Plant Genome最新文献

Powdery mildew, caused by the fungal pathogen Blumeria graminis (DC.) E. O. Speer f. sp. tritici Em. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivum L.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimize Bgt's fast evolving virulence. In tetraploid wheat (Triticum turgidum L.), wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed many Pm resistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction to Bgt isolate OKS(14)-B-3-1 and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis of Bgt resistance in the panel, genome-wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype-by-sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty-five significant SNP markers were identified to be associated with Bgt resistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derived Pm4a, Pm5a, PmG16, and Pm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhance Bgt resistance in wheat.

Climate change represents a significant challenge to global food security by altering environmental conditions critical to crop growth. Plant breeders can play a key role in mitigating these challenges by developing more resilient crop varieties; however, these efforts require significant investments in resources and time. In response, it is imperative to use current technologies that assimilate large biological and environmental datasets into predictive models to accelerate the research, development, and release of new improved varieties that can be more resilient to the increasingly variable climatic conditions. Leveraging large and diverse datasets can improve the characterization of phenotypic responses due to environmental stimuli and genomic pulses. A better characterization of these signals holds the potential to enhance our ability to predict trait performance under changes in weather and/or soil conditions with high precision. This paper introduces characterization and integration of driven omics (CHiDO), an easy-to-use, no-code platform designed to integrate diverse omics datasets and effectively model their interactions. With its flexibility to integrate and process datasets, CHiDO's intuitive interface allows users to explore historical data, formulate hypotheses, and optimize data collection strategies for future scenarios. The platform's mission emphasizes global accessibility, democratizing statistical solutions for situations where professional ability in data processing and data analysis is not available.

End-use and processing traits in wheat (Triticum aestivum L.) are crucial for varietal development but are often evaluated only in the advanced stages of the breeding program due to the amount of grain needed and the labor-intensive phenotyping assays. Advances in genomic resources have provided new tools to address the selection for these complex traits earlier in the breeding process. We used association mapping to identify key variants underlying various end-use quality traits and evaluate the usefulness of genomic prediction for these traits in hard red spring wheat from the Northern United States. A panel of 383 advanced breeding lines and cultivars representing the diversity of the University of Minnesota wheat breeding program was genotyped using the Illumina 90K single nucleotide polymorphism array and evaluated in multilocation trials using standard assessments of end-use quality. Sixty-three associations for grain or flour characteristics, mixograph, farinograph, and baking traits were identified. The majority of these associations were mapped in the vicinity of glutenin/gliadin or other known loci. In addition, a putative novel multi-trait association was identified on chromosome 6AL, and candidate gene analysis revealed eight genes of interest. Further, genomic prediction had a high predictive ability (PA) for mixograph and farinograph traits, with PA up to 0.62 and 0.50 in cross-validation and forward prediction, respectively. The deployment of 46 markers from GWAS to predict dough-rheology traits yielded low to moderate PA for various traits. The results of this study suggest that genomic prediction for end-use traits in early generations can be effective for mixograph and farinograph assays but not baking assays.

Alfalfa (Medicago sativa L.) is a perennial forage legume esteemed for its exceptional quality and dry matter yield (DMY); however, alfalfa has historically exhibited low genetic gain for DMY. Advances in genotyping platforms paved the way for a cost-effective application of genomic prediction in alfalfa family bulks. In this context, the optimization of marker density holds potential to reallocate resources within genomic prediction pipelines. This study aimed to (i) test two genotyping platforms for population structure discrimination and predictive ability (PA) of genomic prediction models (G-BLUP) for DMY, and (ii) explore optimal levels of marker density to predict DMY in family bulks. For this, 160 nondormant alfalfa families were phenotyped for DMY across 11 harvests and genotyped via targeted sequencing using Capture-seq with 17K probes and the DArTag 3K panel. Both platforms discriminated similarly against the population structure and resulted in comparable PA for DMY. For genotyping optimization, different levels of marker density were randomly extracted from each platform. In both cases, a plateau was achieved around 500 markers, yielding similar PA as the full set of markers. For phenotyping optimization, models with 500 markers built with data from five harvests resulted in similar PA compared to the full set of 11 harvests and full set of markers. Altogether, genotyping and phenotyping efforts were optimized in terms of number of markers and harvests. Capture-seq and DArTag yielded similar results and have the flexibility to adjust their panels to meet breeders' needs in terms of marker density.

The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids; thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (∼370 Mb) and the B genome being the largest (∼700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which ∼65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.

Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F₂ individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1M^b could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the M^b sub-genome (425 markers) and the U^b sub-genome (495 markers). Chromosomes of the M^b sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the U^b sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1U^b, 3U^b, and 5U^b retaining a substantial level of collinearity with Triticum aestivum, while 2U^b, 4U^b, 6U^b, and 7U^b show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3M^b, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.

