Plant Genome最新文献

Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is the tetraploid progenitor of hexaploid bread wheat (Triticum aestivum L.) and is known to be a valuable source of genetic variation for wheat improvement. However, direct evaluation of wild emmer diversity for agronomic potential has limited value unless performed in the backgrounds of adapted cultivars. Here, we present a genetic characterization of a population of 1601 backcross recombinant inbred lines, with an average genome composition of 75% bread wheat and 25% wild emmer. Low-coverage whole-genome sequencing allowed introgressions and aneuploidies to be identified at a relatively low cost per sample. We identified a relatively large proportion of small introgressions (median length 38 Mb), and we found introgressions to be distributed across all chromosomes. Approximately 44% of genotyped progeny carried at least one aneuploidy, with monosomies being by far the most common. This population, which we have denoted as the Great Plains Wild Emmer/Hard Winter Wheat introgression population (GPWEW-IP), is, to our knowledge, the first introgression population developed through the direct hybridization of wild emmer wheat and US-adapted hard winter wheat. We believe that this population represents a valuable resource for wheat breeders and will accelerate the discovery and integration of useful variation from wild emmer wheat.

Potato wild relatives (Solanum section Petota) are a source of genetic diversity for climate-smart improvement of modern cultivars (Solanum tuberosum). The allotetraploid Solanum acaule Bitter. has been previously used to introgress frost tolerance into potato cultivars such as Yukon Gold and Viking. The current study presents the subgenomes of S. acaule. In a phylogenetic context, the placement of the individual subgenomes shows that Solanum megistacrolobum (Clade 4) is the progenitor species of S. acaule subgenome 2, while the progenitor species of subgenome 1 (mapping to Clade 3) is still unknown and may be extinct. The genome assembly is 1.34 Gb in 24 chromosomes with an N50 of 56.2 Mb, making the theoretical tetraploid S. acaule genome 2.68 Gb. The C-repeat binding factor (CBF) cold response genes were identified in the subgenomes, and in a freeze-challenged transcriptome analysis of S. acaule compared with autotetraploid S. tuberosum 'Atlantic', CBF1 was induced in both species, while CBF4 (subgenome 2) was induced only in S. acaule. A general subgenome expression bias was not detected in a set of homoeologous genes, though the subgenomes diverged in the number of differentially expressed genes and their functional roles.

Maize (Zea mays L.) is a globally significant crop, with its kernel sugar content playing a crucial role in determining nutritional quality and industrial applications. This study aimed to elucidate the genetic mechanisms underlying sugar-related traits in maize kernels through genome-wide association studies. We evaluated 495 maize inbred lines for reducing sugar content, soluble sugar content, and the reducing/soluble sugar ratio. Phenotypic analysis revealed substantial variation, with coefficients of variation ranging from 28.84% to 53.86%, and high broad-sense heritability (87.90%-93.98%). Using 12,617,573 high-quality single-nucleotide polymorphisms, we identified 93 significant quantitative trait nucleotides associated with these traits. Transcriptomic data from the maize inbred line B73 highlighted six candidate genes (Zm00001d040189, Zm00001d032517, Zm00001d052399, Zm00001d028974, Zm00001d036971, and Zm00001d022316) with high expression during kernel development. Protein-protein interaction and coexpression network analyses suggested that these genes are involved in metabolic processes, cell communication, and carbohydrate metabolism. Haplotype analysis further revealed that the optimal haplotypes of the six candidate genes could increase the kernel sugar content without affecting the yield traits of maize. These findings advance our understanding of the genetic basis of sugar-related traits in maize and offer valuable molecular markers for future breeding programs.

CONSTANS, CONSTANS-LIKE, TIMING OF CAB EXPRESSION1 (CCT) motif genes play a key role in barley (Hordeum vulgare L.) development and flowering, yet their genetic diversity remains underexplored. Leveraging a barley pangenome (76 genotypes) and pan-transcriptome (subset of 20 genotypes), we examined CCT gene variation and evolutionary dynamics. Motif-based searches, combined with genome assembly validation, revealed annotation limitations and novel frameshift variants (e.g., HvCO10, where Hv is Hordeum vulgare L.), indicating active diversification. Pangenome-wide phylogenetic analysis identified clade-specific domain expansions, including B-box domain additions in HvCO clades. Tissue-specific expression patterns further supported functional divergence among paralogs. Notably, VRN2, a canonical floral repressor associated with winter growth, was retained in spring genotypes, challenging its presumed exclusive role in vernalization. Discrepancies between VRN1 expression, VRN2 deletion, and growth habit implicated additional regulatory mechanisms. These findings highlight the power of pangenomes in resolving gene family complexity, refining annotations, and advancing the understanding of CCT genes to enhance barley resilience and adaptability.

