Theoretical and Applied Genetics最新文献

Message: A QTL from rye chromosome 5R confers resistance to root-lesion nematode in triticale.Root-lesion nematode (Pratylenchus neglectus, RLN) poses a significant threat to global wheat production. High levels of RLN resistance are rare in wheat. Triticale, an amphiploid generated by combining wheat and rye genomes that naturally carries rye-derived defense alleles, offers an untapped reservoir of nematode resistance. Here, we evaluated the response to RLN in 137 recombinant inbred lines (RILs) derived from a cross between two triticale cultivars: Siskiyou (susceptible) and Villax St. Jose (resistant). Genotyping-by-sequencing identified 1054 high-quality single-nucleotide polymorphism (SNP) markers, which, along with seven simple sequence repeat (SSR) markers, were assembled into 21 linkage groups covering the triticale genome. A single quantitative trait locus (QTL) on the rye-derived chromosome 5R was identified that explained approximately 20% of the phenotypic variance across experiments. A high-throughput Kompetitive allele-specific PCR (KASP) assay based on the most significant SNP marker was developed, providing a rapid genotyping platform for selecting the resistance allele and reducing reliance on labor-intensive phenotyping for P. neglectus resistance in triticale. This study reports the first mapped RLN-resistance QTL in triticale, laying the fundamental foundation for introgressing the 5R resistance allele into wheat via marker-assisted selection combined with chromosome engineering, thereby broadening the genetic basis for nematode resistance in cereal crops.

Key message: Integrated genome-wide and haplotype-based association analyses identified a key genomic locus governing plant growth habit (PGH) traits in chickpea. Identification of molecular markers governing plant growth habit (PGH) traits that enable mechanical harvestability is pivotal for boosting production efficiency of crops under changing climates and increasing global food demand. With a combinatorial integrated genomics-assisted breeding strategy comprising of association mapping, haplotype-based association, molecular haplotyping and gene expression analysis in a 286 association panel of chickpea (Cicer arietinum), we dissected the genetic basis of PGH traits. This study employed 382,171 genome-wide SNPs (single-nucleotide polymorphisms) obtained from whole-genome sequencing (WGS) of 286 desi and kabuli chickpea accessions and delineated a major genomic locus associated with PGH traits variation, particularly between erect (E)/semi-erect (SE) versus spreading (S)/semi-spreading (SS) types. Within this genomic loci, CaPAR1 (Cicer arietinum PAR1) and its derived natural alleles/haplotypes was identified as the candidate gene. These findings can facilitate generation of high-yielding, erect/semi-erect, mechanically harvestable cultivars through translational genomics and molecular breeding for genetic enhancement of chickpea.

Key message: A core set of sequence tagged microsatellite sites (STMS) markers for Oryza sativa complex were developed, validated and utilized for pre-breding and characterization of Oryza germplasm from different taxa.   Development of genome-wide distributed cross-transferable molecular markers applicable to different species can enhance pre-breeding efficiency. Screening of 23.5K primer pairs across nine reference genomes identified 1,008 cross-amplifiable sequence-tagged microsatellite site (STMS) markers, including 520 genic ones, for the Oryza sativa complex. Predicted amplicon lengths of the markers were validated using polymerase chain reaction (PCR). Additionally, 3,628-13,280 markers were identified for individual species. Most cross-amplifiable markers were syntenic across the A-genome. However, substantial intra- and inter-chromosomal translocations were detected in O. longistaminata, O. nivara, and O. meridionalis compared to other A-genome species and subspecies. Notably, four markers exhibited contrasting inter-chromosomal translocations between the three Asiatic A-genome species and the five other species from Africa, South America, and Australia. Among the 1K cross-amplifiable core markers, 629 syntenic STMS loci were considered cross-transferable across the A-genome, within which three markers showed distinct species-specific amplicon lengths. Additionally, 42 markers were predicted to be cross-amplifiable among O. sativa complex, O. punctata, and O. coarctata. PCR-based cross-amplification of the markers in 21 Oryza species revealed hyper-variable amplicon lengths, though their synteny could not be confirmed. The A-genome core markers, along with the species combination-wise markers, provide a reliable genomic resource for developing chromosome segment substitution lines (CSSLs), molecular mapping, and transferring diverse traits from multiple wild species to all types of cultivated rice, including O. sativa, O. glaberrima, and New Rice for Africa (NERICA). Selected cross-transferable markers were used to develop CSSLs by introgressing O. rufipogon genomic segments into the O. sativa background.

