolution studies in Arachis species have encountered significant challenges due to the absence of consensus karyotypes. In this study, we developed the first "barcode" consensus karyotype for peanut using single-copy oligonucleotide probe libraries. This karyotype was applied to identify interspecific hybrids and radiation-induced chromosomal variants, correlate pseudochromosomes with physical chromosomes, and determine chromosomal homoeologous relationships among Arachis species. Analyses of karyotype, chloroplast phylogeny, and similarity heatmaps revealed that A. duranensis and A. ipaensis exhibited the highest similarity to the subgenome of A. hypogaea; certain A-genome species displayed high heterozygosity; and, despite harboring distinct chloroplast genomes, the nuclear genomes of various botanical varieties of peanut were all most similar to A. duranensis accessions from the Rio Seco region in Argentina. Combined with the geographical distribution of A. ipaensis, we propose that outcrossing events may have contributed to the generation of A. duranensis accessions with distinct chloroplasts; subsequently, these accessions likely hybridized with A. ipaensis, leading to the formation of different peanut botanical varieties within an area extending from southern Bolivia to the Rio Seco region. These findings underscore the broad applicability of our new karyotype for distant hybridization, chromosomal identification, and genome evolution research in peanut.

Key message: A novel gene, TaqW-6AS was discovered on chromosome 6AS which encodes a Class III heme peroxidase influencing WE-AX content in wheat grain. Water-extractable arabinoxylan (WE-AX), a key soluble dietary fiber component, provides various significant health benefits and exhibits notable functional properties. In this study, we detected QTLs for WE-AX content in two populations: a natural population of 163 varieties (ZZ population) genotyped with the Axiom wheat 90 K single nucleotide polymorphism (SNP) array, and a recombinant inbred line (RIL) population with 175 lines derived from a cross between Avocet and Huites (AH population) genotyped with diversity array technology (DArT). QWE-AX.haust-6A, a major-effect and stable co-localized locus associated with WE-AX content was detected by GWAS and linkage analysis which was on the short arm of chromosome 6A with the physical interval 1.09 Mb from 14.61 to 15.70 Mb in five environments. In the candidate region of QWE-AX.haust-6A, a gene temporarily named TaqW-6AS was cloned, which encodes a Class III heme peroxidase. TaqW-6AS protein was localized in the ER-Golgi secretory pathway. Furthermore, three functional markers (kasp-qw6A-1, kasp-qw6A-4, and kasp-qw6A-6) and two favorable haplotypes (Hap4 and Hap5) of TaqW-6AS were deployed effectively in marker-assisted selection (MAS) for biofortification breeding.

Key message: The desirable yield gene extra-large panicle 1 (ELP1), which increased grain yield per plant by approximately 30%, was cloned from wild rice Oryza officinalis through a map-based cloning strategy. Grain number per panicle (GNP) is a crucial determinant of rice yield. The wild rice Oryza officinalis, an accession of extra-large panicle (ELP) type, produces numerous grains (700 ± 100 grains) in its main stem panicle. However, mainly due to weedy traits, incompatibility barrier and linkage drag, this desirable yield trait ELP in O. officinalis has not yet been successfully exploited. Here, interspecific distant hybridization between 93-11 and O. officinalis was performed. One plant with 700 grains in its main stem panicle was obtained from BC4F4 progeny. Genetic analysis showed that the ELP trait was quantitatively controlled. By coupling bulked segregant analysis with whole genome re-sequencing and association analysis, three quantitative trait loci (QTLs) controlling the ELP trait were identified, and the QTL mapped on chromosome 4 was identified as one major QTL (designated ELP1) and thereafter finely mapped to a 44-kb region. The ELP1 encodes a putative F-box domain-containing protein (OsFBX148) with a previously poorly characterized function and undergoes alternative splicing. The two resulting isoforms, ELP1L and ELP1S, oppositely regulate the GNP. Overexpression of the short isoform ELP1S increased tiller number and GNP by approximately 37.5% and 37.6%, respectively, consequently increasing grain yield per plant by approximately 30%. Haplotype analysis showed that ELP1 ^{O. officinalis} allele was a valuable and novel haplotype. Our work not only provides one successful story of identifying a favorable yield gene from O. officinalis but also uncovers a novel regulatory mechanism by which alternative splicing regulates rice GNP.

