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Identification of genome-wide single-nucleotide polymorphisms (SNPs) associated with tolerance to chromium toxicity in spring wheat (Triticum aestivum L.)

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Abstract

Background and aims

Chromium (Cr) toxicity is a rapidly increasing environmental concern and poses a major threat to plant growth as well as food chain. This study was carried out to screen spring wheat diversity panel against Cr toxicity to assess yield reduction, grain contamination extents and genomic regions associated with tolerance to Cr toxicity.

Methods

The diversity panel was planted in control and Cr stress (26 mg Cr/kg soil) in paved plots, and several morphological and physiological traits were recorded. Wheat 90 K Infinium iSelect SNP array was used to identify genomic regions underpinning tolerance to Cr toxicity.

Results

Some wheat cultivars (Khosar-95, Miraj-08, Millet-11, Sarsabaz and NARC-11) had Cr concentration within international edible threshold limit (1 ppm), but showed greater reduction to grain yield (63–95%) due to higher leaf Cr concentrations (2.35–8.95 ppm). Contrastingly, wheat cultivars Auqab-00 and Pakistan-13 had lower yield reduction up to 9% and 39%, respectively but had higher concentration of Cr in seeds (2.1 and 3.5 ppm, respectively). Genome-wide association studies identified 71 loci linked with yield related traits under Cr stress and 48 loci for differences between control and Cr stress treatments. Further, gene ontology of trait-associated SNPs revealed proteins with significant importance in plant development and tolerance against heavy metal stress.

Conclusion

To our knowledge, this is the first study for identification of genomic regions linked to Cr stress, suggesting that this could be useful to identify complex architecture of genetic factors as well as molecular breeding opportunities for tolerance to Cr stress.

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Authors and Affiliations

  1. Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan

    Fakhrah Almas, Adeel Hassan, Arfa Bibi, Masab Ali, Sadia Lateef, Tariq Mahmood & Umar Masood Quraishi

  2. International Maize and Wheat Improvement Centre (CIMMYT), c/o Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Awais Rasheed

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  1. Fakhrah Almas
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  2. Adeel Hassan
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  3. Arfa Bibi
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  4. Masab Ali
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  5. Sadia Lateef
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  6. Tariq Mahmood
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  7. Awais Rasheed
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Correspondence to Umar Masood Quraishi.

Additional information

Responsible Editor: Fangjie Zhao

Fakhra Almas and Arfa Bibi have performed the experimental work. Adeel Hassan, Masab Ali and Sadia lateef have helped in analysis and computation. Tariq Mahmood has provided the logistics necessary for analysis. Umar masood Quraishi and Awais Rasheed wrote the article.

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Almas, F., Hassan, A., Bibi, A. et al. Identification of genome-wide single-nucleotide polymorphisms (SNPs) associated with tolerance to chromium toxicity in spring wheat (Triticum aestivum L.). Plant Soil 422, 371–384 (2018). https://doi.org/10.1007/s11104-017-3436-1

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