Genome-Wide Association Studies Predicted Drought Stress Occuring at Anthesis and Post-Anthesis Stages in Novel Diverse Germplasm of Bread Wheat (Triticum aestivum)

Authors: SHOKAT, SAJID - University Of Copenhagen; REHMAN ARIF, MIAN ABDUR - Nuclear Institute For Agriculture And Biology; FAVERO, BRUNO - University Of Copenhagen; BHATNAGAR, POOJA - International Atomic Energy Agency (IAEA); LOPES, MARTA - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); LIU, FULAI - University Of Copenhagen; Singh, Sukhwinder

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2024
Publication Date: 8/27/2024
Citation: Shokat, S., Rehman Arif, M., Favero, B.T., Bhatnagar, P.M., Lopes, M.S., Liu, F., Singh, S. 2024. Genome-Wide Association Studies Predicted Drought Stress Occuring at Anthesis and Post-Anthesis Stages in Novel Diverse Germplasm of Bread Wheat (Triticum aestivum). Plant Breeding. https://doi.org/10.1111/pbr.13219.
DOI: https://doi.org/10.1111/pbr.13219

Interpretive Summary: Efforts are being made to improve crop plants to ensure global food security. Wheat is a widely grown crop worldwide, but it is susceptible to various biotic and abiotic stresses (Shokat et al., 2020; Akram et al., 2022; Saleem et al., 2022). This crop has been improved in the past, and hunger was globally eradicated by supplying semi-dwarf and input-efficient cultivars (Syme, 1969). However, the current genetic gain through plant improvement efforts is only around one percent, which is not enough to meet the growing demand for food due to the increasing unpredictability of climate and the shortage of arable land (Ray et al., 2012; Sehgal et al., 2017). Some stresses are particularly devastating when they occur during the anthesis and post anthesis stages, significantly reducing grain yield (Farooq et al., 2009; Reynolds and Langridge, 2016; Shokat, Großkinsky, et al., 2021; Shokat, Novák, et al., 2021). The recent climate change scenario has indicated low to no rainfall during the anthesis and post anthesis stages in many arid regions of the world (Iizumi et al., 2021; Yang et al., 2021), which requires wheat genotypes that are tolerant to water stress during these stages. Bridging the genetic diversity of landraces and synthetic bread wheat derivatives has shown great potential in improving wheat crops against biotic and abiotic stresses (Singh et al., 2018, 2021). Recent advances in quantitative genetics and statistical tools have made it possible to identify rare genetic diversity from complex gene pools using modifications in genome-wide association studies (Singh et al., 2021; Sehgal et al., 2024). However, identifying stage-specific tolerance and its association with genetic markers remains challenging. Achieving stage-specific tolerance is crucial for achieving food security.Our previous studies have shown that using more extensive and diverse germplasm and advanced statistical tools can help identify stage-specific tolerance genes against heat stress (Singh et al., 2018; Shokat, Novák, et al., 2021). In this study, we aim to utilize diverse germplasm, including synthetic derivatives and landraces of bread wheat. We attempted three parent crosses of landraces or synthetic bread wheat derivatives with 25 different commercial cultivars. We evaluated 124 stable genotypes for two years and imposed flowering stage drought stress by withholding irrigation during anthesis and post-anthesis. We hypothesize that the diverse germplasm from the crossing mentioned above schemes has the potential to cope with flowering stage water stress, and the marker data generated through genotype by sequencing can effectively be associated with advanced statistical tools.

Technical Abstract: A study was conducted to identify new germplasm with significant marker-trait associations (MTAs) during drought stress at the anthesis and post-anthesis stages. A stable germplasm of 124 genotypes derived from three-way crosses of landraces and synthetic bread wheat was evaluated for two years in the field conditions of CIMMYT Obregon, Mexico. During the drought treatment, irrigation was not provided at anthesis and post-anthesis, and data from 12 traits were recorded. In total, 6,887 single nucleotide polymorphism (SNP) markers were used for MTAs. Nine of the 12 traits were significantly reduced under drought conditions; genotypes differed for seven traits, and differences were also significant for five traits between the two years. The genome-wide association studies (GWAS) showed that 117 significant (p-value < 0.001) MTAs were distributed on all the wheat chromosomes except chromosomes 4B and 4D, explaining from 10 to 21.49% of the phenotypic variation of the corresponding traits. Moreover, 22 MTAs were recorded for grain yield, explaining the phenotypic variations up to 14.71%, with one common association for irrigated and drought conditions. Additionally, associations were identified for normalized difference vegetation index (NDVI), canopy temperature depression (CTD), and spike length at chromosome 1B. The results identified the plant genotypes with minimum reduction in grain yield and significant marker-trait associations for important traits at chromosome 1B. This indicates that genotypes are maintaining better grain yield probably due to better NDVI, CTD, and spike length under anthesis and post-anthesis stage drought stress. However, further validations are required by developing Kompetitive allele-specific PCR and virus-induced gene silencing.