Key message: Eleven QTLs controlling maize ESL were identified via high-resolution QTL mapping of 866 maize-teosinte RILs and three promising candidate genes for qESL1-1 were further screened through integrated RNA-seq and qRT-PCR. Ear shank length (ESL) represents a critical architectural trait in maize that significantly influences yield formation, kernel dehydration, and mechanical harvesting efficiency. To dissect the genetic architecture underlying ESL variation, we conducted a high-resolution quantitative trait locus (QTL) mapping using 866 maize-teosinte BC₂S₃ recombinant inbred lines genotyped with 19,838 single nucleotide polymorphism markers. Phenotypic evaluation across three environments revealed extensive ESL variation with values ranging from 9.9 to 18.7 cm. Correlation analysis demonstrated that ESL showed positive correlations with most agronomic traits but negative correlations with most yield-related traits, while having relatively limited effects on nutritional traits. Multiple QTL mapping identified 11 QTLs distributed across eight chromosomes, collectively explaining 35.8% of phenotypic variation with individual effects ranging from 1.6% to 4.7%. Notably, 10 of 11 QTLs carried teosinte alleles that increased ESL values, indicating strong directional selection during the prolonged domestication and improvement process. The target QTL qESL1-1 was validated using near-isogenic lines, confirming its significant effect on ESL and pleiotropic effects. RNA-sequencing (RNA-seq) transcriptome analysis using near-isogenic lines identified 773 differentially expressed genes, with three promising candidate genes within the qESL1-1 locus: Zm00001d028720 (phosphatidylinositol transfer protein), Zm00001d028761 (chloroplast unusual positioning protein), and Zm00001d028766 (asparagine synthetase). Gene ontology enrichment analysis revealed significant enrichment in terms related to floral organ development, while pathway analysis highlighted roles in amino acid metabolism and mitogen-activated protein kinase (MAPK) signaling. This study provides insights into the polygenic architecture of ESL and identifies genetic resources from teosinte for optimizing maize plant architecture in modern breeding programs.

Key message: HvEMF1L mutants display pleiotropic defects in spike morphology, especially awn development in barley. The study integrates mutagenesis, genetic mapping and sequencing technologies for trait dissection Awns are apical extensions of the lemma that are prevalent in many wild and cultivated grass species. In cultivated cereals they are relevant, given their influence on grain yield through contributions to photosynthesis, transpiration, carbohydrate accumulation and drought stress mitigation. While several genetic factors controlling barley awn traits have been identified, their complex network and interactions are not fully understood. This study characterizes a "pendant awn" mutant derived from an ethyl methanesulfonate (EMS)-mutagenized population of the two-rowed winter barley cultivar 'Igri' which is marked by shorter, thinner, and less upright awns. Segregation analyses in an F₂ population of 149 individuals indicated a monogenic recessive inheritance of the mutant trait. Molecular genetic mapping identified a 356.8 Mbp region on chromosome 3H associated with the pendant awn mutant trait. Whole-genome re-sequencing of mutant and wild-type individuals led to the discovery of a premature stop codon mutation specific to the pendant awn mutant in the EMBRYONIC FLOWER 1 LIKE (HvEMF1L) gene, predicted to truncate the protein by 62.3%. Pan-genomic and -transcriptomic analyses revealed a high level of sequence conservation of HvEMF1L in global barley germplasm and an inflorescence-specific gene expression profile. The study highlights HvEMF1L as a putative regulator of barley awn development and underscores the scope of combining mutagenesis, genetic mapping, and genome sequencing for trait dissection.

