High-throughput phenotyping and genotyping for maize disease resistance selection: assessing both data sources’ power for prediction

Brief description of the Research Topic

High-throughput phenotyping and genotyping for maize disease resistance selection: assessing both data sources’ power for prediction  

Plant phenotyping is one of the most costly and laboring intensive activities within a breeding program. High-throughput phenotyping (HTP) methods have been broadly used to estimate crop traits under abiotic and biotic stresses environment using different tools, and remote sensing is one of the most promise technology that can provide rapid access at large number of plots in short periods of time. Canopy temperature acquired through thermal cameras and biomass dynamics through multispectral vegetative indices, both using unmanned aerial vehicle (UAV), are already reality at CIMMYT. This technology is currently being tested in maize and wheat research programs and has proved to be efficient, for instance, for disease severity scoring.

High-throughput genotyping is also an emerge technology that comes with the potential of developing massive amount of genotypic data from reduced representations of the genome (fragments), through the use of restriction enzymes. Next Generation Sequencing (NGS) has increased our ability to sequence by several orders of magnitude, this has made it feasible to discover, sequence and genotype not only tens, but hundreds of thousands of molecular markers in almost any type of genome, regardless of whether there is previous genetic information of the organism. High-throughput genotyping technologies have a wide variety of purposes, to uncover the genetic underpinnings of complex traits, to assess genetic diversity, phylogeny, and population structure analysis, for marker-assisted and genomic selection in plant breeding for fingerprinting and genetic diagnosis.

Although both technologies have their own potential into breeding programs, the potential and feasibility of merging both data sources for predictions is quite unexplored – being researches in this field of expertise of extreme importance, where real advances will have impact within CIMMYT and in the global research community of phenotyping and genotyping. 

Expectations of work to be performed by candidate
 

The suitable candidate will be responsible for the entire HTP component of the experiments. This includes the UAV flight campaign - having a trainee on the use of UAV for making a flight plan and executing flights with different sensors, on different locations; image processing, data extraction and analysis are going to be essential tasks. Further field measurements may be required for ground-truthing.

It is also expected to have the candidate involved together with biometricians and quantitative geneticists in the data analysis and its merge with HTP data through statistical models.

Discipline

Remote Sensing / HTP&G

Desirable level

PhD

 Any specific or special skills required

Background on Remote Sensing with excellent skills in GIS and statistics are essential. Basic knowledge on SNP markers and GWAS analysis is a plus.

Duration

12-24 months