Analytical and Decision Support Tools for Genomics-Assisted Breeding

Varshney, Rajeev K.; Singh, Vikas K.; Hickey, John M.; Xu, Xun; Marshall, David; Wang, Jun; Edwards, David; Ribaut, Jean-Marcel

doi:10.1016/j.tplants.2015.10.018

Cited by 67 publications

(43 citation statements)

References 81 publications

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“…The rate of historical genetic gains has indicated that reliance on conventional breeding methods alone is unsustainable to fulfill the need of the burgeoning population (Ray et al, 2012), and we need innovative breeding strategies to accelerate the rate of genetic gains in crop breeding (Barabaschi et al, 2016;Bevan et al, 2017;Xu et al, 2017b). For this reason the scientific community has made heavy investment in developing genomic resources and intelligent decision support systems that would likely reduce the genotype-phenotype gap and provide the effective tools to develop next-generation cultivars (Batley and Edwards, 2016;Varshney et al, 2016). The most commonly applied molecular tools for crop breeding are molecular markers, which are used for parental selection, genetic diversity estimation, and reducing the linkage drags and genomicsassisted breeding.…”

Section: Potential Of Molecular Breeding In Developing Next-generatiomentioning

confidence: 99%

“…This tool comprises six modules including data validation, phenotyping, linkage map building, QTL analysis, genome display, and MABC sample size. Apart from these modules, several other analytical and decision support tools for data analysis software, data storage, and data management will usher crop breeding programs into a modern, knowledge-based crop breeding era, leading to sustainable crop production (Varshney et al, 2016).…”

Section: Genotyping Scenarios and Decision Support Toolsmentioning

confidence: 99%

“…Several high-throughput multiplex and single-plex marker platforms in rice (Masouleh et al, 2009), wheat (Berard et al, 2009;Bernardo et al, 2015;Rasheed et al, 2016), legumes (Varshney et al, 2016), and other crops have been proposed for marker-assisted selection (MAS), but the implementation of such platforms in crop breeding is hindered due to the lower efficiency of customization, higher cost, desired flexibility, and costly equipment needed for application. The development of ultra-high-throughput, cost-effective genotyping platforms for practical breeding still has a long way to go, but is an ultimate objective.…”

Section: Introductionmentioning

confidence: 99%

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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

et al. 2017

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There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.

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Section: Potential Of Molecular Breeding In Developing Next-generatiomentioning

confidence: 99%

Section: Genotyping Scenarios and Decision Support Toolsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

et al. 2017

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“…A number of analytical and decision support tools for genomics-assisted breeding are freely available [175]. For example, CIMMYT offers several software packages to facilitate various specialized analyses (see.…”

Section: Modern Approaches Technologies and Tools To Support Commermentioning

confidence: 99%

Past, Present and Future Perspectives on Groundnut Breeding in Burkina Faso

Konaté¹,

Sanou²,

Miningou³

et al. 2019

Preprint

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Groundnut (Arachis hypogaea L.) is a major food and cash crop in Burkina Faso. Due to growing demand for raw oilseeds, there is an increasing interest in groundnut production from traditional rain-fed areas to irrigated environments. However, despite implementation of many initiatives in the past to increase groundnut productivity and production, the groundnut industry still struggles to prosper, due to several constraints including minimal development research and fluctuating markets. Yield penalty due to drought and biotic stresses continue to be a major drawback for groundnut production. This review traces progress in the groundnut breeding that started in Burkina Faso before the country’s political independence in 1960 through to present times. Up to the 1980s, groundnut improvement was led by international research institutions such as IRHO (Institute of Oils and Oleaginous Research) and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics). However, international breeding initiatives were not sufficient to establish a robust domestic groundnut breeding programme. This review also provides essential information about opportunities and challenges of groundnut research in Burkina Faso, emphasising the need for institutional attention to genetic improvement of the crop.

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“…Amalgamation of the genomics with the integrated classical breeding has calibre to boost the yield of peanut by overcoming selected genetic barriers. Since a decennary, enormous progress has been made in the peanut genomics leading to the development of enormous genetic and genomic resources such as genome sequences, whole genome re-sequencing (WGRS), molecular markers, mapping populations, genetic maps, high throughput sequencing and genotyping platforms, transcriptome sequencing and proteome (Pandey et al 2012aVarshney et al 2013Varshney et al , 2015a. These resources have been exploited and utilized in genetic map construction, quantitative trait loci (QTL) mapping for traits, association mapping and ultimately transform it in the translational genomics for the improvement of peanut (Pandey et al 2014aVarshney et al 2015b).…”

Section: Introductionmentioning

confidence: 99%

Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut

Vishwakarma

Nayak

Guo

et al. 2017

Compendium of Plant Genomes

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Advances in availability of genomic resources coupled with genetic resources have accelerated the process of developing better understanding of cytogenetics and genetics of peanut using modern technologies. The cytogenetic studies provided greater insights on chromosomal structures and behaviour of different Arachis species along with their genetic relationship with each other. Researchers are moving faster now in using single nucleotide polymorphism (SNP) markers in their genetic studies as simple sequence repeats (SSRs) did not provide optimum genome density for genetic mapping studies in peanut. Due to availability of reference genome of diploid progenitors, resequencing of some genotypes and soon to be available tetraploid genome, a high-density genotyping array with 58 K SNPs is now available for conducting high-resolution mapping in peanut. ICRISAT has developed next generation genetic mapping populations such as multi-parent advanced generation intercross (MAGIC) and nested association mapping (NAM) populations for conducting high-resolution trait mapping for multiple traits in one go. Affordability of sequencing also encouraged initiation of sequence-based trait mapping such as QTL-seq for dissecting foliar disease resistance trait. Few successful examples are available in peanut regarding development of diagnostic markers and their deployment in breeding to develop improved genotypes, which may see a significant increase in coming years for developing appropriate genomics tools for breeding in peanut.

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Analytical and Decision Support Tools for Genomics-Assisted Breeding

Cited by 67 publications

References 81 publications

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Past, Present and Future Perspectives on Groundnut Breeding in Burkina Faso

Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut

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