In Japan, rice cultivars with high eating quality such as Koshihikari are often highly susceptible to the fungus Pyricularia oryzae, which causes rice blast, the most serious disease of rice; however, little is known about the genetic factors leading to this high susceptibility to blast. Here, after our initial inoculations with P. oryzae, the expression of the pathogenesis-related protein 1b (PR1b) gene was not detected in Koshihikari using RT-qPCR, but it was detected in Nipponbare, a moderately resistant cultivar. This unexpected result was due to the insertion of the nonautonomous retrotransposon Dasheng in the coding region of PR1b in Koshihikari. We then showed that blast resistance was higher in transgenic Koshihikari lines that overexpressed PR1b, suggesting that the PR1b mutation was one of the causes of high blast susceptibility of Koshihikari. When we checked for this PR1b mutation in the top 10 most widely grown rice cultivars in Japan and the current leading cultivars in Hokkaido Prefecture as examples, at least the top eight cultivars and all current leading cultivars in Hokkaido Prefecture had this mutation. Thus, the deleterious PR1b mutation seems to be fixed in nearly the entire rice population in Japan. Moreover, our survey of genomic sequences of 36 rice cultivars in public databases showed that Dasheng was inserted into the PR1b gene in two japonica cultivars and an indica cultivar, all bred in China, at a site identical to that in Koshihikari.

The whitefly-transmitted begomovirus can devastate Solanaceae crops worldwide. Despite a strong demand for the genetic introgression of begomovirus resistance, only the begomovirus resistance gene in tomatoes and peppers has been cloned. Here, we aimed to identify a begomovirus resistance gene in eggplant (Solanum melongena). Previously, we identified accession No.820 as a resistance source against tomato yellow leaf curl Kanchanaburi virus (TYLCKaV). A dominant locus, Eggplant yellow leaf curl disease virus resistance 1 (Ey-1), conferring resistance against TYLCKaV was identified on chromosome 1 by genetic mapping using the F₂ and F_2:3 segregating populations obtained from cross-pollination of No.820 and begomovirus susceptible No.47. From whole-genome and transcriptome sequencing of No.820 and No.47, we selected 5 genes as candidates among 10 genes on the final 113-kb target region. Reverse genetic analysis using virus-induced gene silencing (VIGS) of these five candidate genes in No.820 revealed that silencing of SmNEN3, which encodes a DEDDh family exonuclease protein, resulted in loss of resistance. Comparison of the genomic and transcript sequences of SmNEN3 from No.820 and No.47 revealed a single amino acid deletion and nonsynonymous mutations that most likely contribute to begomovirus resistance. No.820 is a highly valuable genetic resource with dominant resistance to begomovirus, and the new DNA markers will greatly aid marker-assisted breeding.

Allopolyploidization is a major driver of plant evolution and crop improvement, influencing both adaptation and diversification. MicroRNAs (miRNAs), 20-24 nt endogenous noncoding RNAs, regulate post-transcriptional gene expression and influence diverse biological processes. MiRNAs regulate a variety of agronomic traits and represent an important genetic resource for crop genetic improvement. While prevalent in plant evolution, the short-term (< 10,000 years) impact of allopolyploidization on miRNA evolution remains unclear. This study systematically compared miRNAs in the A genomes of Brassica rapa, Brassica juncea, and Brassica napus to reveal the short-term effects of allopolyploidization on miRNAs. The results showed that allopolyploidization caused loss of over half of the miRNAs in the A genomes of B. juncea and B. napus and accelerated miRNA cluster loss. The subgenome dominance (LF > MF1/MF2) resulting from ancient whole-genome triplication persisted post-allopolyploidization. Following allopolyploidization, the nucleotide divergence of miRNAs did not change significantly, and the maximum nucleotide divergence was only 0.11. Multi-copy miRNA retention rates differ between B. juncea and B. napus, potentially due to the influence of B and C genomes. MiRNA retention was affected by flanking protein-coding genes, with those adjacent to multi-copy protein-coding genes more likely retained as multiple copies post-allopolyploidization. Retained single miRNAs may form miRNA clusters via tandem duplication events. Additionally, homoeologous exchanges may affect the protein-coding genes flanking miRNAs. These findings indicated that short-term allopolyploidization significantly affected miRNA retention in Brassica A genome, providing new insights into allopolyploidization impacts on miRNA evolution.

