Genetics have been identified that can protect barley yield and grain quality from heat-stress damage. While these genetics are complex, ways have been identified to deploy these genes in cultivated varieties in the near future

A key issue for barley crops is the downgrade from malting to feed quality as a result of crops experiencing heat stress. This impacts price, resulting in up to a 30 per cent drop in profit. When combined with drought stress, heat is the largest factor in both the loss of quality premiums and yield reductions.

Since 2016, Professor Chengdao Li has led a GRDC investment that investigated the genetic response to heat stress in barley and the potential to increase the crop’s tolerance levels.

This GRDC project was run through the Western Crop Genetics Alliance, a joint venture between Murdoch University and the Department  of Primary Industry and Regional Development (DPIRD). The project has since produced a comprehensive  set of resources for improving barley heat tolerance.

These encompass:

• new genetic sources of heat tolerance traits;
• an understanding of the physiology associated with heat tolerance;
• tools to screen for physiological traits; and
• DNA markers associated with newly identified heat tolerance genetics.

As is the case for other crops, the newly identified traits are complex and not easily deployed by barley breeders. However, the understanding, data and resources generated by this project have mapped a viable way to overcome this limitation and get the genetics into growers’ paddocks.

How it was done

Professor Li first established a consortium to undertake extensive field and glasshouse trials of genetically diverse barley germplasm. Consortium members were Murdoch University, DPIRD, and commercial breeding companies InterGrain and Australian Grain Technologies (AGT).

Key members of the team that has identified heat-tolerant barley germplasm. From left: Dr Tefera Angessa, Professor Chengdao Li and Dr Camilla Hill. Photo: Western Crop Genetics Alliance

A population of barley germplasm was assembled that maximised genetic diversity and the likelihood of capturing heat tolerance-related traits.

This set included barley lines from the Australian gene pool as well as exotic landraces and wild relatives from across the globe, such as material imported from the International Center for Agricultural Research in the Dry Areas (ICARDA) through the CAIGE project (a GRDC-supported initiative involving collaboration between Australia and two international research centres).

The initial target for genetic improvement was the impact of heat on grain filling. However, as new knowledge was accumulated, the scope expanded to include impacts of heat stress at grain set (fertilisation). This revision reflects the evolving shift in occurrence of heat-stress events in paddocks, now tending to hit crops earlier in the season.

Consequently, the novel barley diversity set was screened for improvement in grain number (grain set) plus grain size and shape (plumpness – to reduce screening) following heat-stress events at different stages of development.

With researchers uncertain as to when (or whether) field trials would be hit by heat events, measures were taken to ensure each year produced data. This involved sowing staggered trials all around the country, on the premise that a site somewhere would experience heat at the right developmental window.

It also included the use of heat chambers in glasshouses and directly in paddocks, plus the tagging of a large numbers of barley spikes each season that received heat stress at the right developmental stage (a formidable task for the researchers).

Analysis of yield and quality characteristics identified genetic variants with improved heat tolerance compared with commercial Australian barley varieties for both grain set and grain filling. The traits were mapped genetically to produce quantitative trait loci (QTLs).

Some of these QTLs have a large and stable effect on heat tolerance and offer promising targets for breeding. The germplasm and DNA markers for the QTLs are available to breeders.

The diversity in grain plumpness observed in barley germplasm in a project headed by Professor Chengdao Li. Photo: Western Crop Genetics Alliance

Heat tolerance traits

In all, more than 20 physiological parameters were tested as indicators of heat tolerance in barley. Two proved useful and reliable. The first is the rate at which carbohydrates are pumped into grain. This is known as the ‘grain-filling rate’ trait (and is similar to the ‘source–sink’ trait targeted in wheat).

The ideal ‘plumpness’ of barley grain. Photo: Western Crop Genetics Alliance

“It turns out that grain size is not a good indicator for heat tolerance,” Professor Li says. “Rather, it is how quickly starch can be pumped in.”

Measuring this trait required taking grain periodically during the grain-filling phase and measuring the grain’s starch content. This allowed the rate of filling to be determined. While this proved an accurate test for heat tolerance, the drawback is that it is labour intensive.

The second indicator involves a reduction in the rate of leaves yellowing following heat stress. Known as the ‘stay green’ trait, even a small improvement in the ability to maintain green leaves in the face of heat stress results in improved grain size. This trait, however, is also not easy to embed in breeding programs.

To circumvent difficulties associated with phenotyping these traits, they were mapped back onto the genome and DNA markers developed. This work identified about 30 QTLs associated with improved grain size and shape following heat stress. But there is a caveat.

“The traits we identified were underpinned by the involvement of many genes,” Professor Li says. “Each gene alone has a relatively small effect and the genes are subject to strong interactions with the state of the environment. That means in some environments and years, each gene can confer heat tolerance; in others, they don’t.”

This type of underlying genetic complexity makes it difficult to include in breeding programs given that breeders are already selecting for an extraordinary number of traits (and their associated genes) when producing better-performing barley varieties.

As an award-winning scientist – one who received the 2019 Award for Excellence in Agricultural Research from the Australian Farmer of the Year Awards – Professor Li is well aware of the difficulties that breeders face.

The next phase of this work is about resolving these difficulties and making heat-tolerant genetics more readily deployable within a breeding program.

Figure 1: Newly identified heat-tolerant genetics (left) can enhance grain yield and reduce screenings for malting barley.

Source: Western Crop Genetics Alliance

Deployable gains

The leverage Professor Li is using to help deploy his heat tolerance genes is the sheer amount of data his team and collaborators have generated. This immense amount of data provides the perfect foundation to employ machine-learning algorithms for genomic selection of the many regions of the genome driving heat tolerance.

Genomic selection uses AI to model the likely outcome of crossing different performing lines. It is a virtual breeding program that can ‘see’ all possible progeny and determine which parents are best to use and which crosses will lead to the best possible gains. This allows ‘breeding values’ to be assigned to various gene combinations before even a single ‘real’ cross or field trial has taken place.

Genomic selection requires enormous amounts of physiological and agronomic data across years and environments. On the genomics front, Professor Li’s team (together with international partners), through another GRDC-supported project (The International Barley Pangenome), has been routinely sequencing the entire genome of the barley material in the heat tolerance project. This means they have the needed critical mass of genomic data.

On the phenomics front, Professor Li has cracked which traits to target and how to measure them, but these methods are slow and labour-intensive. This means platforms that are high-throughput are needed.

“Before the genomic information is useful, we need a lot of phenotyping data,” he says.

High-throughput phenotyping is going to be the bottleneck to effectively deploy heat-tolerant genetics in barley.

The phenotyping methods developed in this project are the first steps towards realising a high-throughput capability. Progress is being made.

In the meantime, Professor Li has brought together the 30 identified QTLs into a combined package that delivers a large and more robust heat-tolerant effect. This will allow breeders to transfer a bundled set of QTLs into their breeding programs. This reduces the number of crosses that breeders need to deploy the new heat tolerance genetics.

More information: Chengdao Li, c.li@murdoch.edu.au