Association mapping across a multitude of traits collected in diverse environments in maize

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter different phenotypes. Quantitative natural variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects variants. Widely adopted community association panels been employed by plant genetics communities study the basis naturally occurring phenotypic variation wide range traits. High-density marker data—18M markers—from 2 partially overlapping maize comprising 1,014 unique genotypes grown field trials across at least 7 US states and scored for 162 distinct trait data sets enabled identification 2,154 suggestive marker-trait associations 697 confident genome using resampling-based genome-wide strategy. The precision was estimated be 3 based on reference set with known Examples were observed both loci associated diverse traits (e.g., above-ground below-ground traits), as well same similar environments. Many significant signals are located near whose functions previously entirely unknown purely via functional homologs. This demonstrates mining panel new higher-density combined tests develop testable hypotheses about gene functions, variants, genotype-by-environment interaction.

Language: Английский

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An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(27)

Published: June 30, 2022

Native Americans domesticated maize ( Zea mays ssp. ) from lowland teosinte parviglumis parviglumis) in the warm Mexican southwest and brought it to highlands of Mexico South America where was exposed lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites plant responses low-temperature phosphorus availability have been suggested influence Here, we combined linkage mapping with genome scans identify High PhosphatidylCholine 1 HPC1 ), a gene encodes phospholipase A1 enzyme, as major driver phospholipid variation highland maize. Common garden experiments demonstrated genotype-by-environment interactions associated at HPC1, allele leading higher fitness highlands, possibly by hastening flowering. The variant resulted impaired function encoded protein due polymorphism highly conserved sequence. A meta-analysis across orthologs indicated association between identity amino acid this position optimal growth prokaryotes. Mutagenesis via editing validated its role regulating metabolism. Finally, showed entered cultivated introgression wild mexicana has maintained breeding lines Northern United States, Canada, Europe. Thus, introgressed underlies large metabolic QTL modulates phosphatidylcholine levels an adaptive effect least part induction early

Language: Английский

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Chromosome-scale assembly and annotation of the perennial ryegrass genome

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: July 12, 2022

Abstract Background The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well for evolutionary comparative genomics. improvement long-read sequencing technologies the advent optical mapping chromosome conformation capture last few years, significantly promoted development model plants crop species. In grasses, recently became available cultivated wild species Triticeae subfamily. Development state-of-the-art genomic resources Poeae subfamily, which includes crops like fescues ryegrasses, lagging behind progress cereal Results Here, we report a new sequence assembly perennial ryegrass, obtained by combining PacBio sequencing, Illumina short-read polishing, BioNano Hi-C scaffolding. More than 90% total size ryegrass (approximately 2.55 Gb) covered seven pseudo-chromosomes that show high levels collinearity orthologous chromosomes transposon fraction was found be relatively low, approximately 35% content, less half repeat content We predicted 54,629 high-confidence gene models, 10,287 long non-coding RNAs 8,393 short genome. Conclusions reference annotation presented here are valuable studies applications will expedite productive varieties related

Language: Английский

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SorghumBase: a web-based portal for sorghum genetic information and community advancement

Planta, Journal Year: 2022, Volume and Issue: 255(2)

Published: Jan. 11, 2022

SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research development in agriculture rely on proper data resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, bioinformaticians, centralizing desirable into user-friendly hub crop systems is essential successful collaborations breakthroughs development. Here, we present the web ( https://www.sorghumbase.org ), community. hosts wide range of genomic information modular framework, built with open-source software, to provide sustainable platform. This initial release includes: (1) five reference genome assemblies pan-genome browser; (2) genetic variant natural diversity panels ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface integrated views various types; (4) links supporting interconnectivity other repositories including genebank, QTL, gene expression databases; (5) content management system support access news training materials. offers investigators improved collation will facilitate growth robust genomics-assisted breeding.

Language: Английский

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Exploring impact of recombination landscapes on breeding outcomes

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(14)

Published: March 27, 2023

Plant breeding relies on crossing-over to create novel combinations of alleles needed confer increased productivity and other desired traits in new varieties. However, crossover (CO) events are rare, as usually only one or two them occur per chromosome each generation. In addition, COs not distributed evenly along chromosomes. plants with large genomes, which includes most crops, predominantly formed close ends, there few the swaths around centromeres. This situation has created interest engineering CO landscape improve efficiency. Methods have been developed boost globally by altering expression anti-recombination genes increase rates certain parts changing DNA methylation patterns. progress is being made devise methods target specific sites. We review these approaches examine using simulations whether they indeed capacity efficiency programs. found that current alter can produce enough benefits for programs be attractive. They genetic gain recurrent selection significantly decrease linkage drag donor loci schemes introgress a trait from unimproved germplasm an elite line. genome sites were also provide advantage when introgressing segment harboring desirable quantitative loci. recommend avenues future research facilitate implementation

Language: Английский

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A key to totipotency: Wuschel‐like homeobox 2a unlocks embryogenic culture response in maize (Zea mays L.)

