Scanning the core

A closer look at a special collection of Capsicum could reveal important crop characteristics not visible to the human eye. New instruments make it possible.

Researchers Seok-beom Kang (left) and Derek Barchenger in the recently planted pepper field. The PlantEye gantry can be seen in the background.

 Crop improvement advances in increments. Improving the field performance of a vegetable crop is a long series of steps—some large, but most small—that lead over time to change in a plant’s structure or response to the environment.

The Capsicum genus is a case in point. From five domesticated Capsicum species (C. annuumC. baccatumC. chinenseC. frutescens, and C. pubescens) we now enjoy the fruit of thousands of different varieties of sweet and hot peppers displaying a vast range of shapes, colors, textures, flavors, and heat, produced by plants with diverse growth habits, leaf shapes, and other characteristics.

Grappling with such immense genetic diversity challenges the skills, patience and budgets of plant breeders. With a new field instrument at World Vegetable Center headquarters in Taiwan, finding the right pepper germplasm for breeding will soon become faster and easier.

Getting to the core

To help breeders sort and select from the plethora of peppers, in 2016 the Horizon 2020 project G2P-Sol, a collaboration of 19 partners including WorldVeg, first created a Capsicum core collection. 

Identifying variation for stress tolerance in large germplasm collections is laborious and costly. Establishing subsets of collections—core collections—that represent the diversity of the whole collection makes screening more practical and manageable.

Understanding the traits present in the recently developed Capsicum core collection is essential to fostering wider use of the germplasm. “The more we learn about the diversity of the core collection, the greater the benefit to breeding programs and ultimately farmers,” said Dr. Derek Barchenger, WorldVeg Vegetable Breeder – Pepper.

Most smallholder farmers grow pepper in open field conditions, and unlike other stresses such as diseases and insects, it is much more difficult to manage the effects of high temperature on crops.

In a new project, “Automated phenotyping of the Capsicum core collection under high temperature conditions” funded by G2PSol – EU H2020 and Korea’s Rural Development Administration (RDA), WorldVeg is leading activities to identify core pepper accessions with high levels of heat tolerance and also to better understand the genetic mechanisms associated with tolerance to high temperature.

Colleagues Dr. Roland Schafleitner, Flagship Leader – Vegetable Diversity and Improvement and Head of Molecular Breeding at WorldVeg, and Dr. Soek-boem Kang, RDA Seconded Scientist, are working with Derek on the phenotyping project.

PlantEye 3D scanners can run 24/7.

Eyes in the field

Field #35 on the WorldVeg headquarters research farm is not a typical experimental plot. It’s girded by steel rails on two sides, upon which a mobile gantry glides back and forth across the field, all day, all night. Mounted on the gantry are two PlantEyes: multispectral 3D scanners that capture certain parameters of plants in a non-destructive way.

The WorldVeg Field Phenotyping Platform was built in 2019 by Phenospex, a Netherlands-based company, with funding from the government of Taiwan. It is part of the WorldVeg Research Infrastructure Modernization (RIM) project, an initiative to upgrade facilities and create an Open Science Center to attract innovative researchers, visiting scientists, and students that will develop resilient, productive horticultural practices for sustainable food systems.

The automated system measures morphological parameters and spectral reflectance, which can be correlated with plant parameters such as plant health, disease, plant senescence, chlorophyll content, etc.

“We hope to be able to determine the flower set rate using this system so we can determine what proportion of flowers turn into fruits,” said Derek. “That’s an important indicator of heat tolerance.”

The primary benefit of the phenotyping platform is that each plant in the field is measured three times a day, every day, no matter how hot, humid or dry. The silent gantry also moves at night, on weekends and holidays.

“We currently have 3,600 plants in the field, and it would be impossible to get so much data and as accurate data without the phenotyping platform,” Derek said. “The continuous measuring allows us to capture traits like growth curves over time in a much more efficient and accurate way than we could otherwise.”

The peppers from the core collection were sown 20 March 2020 and transplanted on 29 April. The experiment will run through July (if typhoon season is late) and the experiment will be repeated in the cool season as well.

Researchers must take extra care when setting up an experiment involving automated phenotyping. For instance, they had to make cardboard templates to ensure every plant was equally spaced and that all would fit in the field. They also must plan ahead and envision future plant growth to be sure today’s seedlings will be within the range of the sensors in July, when they will be much larger, fully grown specimens.

“Our aim is to phenotype the core collection as accurately as possible during the hot and dry season in Taiwan, and then identify the genomic loci associated with those traits,” said Derek. “Luckily for us, the Capsicum core collection already has been sequenced. Therefore, it is possible to conduct genome wide association studies (GWAS) for any trait of interest that we can phenotype accurately.”

GWAS is useful in identifying genes contributing to complex traits, such as tolerance to abiotic stress.

In addition to the field scanning, the team will use an impedance flow cytometer to screen the core collection for pollen traits related to heat tolerance.   

Can the peppers take the heat?

A recent study published in the Proceedings of the National Academy of Sciences indicates that if no substantial action is taken to cut greenhouse-gas emissions, one-third of the global population will experience temperatures similar to the Sahara’s within 50 years. Even under optimistic scenarios, the homelands of more than 1 billion people will become unbearably hot by 2070 — with catastrophic consequences for food production.

We know that climate change does not affect us all equally. Tropical and subtropical countries are more affected by the negative effects of climate change and these countries typically have a higher proportion of smallholder farmers.

Approximately 65% of global pepper production occurs in Asia, predominantly the tropics and subtropics. Understanding the genetic mechanisms associated with high temperature stress will allow WorldVeg plant breeders to efficiently develop more heat-tolerant cultivars for farmers in Asia and Africa. The results could be applied to other vegetables as well.

“I am passionate about peppers, and I think there is a possibility to do something meaningful and novel with this experiment,” said Derek. “It will expand the boundaries of our knowledge of heat tolerance and allow farmers to produce pepper under high temperatures. That’s exciting!”

Barchenger and Kang: Excited about the prospect of discovery to benefit farmers and consumers!

Contributors: Maureen Mecozzi, Derek Barchenger

Return to FRESH!

Correct spacing between plants must be followed when setting out seedlings for a phenotyping experiment.

The growth of thousands of pepper accessions will be tracked by the phenotyping system to find those that perform best under high temperature conditions.

A field barcode. The scanners read the barcodes on each pass across the field to automatically calibrate data.