Vol.:(0123456789) 1 3 Journal of Plant Biology https://doi.org/10.1007/s12374-020-09289-9 RESEARCH ARTICLE Exploration of Heat Stress‑Responsive Markers in Understanding Trait Associations in Wheat P. B. Manjunatha 1  · Nivedita Sinha 1  · Hari Krishna 1  · Divya Chauhan 1  · Pawan Kumar 2  · Ranjeet R. Kumar 1  · Neelu Jain 1  · P. K. Singh 1  · G. P. Singh 3 Received: 14 January 2020 / Revised: 29 October 2020 / Accepted: 2 November 2020 © Korean Society of Plant Biologist 2020 Abstract Heat stress (HS) is detrimental to wheat production and productivity globally. To combat HS, several genetic, molecular, and genomic approaches have been employed in the past. Analyzing the physiochemical mechanisms and the important regulatory genes involved is the key to develop HS tolerant plants. In the present work, a total of 243 novel simple sequence repeat (SSR) markers developed from stress-associated genes identifed through RNA-seq were used for understanding marker–trait associations. 37 SSRs were found to be clearly polymorphic and among these, 28 SSR loci were signifcantly associated with component traits of HS tolerance. The polymorphic SSRs were validated for diversity analysis on a subset of 85 genotypes. The genotypes were grouped into four clusters representing diverse and similar alleles imparting HS toler- ance in Indian and exotic genotypes. Additionally, 28 genes selected for the expression analysis confrmed that 15 genes were induced under HS in the thermotolerant WH1021 and Raj3765 and repressed in thermosusceptible HD2009 cultivar. Hence, the information on traits associated with candidate genes and the SSR markers overlying on the gene will enhance our understanding of thermotolerance mechanism operating in wheat and will help the breeders in the precise development of heat-tolerant genotypes through marker-assisted selection (MAS). Keywords Wheat · Ssrs · Association · Gene expression · Diversity · Heat stress Introduction Wheat (Triticum aestivum L.) is one of the most important staple food grains on earth. After years of domestication in fertile crescent region, the present day wheat varieties evolved that are adapted to a wide range of environmental conditions ranging from high-humidity regions like South America to low-humidity regions like India, Nigeria, Egypt, and Australia (Pont et al. 2019). Wheat yields are afected by both biotic and abiotic stresses. Among the abiotic stresses, drought and heat are the most severe stresses that afect the life cycle of the crop (Zampieri et al. 2017). These two fac- tors progressively became important due to global climate change (Akbarian et al. 2011; Zampieri et al. 2017). The global temperature has been presumed to increase by 0.18 °C per decade (Hansen et al. 2012). An estimated 6% loss in wheat production occurs globally for every 1 °C rise in tem- perature (Asseng et al. 2015). Higher temperatures have a direct infuence on plant growth and crop yields owing to reduced opportunities for photosynthesis since the life cycle is truncated (Bita and Gerats 2013; Stocker et al. 2013). At grain-flling stages, the rise in temperature adversely afects the quantity and quality of wheat grains thereby inducing various cellular and metabolic changes. The advances in biotechnology including recent pro- gress in genomics and molecular breeding have enabled wheat researchers to use the technology in mitigating the detrimental efects of HS (Lamaoui et al. 2018). Molecular markers improve the efciency of conventional plant breed- ing by indirectly selecting for the gene of interest. Simple Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12374-020-09289-9) contains supplementary material, which is available to authorized users. * Neelu Jain 2012jainn@gmail.com 1 Indian Agricultural Research Institute, New Delhi 110012, India 2 Indian Institute of Soil and Water Conservation, Dehradun, India 3 Indian Institute of Wheat and Barley Research, Karnal, India