Grains Convo

Genetic, genomic tools and soil management practices offer hope for overcoming soil constraints 

DPIRD Research Scientist Dr Roopali Bhoite

In July 2023, a journal review article was published in The Plant Genome, focusing on genetic and genomic solutions for breeding stable and high-yielding wheats in the face of climate change and soil constraints.

Climate change is increasingly having an impact on soil constraints, which is affecting crop productivity. 

Plants adapt to environmental cues by adjusting component traits - this ability is called plasticity. 

While genetic studies can capture the adaptative ability in certain wheat lines, soil amendment effects, when combined with genetic effects, can provide greater benefits in the long term.  

A team of researchers from DPIRD have summarised the specific genetics and genomic tools that can be integrated to improve yield and overall performance on constrained soils. 

Dr Roopali Bhoite said these tools look at gene-rich regions that can be directly linked to the complex soil constraints tolerance.  

“By looking at the genes directly and carrying out genetic analysis using specific gene-based locations, gene-based markers can be developed for breeding purposes,” Dr Bhoite said. 

“In the case of soil constraints there are many genes contributing to the performance of wheat lines. 

“This is in contrast with qualitative traits that we usually see in disease resistance, where we have a minimal number of genes contributing to disease resistance.” 

Soil problems are complex and vary with location and climatic conditions. 

Genetic solutions to abiotic stresses, both climatic and soils, provide permanent means to adapt against constraints while soil improvement practices mitigate these constraints.

Dr Bhoite said efforts must be made on both fronts. 

"We can model genotype x environment x management practices to identify the best solutions for our declining crop productivity resulting from soil constraints," she said.

Advancements in genetic tools hold promise for wheat cultivation in constrained soils of arid regions 

Wheat cultivation faces significant challenges due to soil constraints, and their impact is increasing with climate change in arid and semi-arid regions.  

Salinity, sodicity and acidity are particularly prevalent in arid and semiarid regions, posing obstacles to global food security and environmental sustainability.  

The scarcity of high-quality water, soil degradation, and a shift away from chemical interventions in agriculture further contribute to the severity of these constraints.  

However, advancements in genetic and genomic tools provide hope for developing climate-resilient wheat varieties.  

By understanding the molecular mechanisms underlying stress tolerance and employing advanced breeding techniques, researchers aim to enhance plasticity traits and improve wheat's adaptability to changing environments.  

These efforts, combined with effective soil management practices, will play a vital role in ensuring global food security and sustainability in the face of climate change. 

A comprehensive strategy has been proposed to improve quantitative traits in wheat by investigating significant alleles, characterising functional variants, validating genes using advanced genomic tools, and developing markers for breeding purposes.  

Additionally, the progress made in gene editing techniques for wheat, such as multiplex gene editing and the discovery of novel alleles for precise gene expression control, has been highlighted.  

These advanced genomic technologies, combined with effective soil management practices, offer a promising approach to building yield, stability, and sustainability in the face of climate change. 

Soil management practices involving the addition of lime and gypsum have been implemented to improve crop performance, but a deeper understanding of the genetic inheritance and mechanisms underlying tolerance to soil constraints is needed to develop climate-resilient wheat cultivars. 

Genomic advances unlock potential for climate-resilient wheat varieties 

Over the past two decades, significant progress has been made in decoding the genomes of various crops, including wheat.  

The completion of the fully annotated reference genome of the Triticum aestivum variety, Chinese Spring, has greatly facilitated research and breeding efforts towards developing next-generation climate-resilient wheat varieties.  

The availability of high-quality pangenome data representing multiple wheat genotypes has further enriched the genetic resources for genome mining and gene editing.  

These advancements offer opportunities for targeted trait improvement and bypassing genotype dependency in wheat transformation. 

The intricate nature of agronomic traits related to soil constraints, which are influenced by complex genotype × environment × management interactions, necessitates the use of efficient genetic and genomic tools.  

Efforts must be concentrated on employing genetic and genomic tools effectively to unravel the genetic basis of plasticity traits.  

Improving crop performance in specific target environments requires comprehensive approaches that consider various factors, including climatic variations, local management practices, soil constraints, genetic variability, heritability of complex traits, and precise phenotyping and genotyping systems.  

Developing climate-proof wheat varieties that exhibit enhanced plasticity for soil constraints has always been a complex task due to the polygenic nature of abiotic stress reactions and the genotype-dependent responses.  

Screening elite germplasm, implementing large-scale and high-throughput phenotyping, generating high-quality genotype data, and utilizing state-of-the-art biotechnologies are crucial for accessing valuable genetic resources and accelerating wheat improvement programs. 

Additionally, chromatin profiling, proteomics, metabolomics, and crop management strategies have emerged as promising complementary research areas to understand traits, soil constraints, and gene expression. 

Rising population and climate change fuel urgency for climate-resilient wheat production 

The global population is expected to reach 8 billion in 2022, 8.5 billion in 2030, and a staggering 9.7 billion by 2050.

To meet the growing demand for food and ensure food security, global agricultural production must increase by at least 70 per cent.  

Wheat, one of the world's major cereal crops, plays a crucial role in feeding 40 per cent of the global population.  

However, the adverse effects of climate change, such as erratic rainfall patterns, are particularly impacting arid and semiarid cropping systems, making wheat cultivation in these regions extremely challenging. 

Soil constraints, including acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5), are major contributors to yield losses in wheat production.  

These constraints are further exacerbated by climate change, leading to an intensification of yield losses.  

To adapt to changing environments, plants employ adaptive strategies, such as phenotypic plasticity, which allows them to shift their traits and responses.  

However, understanding the molecular basis of stress tolerance, particularly for plasticity traits, has proven to be a significant challenge. 

Advancements in sequencing and high-throughput genomics technologies have provided valuable insights into the molecular mechanisms underlying stress tolerance in plants.  

Functional alleles, haplotypes, candidate genes, and gene expression profiles at various growth stages have been identified using these technologies.  

More information

Click here to read the journal review article published in The Plant Genome

Project collaborators: 

  • Grains Genetics Portfolio, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia 
  • The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia 
  • Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia 
  • Western Crop Genetics Alliance (MU, DPIRD) 
  • University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland, Australia 


Dr Roopali Bhoite 
DPIRD Research Scientist