High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field

Shakoor, Nadia; Lee, Scott; Mockler, Todd C.

doi:10.1016/j.pbi.2017.05.006

Cited by 243 publications

(154 citation statements)

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“…High-throughput plant phenotyping facilities provide accurate screening of thousands of plant breeding lines, clones or populations over time (Fu, 2015) are critical for accelerating genomics-based breeding. Automated image collection and analysis, phenomics technologies allow accurate and nondestructive measurements of a diversity of phenotypic traits in large breeding populations (Gegas, Gay, Camargo & Doonan, 2014;Goggin, Lorence, & Topp, 2015;Ludovisi et al, 2017;Shakoor, Lee, & Mockler, 2017). One important consideration is the identification of relevant and quantifiable target traits that are early diagnostic indicators of biomass yield.…”

Section: Phenomics-assisted Breeding Technologymentioning

confidence: 99%

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

et al. 2018

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Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

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Section: Phenomics-assisted Breeding Technologymentioning

confidence: 99%

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

et al. 2018

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“…The genomic scan for LA represents today the first, most affordable step towards the exploitation of the positive features of crop landraces, mainly because of the resources needed for the phenotypic characterization of ample populations in different environments. Advances in high-throughput plant phenotyping facilities give reasons to believe that in the near future landraces characterization will be accelerated [107][108][109].…”

Section: Current Opportunities and Challengesmentioning

confidence: 99%

Towards the Genomic Basis of Local Adaptation in Landraces

Corrado

Rao

2017

Diversity

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Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces' genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of 'omics' sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.Keywords: genomics; differentiation; genome-environment association Crop LandracesPublic awareness on the importance of biodiversity conservation is strengthening over time [1]. Climate change, pollution, environmental disasters, loss of natural habitats, environmental degradation, and overexploitation of resources regularly make front-page news. Without taking into consideration the impact of the measures implemented to avoid biodiversity loss, large attention is generally given to wild species, especially those at risk of extinction [1,2]. Agricultural biodiversity (i.e., the variety and variability of animals, plants, and microorganisms that are used directly or indirectly for food and agriculture [3]) is largely regarded as a subset of biodiversity. However, agriculture and biodiversity are closely tied. Their mutual dependence is crucial not only to ensure yield today, but also to contribute to a more resilient, sustainable agriculture. This includes the development of solutions for water-saving technologies and for minimizing the detrimental effects of global climate change on crops [4,5].Plant genetic resources for food and agriculture (PGRFA) are the central components of agricultural biodiversity because they constitute the primary elements of the production process. Crop improvement relies on genetic diversity. Taking into account the trends and efforts of modern breeding, the main part of genetic diversity of cultivated species is expected to be found in traditional varieties, also known as landraces. It is not easy to provide an all-p...

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“…The reason for this ‘phenotyping bottleneck’ is that plants are highly plastic; one genotype may exhibit many different phenotypes depending on environmental conditions. Considerable efforts have been invested into the automation of plant phenotyping (Fiorani and Schurr, ; Fahlgren et al ., ; Shakoor et al ., ), which has dramatically improved the consistency and throughput of plant phenotyping.…”

Section: Introductionmentioning

confidence: 99%

Computational aspects underlying genome to phenome analysis in plants

et al. 2019

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Summary Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high‐throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait−trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.

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High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field

Cited by 243 publications

References 56 publications

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Towards the Genomic Basis of Local Adaptation in Landraces

Computational aspects underlying genome to phenome analysis in plants

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