TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

PLoS ONE, Journal Year: 2014, Volume and Issue: 9(2), P. e90346 - e90346

Published: Feb. 28, 2014

Genotyping by sequencing (GBS) is a next generation based method that takes advantage of reduced representation to enable high throughput genotyping large numbers individuals at number SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol currently being applied in numerous species researchers. Herein we describe bioinformatics pipeline, tassel-gbs, designed for the efficient processing raw sequence data into genotypes. tassel-gbs pipeline successfully fulfills following key design criteria: (1) Ability run on modest computing resources are typically available small breeding or ecological research programs, including desktop laptop machines with only 8–16 GB RAM, (2) Scalability from extremely studies, where hundreds thousands even millions SNPs can be scored up 100,000 (e.g., programs genetic surveys), (3) Applicability an accelerated context, requiring rapid turnover tissue collection Although reference genome required, also unfinished "pseudo-reference" consisting contigs. We detail benchmark it upon scale, wide analysis maize (Zea mays), average error rate was 0.0042 through application population genetic-based filters. Overall, assay provide robust tools studying genomic diversity.

Language: Английский

---

Drought Stress Impacts on Plants and Different Approaches to Alleviate Its Adverse Effects

Plants, Journal Year: 2021, Volume and Issue: 10(2), P. 259 - 259

Published: Jan. 28, 2021

Drought stress, being the inevitable factor that exists in various environments without recognizing borders and no clear warning thereby hampering plant biomass production, quality, energy. It is key important environmental stress occurs due to temperature dynamics, light intensity, low rainfall. Despite this, its cumulative, not obvious impact multidimensional nature severely affects morphological, physiological, biochemical molecular attributes with adverse on photosynthetic capacity. Coping water scarcity, plants evolve complex resistance adaptation mechanisms including physiological responses, which differ species level. The sophisticated regularity network improves tolerance are briefly discussed. Growth pattern structural reduction transpiration loss through altering stomatal conductance distribution, leaf rolling, root shoot ratio length increment, accumulation of compatible solutes, enhancement efficiency, osmotic hormonal regulation, delayed senescence strategies adopted by under deficit. Approaches for drought alleviations breeding strategies, genomics perspectives special emphasis omics technology alteration i.e., metabolomics, proteomics, genomics, transcriptomics, glyomics phenomics improve plants. For induction, seed priming, growth hormones, osmoprotectants, silicon (Si), selenium (Se) potassium application worth using conditions In addition, microbes, hydrogel, nanoparticles applications metabolic engineering techniques regulate antioxidant enzymes activity plants, enhancing maintenance cell homeostasis ameliorates effects great potential agriculture.

Language: Английский

---

Evolution of crop species: genetics of domestication and diversification

Nature Reviews Genetics, Journal Year: 2013, Volume and Issue: 14(12), P. 840 - 852

Published: Nov. 18, 2013

Language: Английский

---

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Proceedings of the National Academy of Sciences, Journal Year: 2013, Volume and Issue: 110(20), P. 8057 - 8062

Published: April 29, 2013

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject during improvement, we developed a high-throughput array interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in worldwide sample 2,994 accessions hexaploid including landraces and modern cultivars. Using SNP-based diversity map characterized impact crop improvement on genomic geographic patterns genetic diversity. We found evidence small population bottleneck extensive use ancestral variation often traceable founders cultivars from diverse regions. Analyzing differentiation among populations extent haplotype sharing, identified allelic variants subjected improvement. Selective sweeps were around genes involved regulation flowering time phenology. An introgression wild relative-derived gene conferring resistance fungal pathogen was detected by haplotype-based analysis. Comparing selective different populations, show that likely acts distinct targets or multiple functionally equivalent alleles portions range wheat. The majority selected present low frequency suggesting either weak pressure temporal directional breeding probably associated with changing agricultural practices environmental SNP chip provide resource for advancing supporting future genome-wide association studies

Language: Английский

---

Natural Variations and Genome-Wide Association Studies in Crop Plants

Annual Review of Plant Biology, Journal Year: 2013, Volume and Issue: 65(1), P. 531 - 551

Published: Nov. 26, 2013

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse that able to adapt various environmental conditions valuable resources for crop improvements meet the food demands increasing population. With completion reference genome sequences, advent high-throughput sequencing technology now enables rapid accurate resequencing a large number genomes detect genetic basis phenotypic variations in crops. Comprehensive maps facilitate genome-wide association studies complex traits functional investigations evolutionary changes These advances will greatly accelerate on designs via genomics-assisted breeding. Here, we first discuss describe development sequencing-based genotyping We then review domestication offer perspective genomics-driven designs.