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(9), P. 1860 - 1872

Published: June 26, 2023

The ability of plant somatic cells to dedifferentiate, form embryos and regenerate whole plants in vitro has been harnessed for both clonal propagation as a key component genetic engineering systems. Embryogenic culture response is significantly limited, however, by genotype most species. This impedes advancements transformation-based functional genomics research crop improvement efforts. We utilized natural variation among maize inbred lines genetically map embryo generation potential tissue identify candidate genes underlying totipotency. Using series derived from crosses involving the culturable parent A188 non-responsive B73, we identified region on chromosome 3 associated with embryogenic focused three within based position expression pattern. Two showed no effect when ectopically expressed but gene Wox2a was found induce embryogenesis callus proliferation. Transgenic B73 strong constitutive coding sequences were produce at similar frequencies, demonstrating that sufficient either allele could rescue phenotype. regenerated without chemical selection pleiotropic effects observed overexpression T0 or two independent events which produced T1 progeny. In addition linking Wox2a, our data support utility enabling transformation recalcitrant genotypes.

Language: Английский

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MDSi: Multi-omics Database for Setaria italica

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: April 27, 2023

Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows high inbreeding rate close relationship to several major foods, feed, fuel bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled data high-quality efficient Agrobacterium-mediated genetic transformation system made xiaomi ideal C4 model system. has been widely shared in research community as result there is growing need for user-friendly portal intuitive interface perform exploratory analysis of data.Here, built Multi-omics Database Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm ), that contains 161,844 annotations, 34,436 protein-coding genes their expression information 29 different tissues (6) JG21 (23) samples can be showed Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, whole-genome resequencing (WGS) 398 germplasms, including 360 millets 38 green foxtails corresponding metabolic were available MDSi. SNPs Indels these germplasms called advance searched compared interactive manner. Common tools BLAST, GBrowse, JBrowse, map viewer, downloads implemented MDSi.The MDSi constructed this study integrated visualized from three levels genomics, transcriptomics metabolomics, also provides on variation hundreds germplasm resources satisfies mainstream requirements supports community.

Language: Английский

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Drought stress in maize: stress perception to molecular response and strategies for its improvement

Functional & Integrative Genomics, Journal Year: 2023, Volume and Issue: 23(4)

Published: Sept. 11, 2023

Language: Английский

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The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(15), P. 4611 - 4624

Published: June 14, 2024

Abstract Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret ever-increasing number of reported PTMs, Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview PTMs tools to assess it. This update includes 62 novel profiling studies, adding a total 112 000 modified peptides reporting including 14 additional types three species (moss, tomato, soybean). Furthermore, open modification re-analysis large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes lysine acylations predominant in seed flower tissues 3-phosphoglycerylation on glycolytic enzymes plants. An extra ‘Protein list analysis’ tool was developed for retrieval assessing enrichment interest. We conducted analysis nuclear proteins, revealing substantial redox nucleus, confirming previous assumptions regarding regulation transcription. encourage use 2.0 hypothesis testing new target discovery, also submit data expand coverage conditions, species, types, thereby enriching our understanding biology.

Language: Английский

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Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 30, 2024

Abstract Background Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying response in maize, though functions of many genes still unknown. To enhance functional annotation maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying traits related stress. Results We mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 seven studies) generated B73 cultivar recent version reference genome (B73v5) deduced stress-related gene models. conducted robust meta-analysis transcriptome profiles identify loci responsive 3,230 differentially expressed (DEGs): 2,555 DEGs regulated 408 during 267 (co-DEGs) that overlap between discovered hub network analyses, among co-DEGs we identified putative NAC domain transcription factor superfamily protein ( Zm00001eb369060 ) IDP275, which previously responded herbivory drought IDP275 was up-regulated our analysis eight four stresses. A set enrichment pathway revealed hormone-mediated signaling processes phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, also demonstrated how evolve adapt changing environments. Conclusions These results will help facilitate multiple models maize. Data can be accessed downloaded at Maize Genetics Genomics Database (MaizeGDB).

Language: Английский

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