Theoretical and Applied Genetics最新文献

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.

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.