Cultivated strawberry Fragaria × ananassa (Duch.) is an economically important small fruit. Flowering habit is a key trait of interest in cultivar development and agricultural production. Two cultivar types are distinguished: seasonal flowering (SF) varieties, which require a sufficiently short day length to initiate flowering; and perpetual flowering (PF) varieties, which are photoperiod-insensitive and continuously flowering at permissive temperatures. Identifying marker-trait associations (MTAs) and genes related to flowering time is an ongoing goal. SF and PF accessions of the ancestral octoploid Fragaria virginiana were used in crossing and backcrossing to generate a BC₁F₁ mapping population, which was genotyped on the IStraw90 SNP array to develop a linkage map using JoinMap 4.1. MTA analysis was done by chi-square test for independence and compared with analyses done using FlexQTL and WinQTLCart. Six MTAs for PF were mapped, suggesting complex genetic regulation. These MTAs were distributed across five linkage groups (LGs) representing four chromosomal homeology groups. Surprisingly, none of these six MTAs were assigned to a member of the F. virginiana subgenome A, the octoploid strawberry subgenome widely agreed to descend from the ancestral diploid Fragaria vesca. This important distinction extended to the strong MTAs on LG14, which our analysis assigned to the same homeology group but not the same homeolog previously assigned to the well-studied FaPFRU locus conferring continuous flowering in F. × ananassa. This alternative localization may help to explain why the gene(s) underlying FaPFRU have remained unidentified in the 13 years since its discovery.

Leaf rust, caused by the obligate fungal pathogen Puccinia purpurea, poses a serious threat to sorghum [Sorghum bicolor (L.) Moench] production leading to significant yield losses and undermining its values as renewable fuel crop. In this study, the United States Department of Agriculture-Agriculture Research Service, National Plant Germplasm System (NPGS) Sudan core collection was evaluated for rust-resistant response across four tropical environments. The analysis identified 18 accessions with rust resistant, among which four accessions (PI 568621, PI 569393, PI 570548, and PI 570974) consistently showed no rust pustules across all environments. Genome-wide association analysis led to the identification of a 57 kbp genomic region on chromosome 8 that encompasses a cluster of five homologous R genes. The resequencing analysis of the first exon from one candidate gene (Sobic.008G178200) found 61 point mutations that generate seven haplotypes. The high homology of these five genes and seven haplotypes indicates that this cluster might be acting as a single locus (Rp2) against P. purpurea. Comparative genome analysis found that the orthologs of Rp2 locus in maize (Zm00001d023311) are associated with the resistant response to Puccinia polysora, the causal agent of southern corn rust and in rice (Os12G29690), with resistance to the brown planthopper (Nilaparvata lugens). The introgression of the Rp2 locus into elite varieties or the inclusion of top-performing Sudanese tropical accessions in pre-breeding germplasm can accelerate the development of improved sorghum germplasm with durable rust resistant.

Fusarium graminearum colonizes the maize ear, causing Gibberella ear rot (GER) and producing harmful mycotoxins, including deoxynivalenol (DON) and zearalenone (ZEA). The disease can be managed in part by breeding and planting resistant maize cultivars. Resistance to GER is a quantitative and complex trait. Evaluation of diverse germplasm to identify regions and candidate genes associated with resistance may be useful for crop improvement efforts. Screening for GER is time-consuming and costly. Thus, identifying other traits that may serve as a proxy for GER resistance may accelerate resistance breeding efforts. We hypothesized that grain phenylpropanoid content and kernel composition are genetically and mechanistically related to GER resistance. We screened a diverse set of maize inbred lines for disease severity, DON, ZEA, ferulic acid, p-coumaric acid, pericarp thickness, and several kernel composition traits. Using a genome-wide association study, we identified markers associated with each phenotype and genomic regions that harbor alleles for both disease and metabolite-related phenotypes. Pathways significantly associated with GER-related traits were related to detoxification, cell wall integrity, and lignin biosynthesis. End-season ferulic acid and p-coumaric acid concentrations are not strong proxies for GER resistance, but secondary metabolites are important components of the maize-Fusarium graminearum pathosystem. Furthermore, lignin-deficient brown midrib mutants exhibited increased susceptibility to GER, underscoring the importance of lignin composition in limiting fungal colonization. The study highlights the multifaceted nature of GER resistance, involving both biochemical and structural defenses. These findings provide valuable targets for breeding programs aiming to enhance GER resistance and reduce mycotoxin contamination in maize.