Language: Английский

---

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

Theoretical and Applied Genetics, Journal Year: 2013, Volume and Issue: 126(4), P. 867 - 887

Published: March 7, 2013

More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping genome-wide association studies for training genomic selection models in plant improvement. Within this framework, the objective of modern is increase accuracy, precision throughput phenotypic estimation at all levels biological organization while reducing costs minimizing labor through automation, remote sensing, improved data integration experimental design. Much like efforts optimize genotyping during 1980s 1990s, designing effective initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians engineers. Robust systems needed characterize full suite genetic factors that contribute quantitative variation across cells, organs tissues, developmental stages, years, environments, species research programs. Next-generation generates significantly more than previously novel management, access storage systems, increased use ontologies facilitate integration, new statistical tools enhancing design extracting biologically meaningful signal from environmental noise. To ensure relevance, implementation efficient informative experiments also familiarity with diverse germplasm resources, population structures, target populations environments. Today, quickly emerging as major operational bottleneck limiting power analysis prediction. The challenge next generation geneticists breeders not only understand basis complex trait variation, but knowledge efficiently synthesize twenty-first century crop varieties.

Language: Английский

---

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

The Plant Journal, Journal Year: 2017, Volume and Issue: 93(2), P. 338 - 354

Published: Nov. 21, 2017

Summary Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass genetic model grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, colinearity with other genomes. In this study, deep sequencing, linkage analysis, transcriptome data were produce annotate high‐quality reference sequence. Reference sequence order was improved, 29.6 Mbp additional incorporated, number genes annotated increased 24% 34 211, average gene length N50 increased, error frequency reduced 10‐fold 1 per 100 kbp. Subtelomeric repeats characteristics Tandem Repeats in Miniature ( TRIM ) elements identified at termini most chromosomes. Nucleosome occupancy predictions nucleosomes positioned immediately downstream transcription start sites different densities across Alignment more than 50 resequenced genomes from sorghum genotypes approximately 7.4 M single nucleotide polymorphisms SNP s) 1.9 indels. Large‐scale variant features euchromatin periodicities 25 A atlas expression constructed 47 RNA ‐seq profiles growing developed tissues major plant organs (roots, leaves, stems, panicles, seed) collected during juvenile, vegetative reproductive phases. Analysis indicated that tissue type protein kinase had large influences on transcriptional profile clustering. The updated assembly, annotation, represent resource research crop improvement.

Language: Английский

---

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Nature Communications, Journal Year: 2013, Volume and Issue: 4(1)

Published: Aug. 27, 2013

Sorghum is a food and feed cereal crop adapted to heat drought staple for 500 million of the world's poorest people. Its small diploid genome phenotypic diversity make it an ideal C4 grass model as complement C3 rice. Here we present high coverage (16–45 × ) resequenced genomes 44 sorghum lines representing primary gene pool spanning dimensions geographic origin, end-use taxonomic group. We also report first S. propinquum, identifying 8 M high-quality SNPs, 1.9 indels specific loss gain events in bicolor. observe strong racial structure complex domestication history involving at least two distinct events. These assembled enable leveraging existing functional genomics data against novel available sorghum, providing unmatched resource genetic improvement other species. drought-resistant used by over half billion authors high-coverage resequencing varying which include number wild relatives.

Language: Английский

---

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

PLoS Biology, Journal Year: 2014, Volume and Issue: 12(6), P. e1001883 - e1001883

Published: June 10, 2014

Rajeev Varshney, Ryohei Terauchi, and Susan McCouch summarize the current future uses of next-generation sequencing technologies, both for developing crops with improved traits increasing efficiency modern plant breeding, as a step towards meeting challenge feeding growing world population.

Language: Английский

---

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data

Methods in molecular biology, Journal Year: 2016, Volume and Issue: unknown, P. 1 - 31

Published: Dec. 17, 2016

Language: Английский

---