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

Methods in molecular biology, Journal Year: 2015, Volume and Issue: unknown, P. 115 - 140

Published: Oct. 30, 2015

Language: Английский

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Strategies for transferring resistance into wheat: from wide crosses to GM cassettes

Frontiers in Plant Science, Journal Year: 2014, Volume and Issue: 5

Published: Dec. 4, 2014

The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed base by introducing extreme levels uniformity on vast spatial and temporal scale. This reduction complexity renders crop vulnerable new emerging pests pathogens. wild relatives represent an important source variation for disease resistance. For nearly century farmers, breeders, cytogeneticists have sought access this improvement. Several barriers restricting interspecies hybridization introgression been overcome, providing opportunity tap extensive reservoir diversity. Resistance introgressed into from at least 52 species 13 genera, demonstrating remarkable plasticity genome importance such natural breeding. Two main problems hinder effective deployment resistance genes improvement: (1) simultaneous introduction genetically linked deleterious traits (2) rapid breakdown when deployed individually. In review, we discuss how recent advances molecular genomics are opportunities overcome these problems.

Language: Английский

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Genome-environment associations in sorghum landraces predict adaptive traits

Science Advances, Journal Year: 2015, Volume and Issue: 1(6)

Published: July 3, 2015

Genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.

Language: Английский

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Drought Tolerance and Water Use of Cereal Crops: A Focus on Sorghum as a Food Security Crop in Sub‐Saharan Africa

Journal of Agronomy and Crop Science, Journal Year: 2016, Volume and Issue: 203(3), P. 177 - 191

Published: Nov. 11, 2016

Abstract Sub‐Saharan Africa ( SSA ) faces twin challenges of water stress and food insecurity – that are already pressing projected to grow. comprises 43 % arid semi‐arid area, which is increase due climate change. Small‐scale, rainfed agriculture the main livelihood source in areas . Because constitutes more than 95 agricultural land use, scarcity a major limitation production. Crop production, specifically staple cereal crop will have adapt improved productivity (output per input) meet requirements. We propose inclusion promotion drought‐tolerant crops agro‐ecological zones where Sorghum uniquely fits production such regions, high stable water‐use efficiency, drought heat tolerance, germplasm variability, comparative nutritional value existing chain However, sorghum socio‐economically geographically underutilized parts and/or , especially among subsistence farmers, improve security.

Language: Английский

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Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

PLoS ONE, Journal Year: 2014, Volume and Issue: 9(5), P. e96758 - e96758

Published: May 6, 2014

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on reference set (300 accessions, including 211 mini-core collection accessions) for related root traits, tolerance, yield component traits from 1-7 seasons 1-3 locations India (Patancheru, Kanpur, Bangalore) three Africa (Nairobi, Egerton Kenya Debre Zeit Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome used determine population structure sub-populations identified using admixture model STRUCTURE. The pairwise linkage disequilibrium (LD) estimated squared-allele frequency correlations (r2; when r2<0.20) was found decay rapidly with distance 5 cM. For establishing marker-trait associations (MTAs), both genome-wide candidate gene-sequencing based approaches conducted 1,872 (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs 36 simple sequence repeats [SSRs]) phenotyping mentioned above employing mixed linear (MLM) analysis optimum compression P3D method kinship matrix. As result, 312 significant MTAs maximum number (70) 100-seed weight. A total 18 genes (ERECTA, 11 SNPs; ASR, 4 DREB, 1 SNP; CAP2 promoter, SNP AMDH, 1SNP) significantly associated different traits. This study provides that can be used, after validation, molecular breeding developing superior varieties enhanced tolerance.

Language: Английский

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Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

Plant Biotechnology Journal, Journal Year: 2016, Volume and Issue: 15(2), P. 149 - 161

Published: Oct. 11, 2016

In the last decade, revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high-throughput of entire populations have proliferated and opened door to wider use molecular tools plant breeding. These new genotyping-by-sequencing (GBS) include over a dozen reduced-representation (RRS) approaches at least four whole-genome resequencing (WGR) approaches. The diversity available, each often producing different types data cost, can make selection best-suited method seem daunting task. We review most common used today compare their suitability for linkage mapping, genomewide association studies (GWAS), marker-assisted genomic genome assembly improvement crops with various sizes complexity. Furthermore, we give an outline bioinformatics analysis data. WGR is well suited biparental cross complex, small- moderate-sized genomes provides lowest cost per marker point. RRS differ tasks, but demonstrate similar costs are generally better de novo applications more cost-effective when large or high heterozygosity. expect that although will remain some time, become widespread as continue decrease.

Language: Английский

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Bulked sample analysis in genetics, genomics and crop improvement

Plant Biotechnology Journal, Journal Year: 2016, Volume and Issue: 14(10), P. 1941 - 1955

Published: March 19, 2016

Biological assay has been based on analysis of all individuals collected from sample populations. Bulked (BSA), which works with selected and pooled individuals, extensively used in gene mapping through bulked segregant biparental populations, by sequencing major mutants genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale cost simplifying procedure. The bulks can be built selection extremes or representative samples any populations types segregants variants that represent wide ranges phenotypic variation for target trait. Methods procedures sampling, bulking multiplexing are described. analysed individual markers, microarrays high-throughput at levels DNA, RNA protein. power is affected size, strategies, genetic architecture trait marker density. will facilitate plant breeding development diagnostic constitutive agronomic genomics, marker-assisted selective phenotyping. Applications genetics, genomics crop improvement discussed their future perspectives.

Language: Английский

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On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

Annual Review of Genetics, Journal Year: 2018, Volume and Issue: 52(1), P. 421 - 444

Published: Oct. 4, 2018

Understanding the quantitative genetics of crops has been and will continue to be central maintaining improving global food security. We outline four stages that plant breeding either already achieved or probably soon achieve. Top-of-the-line programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us start on predicted instead measured phenotypes. focus three major questions must answered move from current 3.0 practices 4.0: ( a) How do we adapt better fit agricultural environments? b) What is nature diversity upon which can act? c) deal deleterious variants? Answering these then translating them actual gains for farmers a significant part achieving security twenty-first century.

Language: Английский

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Breeding for plant heat tolerance at vegetative and reproductive stages

Plant Reproduction, Journal Year: 2016, Volume and Issue: 29(1-2), P. 67 - 79

Published: Feb. 13, 2016

Thermotolerant crop research. Global warming has become a serious worldwide threat. High temperature is major environmental factor limiting productivity. Current adaptations to high via alterations technical and management systems are insufficient sustain yield. For this reason, breeding for heat-tolerant crops in demand. This review provides an overview of the effects on plant physiology, fertility yield discusses strategies cultivars. Generating thermotolerant seems be challenging task as heat sensitivity highly variable across developmental stages processes. In response heat, plants trigger cascade events, switching numerous genes. Although made substantial advances developing lines, genetic basis diversity tolerance remain largely unknown. The development new varieties expensive time-consuming, knowledge mechanisms would aid design screen germplasm traits. However, gains limited by often narrow diversity. Exploration use wild relatives landraces can increase useful current crops. Due complex nature its immediate global concern, it essential face challenge multidisciplinary holistic approach involving governmental agencies, private companies academic institutions.

Language: Английский

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Genomic prediction contributing to a promising global strategy to turbocharge gene banks

Nature Plants, Journal Year: 2016, Volume and Issue: 2(10)

Published: Oct. 3, 2016

Language: Английский

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