The field elm (Ulmus minor) is an emblematic species of the European landscape, which has been severely affected by Dutch elm disease (DED) since the 20th century. To support restoration and conservation of this species and congeners, we present a de novo assembly and annotation of a wild genotype tested positive for DED resistance, along with a comprehensive phylogenetic analysis with related species. Cutting-edge sequencing technologies were used alongside high-throughput chromosome conformation capture technologies for chromosome conformation capture. Our assembly spans approximately 2.1 Gb, with scaffold and contig N50 sizes of 133.765 and 8.189 Mb, respectively. Repetitive elements account for 81.45% of the genome size. Using transcriptomic information from 19 tissues in varying developmental stages and gene model prediction techniques, a total of 46,357 protein-coding genes were annotated, 99.70% of which were functionally characterized. An analysis of the presence and arrangement of resistance genes on U. minor, and sister species Ulmus glabra and Ulmus parvifolia, revealed a clustered and syntenic distribution across all of them, with a higher density in U. minor. This genomic resource and its analytical dissection herein introduced represent valuable tools for future in-depth studies on the resistance mechanisms to DED. Additionally, this study completes the phylogenetic context within the order Rosales and provides a robust framework for future research.

Ipomoea trifida G. Don (2n = 2x = 30) is considered the closest known diploid relative and a wild ancestor of the autohexaploid sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90). This study aimed to map quantitative trait loci (QTLs) in a diploid full-sib population (M9 × M19) consisting of 210 progenies based on a high-density genetic linkage map constructed with single-nucleotide polymorphisms (SNPs). In a randomized complete block design with four replications, the phenotypic evaluation of 11 morphological traits was conducted for 188 individuals in 2016 at the International Potato Center under screenhouse conditions in San Ramón, Peru. Heritabilities ranged from 0.30 to 0.80, and genetic correlations varied from -0.22 to 1. An integrated genetic map was constructed with 15 linkage groups and 6410 SNPs spanning 2440.47 cM using the Onemap v.3.0 R package. Major misassemblies were identified and properly fixed on chromosomes 2, 3, and 7. QTL mapping was performed using the composite interval mapping approach for each trait with fullsibQTL v.0.0.901 R package. A total of 37 QTLs were identified, with up to 42.39% of the proportion of phenotypic variance explained by a major QTL on chromosome 3 for a leaf shape-related trait. Reference genome refining and QTL-linked markers contribute to advancing genetic and genomic research on I. trifida and may support sweetpotato breeding programs targeting ornamental traits.

PhasiRNAs (phased small interfering RNAs) are a major class of plant small RNAs (sRNA) known to be key regulators in male reproductive development of maize (Zea mays) and rice (Oryza sativa), among other plants. Earlier research focused primarily on premeiotic 21-nucleotide (nt) phasiRNAs and meiotic 24-nt phasiRNAs, while new studies uncovered a premeiotic class of 24-nt phasiRNAs. The biogenesis and function of these phasiRNAs remain unclear. We conducted an integrative analysis combining sRNA sequencing and transcriptomic profiling of sRNA-associated genes across 10 developmental stages of anther in Kitaake rice to map associations between expression of the transcripts encoding sRNA-related proteins and accumulation of phasiRNA classes. We identified previously undescribed classes of postmeiotic 21- and 24-nt phasiRNA-producing loci and characterized their unique accumulation patterns. Additionally, our findings reveal distinct nucleotide composition and register accumulation among the phasiRNA classes, suggesting the presence of diverse mechanisms of biogenesis and function. Our results provide new insights into the regulatory complexity of phasiRNAs, establishing a foundation for further functional studies and advancing our understanding of their roles in anther development and their underlying mechanisms.