Key message: Arachis hypogaea High Antioxidant Activity gene 1 (AhHAA1), likely encoding an anthocyanidin reductase, enhances nutritional quality of testaless peanut seeds. Improving the antioxidant activity of peanut (Arachis hypogaea) seeds is critical for extending their shelf life and enhancing their nutritional quality. Mining of genetic resources to identify loci associated with antioxidant activity could facilitate the breeding of new cultivars with high antioxidant activity in seeds. Here, we developed a population of advanced recombinant inbred lines containing 175 F_5:6 families derived from the parents 'JiHua 11' (JH11) and 'JiHuaTian 1' (JHT1). We constructed a high-resolution genetic map covering 2870.3 cM, with an average length of 143.5 cM per linkage group, using 1108 polymorphic single-nucleotide polymorphisms to identify quantitative trait loci (QTLs) associated with antioxidant activity and the contents of antioxidant components. The major QTL qIAA_A03_2 made the greatest contribution to standing genetic variation (53.75%). We mapped qIAA_A03_2 to a physical interval of approximately 80 kb on chromosome A03. Analysis of whole-genome variation between parents uncovered a strong candidate gene encoding an anthocyanin reductase, designated Arachis hypogaea High Antioxidant Activity 1 (AhHAA1). Analysis of the genotypes and phenotypes of near-inbred lines with high and low antioxidant levels as well as 50 peanut accessions suggested that AhHAA1 increases the antioxidant activity of processed testaless seeds, primarily by affecting the contents of antioxidant component_3 (AC3) and AC4. Our results provide insights into the genetic regulation of antioxidant activity in peanut seeds that can survive testa removal during processing. In addition, the polymorphic markers linked to AhHAA1 could facilitate the selection of germplasm and the breeding of peanuts with high nutritional quality via marker-assisted selection.

Key message: A stable QTL for petiole length, qPL6, was mapped in a RIL population over three consecutive growing seasons, with two candidate genes identified through integrated RNA-seq analysis. Petiole length is a critical determinant of canopy architecture in soybean (Glycine max (L.) Merr.), directly modulating yield potential through its effects on photosynthetic efficiency. Consequently, identifying genes controlling petiole length is essential for developing an ideal plant architecture adapted to high-density planting, ultimately increasing yield per unit area. Here we identified a stable quantitative trait locus (QTL) for petiole length on chromosome 6, designated qPL6, across three consecutive growing seasons, which explained 6.13-19.42% of the phenotypic variance. By comparing the longitudinal anatomical structures of petioles from Qi Huang No34 (QH34) and Ji Dou No17 (JD17), we determined that the difference in petiole length was attributed to variations in parenchyma cell lengths. Through RNA-seq analysis of two near-isogenic lines (NILs), we identified 90 differential expressed genes (DEGs) common to the upper, middle and lower petioles. These DEGs were significantly enriched in GO terms related to hormone signaling pathways and cell wall organization. By integrating analysis of sequence variations with transcriptional profiles, we selected two candidate genes, Glyma.06G258000 and Glyma.06G260800, both implicated in the auxin-responsive pathway. Glyma.06G258000 showed differential expression in the petiole, pulvinus and leaf, and carried a 626-bp InDel located 737 bp upstream of its coding region. Glyma.06G260800 contained two SNPs in its second exon that induced two nonsynonymous mutations. The novel QTL and candidate genes identified in this study offer valuable genetic resources for soybean molecular breeding aimed at optimizing plant architecture and increasing yield.

Cis-regulatory elements (CREs) govern gene expression, and the relationship between non-coding regulatory elements and gene expression is inherently complex. To further elucidate how these elements influence gene expression, we refined previous models and developed an interpretable deep learning model, termed L-CRE. By analyzing the flanking regions of genes from four distinct tomato varieties, this model successfully predicted high and low levels of gene expression, achieving a peak accuracy of 86.9%, demonstrating robust performance. To gain deeper insights into the model's predictive mechanisms, we conducted an interpretability analysis, calculating and evaluating the contribution scores of different genomic regions to the prediction outcomes. Through further exploration of these contribution scores, we identified several critical genomic regions that significantly influence the prediction of gene expression levels. Notably, these regions frequently encompass transcription factor binding sites. Moreover, based on the analysis of contribution scores, we successfully identified several experimentally validated regulatory elements. This study not only enhances our understanding of gene regulatory mechanisms in tomatoes but also provides novel insights and methodologies for future research in crop genetic improvement and functional genomics.

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.