The R2R3-MYB transcription factor StAN1, a crucial regulator of anthocyanin biosynthesis in potato tubers, exerts previously unexplored global control over flavonoid diversification. Integrated transcriptomics (RNA-seq) and flavonoid metabolomics (UPLC-MS/MS) of StAN1-overexpressing tubers revealed its dual role in metabolic reprogramming: among 186 identified flavonoids, 122 exhibited tissue-specific accumulation shifts, with anthocyanins (e.g., pelargonidin/cyanidin), flavanones, and flavanonols upregulated in red flesh while flavonols (kaempferol/quercetin derivatives) were suppressed. Transcriptomic analyses identified 4783 flesh-specific and 2935 skin-specific differentially expressed genes (DEGs), pinpointing key biosynthetic genes and novel co-regulators (ERF, WRKY, bHLH TFs). Mechanistically, DAP-seq demonstrated StAN1 binding to promoters of flavonoid genes (e.g., StDFR), and dual-luciferase assays confirmed its direct activation of StDFR expression. Regulatory network expansion was evidenced by co-upregulation of RLKs (e.g., LRK10-like kinases), implicating kinase signaling in flavonoid partitioning. This study elucidates StAN1's multifaceted role beyond anthocyanin activation-orchestrating metabolic flux, engaging novel TF/kinase networks, and directly targeting structural genes-providing a foundation for engineering potatoes with enhanced nutraceutical properties via targeted manipulation of the StAN1 regulatory network.

Key message: We identified sources of resistance and a major QTL for resistance to bacterial leaf streak in durum. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa, has reemerged as a significant disease impacting bread wheat and durum production worldwide. The lack of resistance sources and limited understanding of the genetics behind host resistance have made breeding for BLS resistance challenging, especially in durum wheat. In this study, we first evaluated the reaction of a set of durum cultivars, mainly from North Dakota State University (NDSU). Our results indicated that most cultivars were susceptible, with only a few exceptions. Next, we utilized a subset of the Global Durum Panel (GDP) to identify sources of resistance and conduct a genome-wide association study (GWAS) to identify BLS resistance loci. Additionally, we performed disease evaluations and quantitative trait locus (QTL) analysis on two durum recombinant inbred line (RIL) populations: one was derived from the resistant NDSU cultivar 'Ben' and the other from the resistant Ethiopian landrace PI 387336. Our findings revealed that several modern durum cultivars from different countries within the GDP exhibited a high level of resistance. Both GWAS and biparental mapping identified a major QTL located at the distal end of chromosome arm 6AS. The physical positions of the single-nucleotide polymorphism (SNP) markers obtained from both experiments strongly suggest that the same locus is responsible for BLS resistance in the tested durum materials. The resistant accessions and SNP markers identified in this study will be valuable for transferring this major QTL into elite durum and common wheat cultivars.

Key message: Genome‑wide association studies, linkage mapping and transcriptomic analysis reveal TraesCS1B02G308200 as a candidate gene associated with nitrogen use efficiency in wheat. Enhancing nitrogen use efficiency (NUE) in wheat production can substantially increase crop productivity while minimizing nitrogen application. In this study, QTLs for NUE-related agronomic traits were detected in two populations: (1) a natural population of 243 wheat accessions from the Yellow and Huai River Valleys in China (CH population) and (2) a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero (AC population). Nine agronomic traits were evaluated under two nitrogen regimes, namely, normal and low-nitrogen stress, at two experimental sites during two growing seasons. A total of 836 and 154 QTLs were identified through association and linkage analyses, respectively, based on the low-nitrogen tolerance index of the nine traits across all environments. By further transcriptome analysis of Chilero at the jointing, anthesis and grain-filling stages, a total of 48 differentially expressed genes were identified within the colocalization interval of the two populations. A stable QTL, QYSI1B.2 (chr1B: 501.04-508.02 Mb), was successfully validated in both populations. By examining local linkage disequilibrium, QYSI1B.2 was refined to a smaller physical region spanning 506.02-507.19 Mb. A possible candidate gene, TraesCS1B02G308200, which encodes a WRKY transcription factor, was identified through evaluation of its expression levels. These findings provide a foundation for exploring the molecular targets underlying wheat NUE.