Genome wide association study of frost tolerance in wheat

Abstract

Winter wheat growing areas in the Northern hemisphere are regularly exposed to heavy frost. Due to the negative impact on yield, the identification of genetic factors controlling frost tolerance (FroT) and development of tools for breeding is of prime importance. Here, we detected QTL associated with FroT by genome wide association studies (GWAS) using a diverse panel of 276 winter wheat genotypes that was phenotyped at five locations in Germany and Russia in three years. The panel was genotyped using the 90 K iSelect array and SNPs in FroT candidate genes. In total, 17,566 SNPs were used for GWAS resulting in the identification of 53 markers significantly associated (LOD ≥ 4) to FroT, corresponding to 23 QTL regions located on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B and 7D). The strongest QTL effect confirmed the importance of chromosome 5A for FroT. In addition, to our best knowledge, eight FroT QTLs were discovered for the first time in this study comprising one QTL on chromosomes 3A, 3D, 4A, 7D and two on chromosomes 1B and 2D. Identification of novel FroT candidate genes will help to better understand the FroT mechanism in wheat and to develop more effective combating strategies.

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

“…Moreover, eight candidate genes associated with abiotic stresses were reported, with three significantly linked to LTG: CsaV3_1G044080 (pentatricopeptide repeat‐containing protein) for gLTG1.2 , CsaV3_4G013480 (RING‐type E3 ubiquitin transferase) for gLTG4.1 , and CsaV3_5G029350 (serine/threonine‐protein kinase) for gLTG5.2 (Li et al, 2023a). Frost tolerance (FroT) QTL were identified in 276 winter wheat genotypes previously phenotyped at field locations in Germany and Russia (Soleimani et al, 2022). From a pool of 17,566 SNPs, 53 were significantly associated with FroT, corresponding to 23 QTL regions on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B, and 7D).…”

“…From a pool of 17,566 SNPs, 53 were significantly associated with FroT, corresponding to 23 QTL regions on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B, and 7D). The QTL regions on chromosome 5A were strongly responsible for FroT (Soleimani et al, 2022).…”

Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops

“…In wheat, GWAS analyses led to the identification of seven QTLs associated with cold tolerance using a diversity panel of 450 Canadian wheat varieties (Chen et al., 2019). Also, 23 QTLs localized on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B, and 7D) were identified by GWAS using a diverse panel of 276 winter wheat accessions (Soleimani et al., 2022). Using GWAS, one major additive effect QTL was identified on wheat chromosome 5B (Zhao et al., 2013).…”

Genome-wide association mapping and candidate genes analysis of high-throughput image descriptors for wheat frost resistance

“…Although Fr-1 and Fr-2 jointly regulate frost resistance in wheat, speci c biological mechanisms remain unclear (Zhu et al, 2014, Galiba et al, 2009. Recently, QTL mapping and genome-wide association studies (GWAS) have revealed new frost resistance hotspots in wheat's homologous groups 4 and 7, but these loci are not su cient to meet improvement needs (Zhang et al, 2022b, Zhao et al, 2020, Soleimani et al, 2022. Additionally, there is only one well-de ned cold signaling pathway, the inducer of CBF expression (ICE)-CBF cold response (COR) pathway (Shi et al, 2018, Liu et al, 2019, emphasizing the urgent need for further research on the genetics and molecular biology of wheat frost resistance.…”