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Genomics-assisted breeding for designing salinity-smart future crops.

Ali Raza1,2, Qamar U Zaman3, Sergey Shabala4,5

  • 1Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.

Plant Biotechnology Journal
|May 20, 2025
PubMed
Summary
This summary is machine-generated.

Developing salinity-smart crops is crucial for agriculture facing climate change. Advanced genomics-assisted breeding tools accelerate the creation of crops with enhanced salinity stress tolerance (SST) and stable yields.

Keywords:
cell‐/tissue‐based phenotypingcrop wild relativesgenome sequencingpan‐genomicssalinity tolerancesingle‐cell genomics

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Area of Science:

  • Plant science
  • Genetics
  • Agricultural science

Background:

  • Climate change exacerbates soil salinity, posing a significant threat to global agriculture and food security.
  • Salinity stress tolerance (SST) is a complex trait vital for crop sustainability and profitability, necessitating the development of salinity-smart crop varieties.
  • Advancements in genomics and breeding technologies offer new avenues for improving crop resilience to salinity.

Purpose of the Study:

  • To review the progress and future prospects of genomics-assisted breeding (GAB) tools for enhancing crop salinity stress tolerance (SST).
  • To explore the integration of high-throughput phenotyping (HTP) and artificial intelligence (AI) in optimizing breeding efficiency for salinity-smart crops.
  • To highlight the potential of GAB tools in ensuring sustainable agriculture and global food security by developing crops for saline environments.

Main Methods:

  • Genome sequencing, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) for identifying key genes and QTLs related to SST.
  • Genomic selection (GS) and haplotype-based breeding (HBB) for accelerating genetic gains and developing improved cultivars.
  • High-throughput phenotyping (HTP) and artificial intelligence (AI) for optimizing breeding efficiency and guiding large-scale breeding efforts.

Main Results:

  • High-quality reference genomes and advanced molecular breeding tools have facilitated the discovery of genes and markers for improved SST.
  • Genomics-assisted breeding (GAB) tools, including GS and HBB, have demonstrated effectiveness in fast-tracking genetic gains and reducing development time/cost for enhanced SST and yield stability.
  • The integration of HTP and AI shows promise in optimizing breeding efficiency and guiding the development of salinity-smart crops.

Conclusions:

  • Genomics-assisted breeding (GAB) offers a powerful suite of tools, including advanced sequencing, QTL mapping, GWAS, GS, and HBB, to exploit the genetic basis of salinity stress tolerance (SST).
  • The synergistic application of HTP and AI can significantly enhance breeding efficiency, leading to the development of 'salinity-smart' crop varieties.
  • Bridging the gap between research and field application through the collective adoption of these tools is essential for delivering stress-resilient crops to saline-affected regions, thereby ensuring global food security.