Panicle exsertion is essential for crop yield and quality, and understanding its molecular mechanisms is crucial for optimizing plant architecture. In this study, the sheathed panicle-I (shp-I) mutant was identified from the ethyl methane sulfonate mutant population of the sorghum [Sorghum bicolor (L.) Moench] variety Hongyingzi (HYZ). While phenotypically similar to the wild type during the seedling stage, shp-I exhibits a significantly shorter peduncle internode at the heading stage. Cytomorphological analysis revealed reduced parenchyma cell size within the mutant's peduncle internode. Phytohormonal profiling showed lower levels of indole-3-acetic acid and higher concentrations of brassinosteroid in the mutant compared to the wild type at the peduncle internode. Genetic analysis confirmed that the mutant phenotype was caused by a recessive single-gene mutation. Through bulked segregant analysis sequencing (BSA-seq) genetic mapping, the causative locus for the mutant phenotype was localized to a 59.65-59.92 Mb interval on chromosome 10, which contains 28 putative genes. Additionally, the gene SbiHYZ.10G230700, which encodes a BTB/POZ and MATH (BPM) domain protein, was identified as a candidate gene. Further analysis revealed that the non-synonymous mutations in the candidate gene were located within the MATH domain, affecting the 3D structure of the protein. In summary, this study provides a new genetic material and candidate genes for future research into the molecular regulation of sorghum peduncle length.

Sweetness is a main component of the table beet (Beta vulgaris L.) flavor profile and a key determinant of its market success for fresh consumption. Total dissolved solids (TDS) is a proxy for sugar content in produce and are easily measured through a refractometer, making TDS valuable in breeding programs focused on increasing sweetness. A diversity panel of 238 accessions from the Beta vulgaris crop complex and wild relatives was assembled and genotyped using genotyping-by-sequencing, yielding 10,237 single nucleotide polymorphisms (SNPs) from 226 full panel accessions and 9,847 SNPs from table beet only accessions after filtering. The panel was phenotyped in field trials over 2 years and mean values were adjusted using best linear unbiased estimates. TDS levels varied among crop types and a broad-sense heritability of 0.90 indicated that phenotypic differences can be attributed in large part to genetic variation. A genome-wide association study (GWAS) uncovered four quantitative trait loci (QTLs) identified across multiple models to significantly associate with TDS. A QTL on chromosome 2 was consistently identified among GWAS models, explaining 12.1%-62.6% of the phenotypic variation in the full panel. Bevul.2G176300, a gene directly involved in the sucrose biosynthesis pathway, was located downstream the significant marker. A second QTL identified on chromosome 7 revealed QTL alleles that may differentiate between table beet accessions, explaining nearly half the phenotypic variation, and is the first QTL reported in association with TDS unique to table beet. The QTL described can be used to efficiently breed for higher TDS levels in Beta vulgaris, avoiding intercrop type crosses and linkage drag.

Phytocytokines belong to a category of small secreted peptides with signaling functions that play pivotal roles in diverse plant physiological processes. However, due to low levels of sequence conservation across plant species and poorly understood biological functions, the accurate detection and annotation of corresponding genes is challenging. The availability of a high-quality apple (Malus domestica) genome has enabled the exploration of five phytocytokine gene families, selected on the basis of their altered expression profiles in response to biotic stresses. These include phytosulfokine, inflorescence deficient in abscission/-like, pathogen-associated molecular pattern induced secreted peptide, plant peptide containing sulfated tyrosine, and C-terminally encoded peptide. The genes encoding the precursors of these five families of signaling peptides were identified using a customized bioinformatics protocol combining genome mining, homology searches, and peptide motif detection. Transcriptomic analyses showed that these peptides were deregulated in response to Erwinia amylovora, the causal agent of fire blight in pome fruit trees, and in response to a chemical elicitor (acibenzolar-S-methyl). Finally, gene family evolution and the orthology relationships with Arabidopsis thaliana homologs were investigated.

Durum wheat (Triticum turgidum ssp. durum L.) is an important world food crop used to make pasta products. Compared to bread wheat (Triticum aestivum L.), fewer studies have been conducted to identify genetic loci governing yield-component traits in durum wheat. A potential source of diversity for durum is its immediate progenitor, cultivated emmer (T. turgidum ssp. dicoccum). We evaluated two biparental populations of recombinant inbred lines (RILs) derived from crosses between the durum lines Ben and Rusty and the cultivated emmer wheat accessions PI 41025 and PI 193883, referred to as the Ben × PI 41025 (BP025) and Rusty × PI 193883 (RP883) RIL populations, respectively. Both populations were evaluated under field conditions in three seasons with an aim to identify quantitative trait loci (QTLs) associated with yield components and seed morphology that were expressed in multiple environments. A total of 44 and 34 multi-environment QTLs were identified in the BP025 and RP883 populations, respectively. As expected, genetic loci known to govern domestication and development were associated with some of the QTLs, but novel QTLs derived from the cultivated emmer parents and associated with yield components including spikelet number, grain weight, and grain size were identified. These QTLs offer new target loci for durum wheat improvement, and toward that goal, we identified five RILs with increased grain weight and size compared to the durum parents. These materials along with the knowledge of stable QTLs and associated markers can help to expedite the development of superior durum varieties.