Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa) DOI Creative Commons

Hasina Begum,

Jennifer Spindel, Antonio G. Lalusin

et al.

PLoS ONE, Journal Year: 2015, Volume and Issue: 10(3), P. e0119873 - e0119873

Published: March 18, 2015

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP utilized order assay a wide range alleles haplotypes monitor breakpoints By contrast, GWAS have not generally been performed breeding populations. In this study we for 19 agronomic traits including yield components population elite irrigated tropical rice lines so that results would be more directly applicable than those from panel. The was 71,710 SNPs using genotyping-by-sequencing (GBS), explicit goal expediting selection program. Using panel identified 52 11 traits, large effect QTLs flowering time grain length/grain width/grain-length-breadth ratio. We also can select plants our short stature (plant height), early time, yield, thus demonstrate utility populations informing decisions. conclude by exploring how newly significant insights into genetic architecture these quantitative leveraged build genomic-assisted models.

Language: Английский

Drought Stress Impacts on Plants and Different Approaches to Alleviate Its Adverse Effects DOI Creative Commons
Mahmoud F. Seleiman,

Nasser Al-Suhaibani,

Nawab Ali

et al.

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

Citations

1228

Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change DOI Open Access
Marta S. Lopes, Ibrahim S. Elbasyoni,

P. Stephen Baenziger

et al.

Journal of Experimental Botany, Journal Year: 2015, Volume and Issue: 66(12), P. 3477 - 3486

Published: March 28, 2015

Climate change has generated unpredictability in the timing and amount of rain, as well extreme heat cold spells that have affected grain yields worldwide threaten food security. Sources specific adaptation related to drought heat, associated breeding genetic traits, will contribute maintaining dry warm years. Increased crop photosynthesis biomass been achieved particularly through disease resistance healthy leaves. Similarly, sources extended increased would also greatly benefit improvement. Wheat landraces cultivated for thousands years under most environmental conditions. They lower input farming systems which those increase duration photosynthesis, conserved. Landraces are a valuable source diversity local conditions according their place origin. Evidence supports hypothesis can provide thousand kernel weight, both important traits tolerate heat. Evaluation wheat stored gene banks with highly beneficial untapped stress adaptation, once characterized, should be used Unified development databases promotion data sharing among physiologists, pathologists, quality scientists, national programmes, breeders improvement climate worldwide.

Language: Английский

Citations

438

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication DOI
Maojun Wang, Lili Tu, Min Lin

et al.

Nature Genetics, Journal Year: 2017, Volume and Issue: 49(4), P. 579 - 587

Published: March 6, 2017

Language: Английский

Citations

385

High-Throughput SNP Genotyping to Accelerate Crop Improvement DOI Creative Commons
Michael J. Thomson

Plant Breeding and Biotechnology, Journal Year: 2014, Volume and Issue: 2(3), P. 195 - 212

Published: Sept. 30, 2014

Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP offers a number of advantages over previous marker systems, including an abundance markers, rapid processing large populations, variety systems meet different needs, straightforward allele calling database storage due the bi-allelic nature markers. NGS technologies have enabled whole genome sequencing, providing extensive discovery pools select informative markers for sets germplasm. Highly multiplexed fixed array platforms powerful approaches such as genome-wide association studies. On other hand, routine deployment trait-specific requires flexible, low-cost smaller numbers SNPs across breeding using Fluidigm’s Dynamic Arrays™, Douglas Scientific’s Array Tape™, LGC’s automated running KASP™ At same time, by (GBS) is rapidly becoming popular high-density scans through sequencing. This review will discuss range options available modern breeders integrating into their programs, whether outsourcing service providers or setting up in-house facilities, provide example rice research demonstrated Genotyping Services Lab at International Rice Research Institute.

Language: Английский

Citations

369

Genomic innovation for crop improvement DOI
Michael W. Bevan, Cristóbal Uauy, Brande B. H. Wulff

et al.

Nature, Journal Year: 2017, Volume and Issue: 543(7645), P. 346 - 354

Published: March 1, 2017

Language: Английский

Citations

360

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement DOI Creative Commons

J E Spindel,

Hamida Begum,

Devrim Akdemir

et al.

Heredity, Journal Year: 2016, Volume and Issue: 116(4), P. 395 - 408

Published: Feb. 10, 2016

To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity environmental sustainability. Current breeding practices, however, unable keep pace with demand. Genomic selection (GS) is a technique helps accelerate rate of genetic gain in using whole-genome data predict value offspring. Here, we describe GS model combines RR-BLUP markers fit as fixed effects selected from results genome-wide-association study (GWAS) on training data. We term this + de novo GWAS. In tropical rice, GWAS outperformed six other models for variety traits environments. On basis these results, propose an extended, two-part design be used efficiently integrate novel variation into elite populations, thus expanding diversity enhancing potential sustainable gains.

Language: Английский

Citations

308

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects DOI Creative Commons

Chittaranjan Kole,

Mehanathan Muthamilarasan, Robert J Henry

et al.

Frontiers in Plant Science, Journal Year: 2015, Volume and Issue: 6

Published: Aug. 11, 2015

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication drastic edible yield loss, which is expected to surge further due global warming. This situation has compelled plant scientists develop climate change-resilient crops, can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood and submergence, pests along with increased productivity. Genomics appears be a promising tool for deciphering stress responsiveness crop species adaptation traits or in wild relatives towards identifying underlying genes, alleles quantitative trait loci. Molecular breeding approaches have been proven helpful enhancing plants, recent advancement next-generation sequencing high-throughput phenotyping platforms transformed molecular genomics-assisted (GAB). In view this, present review elaborates progress prospects GAB improving resilience plants circumventing insecurity.

Language: Английский

Citations

303

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application DOI Creative Commons
Armin Scheben, Jacqueline Batley, David Edwards

et al.

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

Citations

269

Haploids: Constraints and opportunities in plant breeding DOI

Sangam L. Dwivedi,

Anne Britt, Leena Tripathi

et al.

Biotechnology Advances, Journal Year: 2015, Volume and Issue: 33(6), P. 812 - 829

Published: July 10, 2015

Language: Английский

Citations

261

Review: Climate change impacts on food security- focus on perennial cropping systems and nutritional value DOI Creative Commons
Courtney P. Leisner

Plant Science, Journal Year: 2020, Volume and Issue: 293, P. 110412 - 110412

Published: Jan. 15, 2020

Anthropogenic increases in fossil fuel emissions have been a primary driver of increased concentrations atmospheric carbon dioxide ([CO2]) and other greenhouse gases resulting warmer temperatures, alterations precipitation patterns, occurrence extreme weather events terrestrial areas across the globe. In agricultural growing regions, climate can challenge plant productivity ways that impact ability world to sustain adequate food production for increasingly affluent population with shifting access affordable nutritious food. While knowledge gap exists regarding potential change impacts is large agriculture, it especially specialty cropping systems. This includes fruit vegetable crops, perennial systems which also contribute (along row crops) our global diet. order obtain comprehensive view true on supply, we must expand narrow focus from improving yield include nutritional value these crops. address questions, need multi-faceted approach integrates physiology genomics tools conducts experiments under realistic depictions future projected climate. review describes gaps relation responses, questions actions are needed develop sustainable supply light change.

Language: Английский

Citations

228