Genomic resources in plant breeding for sustainable agriculture

Journal of Plant Physiology, Journal Year: 2020, Volume and Issue: 257, P. 153351 - 153351

Published: Dec. 17, 2020

Climate change during the last 40 years has had a serious impact on agriculture and threatens global food nutritional security. From over half million plant species, cereals legumes are most important for Although systematic breeding relatively short history, conventional coupled with advances in technology crop management strategies increased yields by 56 % globally between 1965−85, referred to as Green Revolution. Nevertheless, demand food, feed, fiber, fuel necessitates need break existing yield barriers many plants. In first decade of 21st century we witnessed rapid discovery, transformative technological development declining costs genomics technologies. second decade, field turned towards making sense vast amount genomic information subsequently moved accurately predicting gene-to-phenotype associations tailoring plants climate resilience this review focus resources, genome germplasm sequencing, sequencing-based trait mapping, genomics-assisted approaches aimed at developing biotic stress resistant, abiotic tolerant high nutrition varieties six major (rice, maize, wheat, barley, sorghum pearl millet), (soybean, groundnut, cowpea, common bean, chickpea pigeonpea). We further provide perspective way forward use including marker-assisted selection, backcrossing, haplotype based prediction machine learning artificial intelligence, speed approaches. The overall goal is accelerate genetic gains deliver resilient sustainable agriculture.

Language: Английский

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(1), P. 263 - 286

Published: Sept. 16, 2020

Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies now enable assembling genomes unprecedented quality contiguity. However, the difficulty in repeat‐rich GC‐rich regions (genomic “dark matter”) limits insights into evolution genome structure regulatory networks. Here, we compare available (short/linked/long reads proximity ligation maps) combinations thereof genomic dark matter. By adopting different de novo assembly strategies, draft to a curated multiplatform reference identify features that cause gaps within each assembly. We show implementing long‐read, linked‐read performs best recovering transposable elements, multicopy MHC genes, microchromosomes W chromosome. Telomere‐to‐telomere not reality yet for most organisms, but leveraging technology choice it is possible minimize downstream analysis. provide roadmap tailor projects optimized completeness both coding noncoding parts nonmodel genomes.

Language: Английский

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Gapless assembly of maize chromosomes using long-read technologies

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: May 20, 2020

Abstract Creating gapless telomere-to-telomere assemblies of complex genomes is one the ultimate challenges in genomics. We use two independent and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed 63 contigs contig N50 162 Mb. This includes chromosome 3 (236 Mb) 9 (162 Mb), 53 Mb Ab10 meiotic drive haplotype. The data also reveal internal structure seven centromeres five heterochromatic knobs, showing that major tandem repeat arrays (CentC, knob180, TR-1) are discontinuous frequently interspersed with retroelements.

Language: Английский

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High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

GigaScience, Journal Year: 2020, Volume and Issue: 9(5)

Published: May 1, 2020

Abstract Background The release of the first reference genome walnut (Juglans regia L.) enabled many achievements in characterization genetic and functional variation. However, it is highly fragmented, preventing integration genetic, transcriptomic, proteomic information to fully elucidate biological processes. Findings Here, we report new chromosome-scale assembly (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative previous genome, features an 84.4-fold increase N50 size, 16 chromosomal pseudomolecules assembled representing 95% its total length. Using full-length transcripts from single-molecule real-time sequencing, predicted 37,554 gene models, a mean length higher than annotations. Most protein-coding genes (90%) present both start stop codons, which represents significant improvement compared Chandler v1.0 (only 48%). We then tested potential impact chromosome-level on different areas research. By studying proteome changes occurring during male flower development, observed that virtual v2.0 presents fewer artifacts enabling identification pollen allergen walnut. Also, facilitates in-depth studies intraspecies diversity revealing previously undetected autozygous regions Chandler, likely resulting inbreeding, 195 genomic differentiated between Western Eastern cultivars. Conclusion Overall, will serve as valuable resource better understand explore biology.

Language: Английский

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Sorghum breeding in the genomic era: opportunities and challenges

Theoretical and Applied Genetics, Journal Year: 2021, Volume and Issue: 134(7), P. 1899 - 1924

Published: March 2, 2021

Language: Английский

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Structural Variation Detection and Analysis Using Bionano Optical Mapping

Methods in molecular biology, Journal Year: 2018, Volume and Issue: unknown, P. 193 - 203

Published: Jan. 1, 2018

Language: Английский

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Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps

G3 Genes Genomes Genetics, Journal Year: 2019, Volume and Issue: 9(3), P. 619 - 624

Published: Jan. 9, 2019

Wild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of all modern cultivated tetraploid wheat. Its genome large (> 10 Gb) and contains over 80% repeated sequences. The successful whole-genome-shotgun assembly wild (accession Zavitan) sequence (WEW_v1.0) was an important milestone for wheat genomics. In effort to improve this assembly, optical map accession Zavitan constructed using Bionano Direct Label Stain (DLS) technology. spanned 10.4 Gb. This another produced earlier by us with Bionano's Nick Repair (NLRS) technology were used current assembly. WEW_v1.0 consisted 151,912 scaffolds. Of them, 3,102 could be confidently aligned on maps. Forty-seven chimeric. They disjoined new scaffolds assembled aid total number reduced from 149,252 N50 increased 6.96 Mb 72.63 Mb. scaffolds, 485 which accounted 97% length, oriented genetic maps, WEW_v2.0 pseudomolecules constructed. included 333 (68.51 Mb) originally unassigned, 226 (554.84 placed into locations, 332 (394.83 re-oriented. improved resource understanding genomic modification that occurred domestication.

Language: Английский

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Assembly methods for nanopore-based metagenomic sequencing: a comparative study

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Aug. 12, 2020

Abstract Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due their potential generate long reads. Nevertheless, there is a lack updated and systematic studies evaluating performance different assembly tools on nanopore data. In this study, we have benchmarked ability assemblers reconstruct two commercially-available mock communities that been sequenced using Oxford Nanopore Technologies platforms. Among tested tools, only metaFlye, Raven, Canu performed well all datasets. These retrieved genomes (or even complete genomes) directly from metagenomic Despite intrinsic high error sequencing, final reached accuracy (~ 99.5 99.8% consensus accuracy). Polishing strategies demonstrated be necessary reducing number indels, had an impact prediction biosynthetic gene clusters. Correction with quality short reads did not always higher draft assemblies. Overall, data-adapted MinION’s current output-proved sufficient assembling characterizing low-complexity communities.

Language: Английский

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Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: unknown

Published: Nov. 20, 2019

The chloroplast genome usually has a quadripartite structure consisting of large single copy region and small separated by two long inverted repeats. It been known for some time that cell may contain at least structural haplotypes this structure, which differ in the relative orientation regions. However, methods required to detect measure abundance are labor-intensive, phenomenon remains understudied. Here, we develop new method, Cp-hap, all possible genomes using long-read sequencing data. We use method conduct systematic analysis quantification 61 land plant species across 19 orders Angiosperms, Gymnosperms, Pteridophytes. Our results show there occur with equal frequency most individuals. Nevertheless, whose lack repeats or have short just haplotype. also constant multiple samples from individual plant, suggesting process maintains operates rapidly, consistent hypothesis flip-flop recombination mediates heteroplasmy. suggest previous claims differences between need be revisited.

Language: Английский

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Comparative evolutionary genetics of deleterious load in sorghum and maize

Nature Plants, Journal Year: 2021, Volume and Issue: 7(1), P. 17 - 24

Published: Jan. 15, 2021

Language: Английский

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