*Article* **New Genomic Regions Identified for Resistance to Spot Blotch and Terminal Heat Stress in an Interspecific Population of** *Triticum aestivum* **and** *T. spelta*

**Sudhir Navathe 1,2, Ajeet Kumar Pandey 1, Sandeep Sharma 1, Ramesh Chand 1,\*, Vinod Kumar Mishra 1, Dinesh Kumar 3,4, Sarika Jaiswal 3, Mir Asif Iquebal 3, Velu Govindan 5, Arun Kumar Joshi 6,7 and Pawan Kumar Singh 5,\***


**Abstract:** Wheat is one of the most widely grown and consumed food crops in the world. Spot blotch and terminal heat stress are the two significant constraints mainly in the Indo–Gangetic plains of South Asia. The study was undertaken using 185 recombinant lines (RILs) derived from the interspecific hybridization of '*Triticum aestivum* (HUW234) <sup>×</sup> *T. spelta* (H+26)' to reveal genomic regions associated with tolerance to combined stress to spot blotch and terminal heat. Different physiological (NDVI, canopy temperature, leaf chlorophyll) and grain traits (TGW, grain size) were observed under stressed (spot blotch, terminal heat) and non-stressed environments. The mean maturity duration of RILs under combined stress was reduced by 12 days, whereas the normalized difference vegetation index (NDVI) was 46.03%. Similarly, the grain size was depleted under combined stress by 32.23% and thousand kernel weight (TKW) by 27.56% due to spot blotch and terminal heat stress, respectively. The genetic analysis using 6734 SNP markers identified 37 significant loci for the area under the disease progress curve (AUDPC) and NDVI. The genome-wide functional annotation of the SNP markers revealed gene functions such as plant chitinases, NB-ARC and NBS-LRR, and the peroxidase superfamily Cytochrome P450 have a positive role in the resistance through a hypersensitive response. Zinc finger domains, cysteine protease coding gene, F-box protein, ubiquitin, and associated proteins, play a substantial role in the combined stress of spot blotch and terminal heat in bread wheat, according to genomic domains ascribed to them. The study also highlights *T. speltoides* as a source of resistance to spot blotch and terminal heat tolerance.

**Keywords:** *Bipolaris sorokiniana*; Indo–Gangetic plain; resistance; terminal heat

#### **1. Introduction**

Wheat is one of the most widely grown and consumed food crops globally, having exceptionally high importance in the food system of South Asia. The eastern part of South Asia, which encompasses the eastern Gangetic Plains (EGP) of India, Nepal, and Bangladesh, is one of the most heavily populated parts of the world. In the EGP, where wheat is grown in about 10 m ha, the two major stresses to the wheat crop are spot blotch (SB) and terminal heat [1–3]. In EGP, SB caused by *Bipolaris sorokiniana* causes considerable yield loss between 15.5 and 19.6% annually [4]. However, when the disease is initiated at

**Citation:** Navathe, S.; Pandey, A.K.; Sharma, S.; Chand, R.; Mishra, V.K.; Kumar, D.; Jaiswal, S.; Iquebal, M.A.; Govindan, V.; Joshi, A.K.; et al. New Genomic Regions Identified for Resistance to Spot Blotch and Terminal Heat Stress in an Interspecific Population of *Triticum aestivum* and *T. spelta*. *Plants* **2022**, *11*, 2987. https://doi.org/10.3390/ plants11212987

Academic Editor: Mingxun Chen

Received: 10 October 2022 Accepted: 3 November 2022 Published: 5 November 2022

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the flag leaf stage, losses of grains are estimated to be up to 24.2% [2]. (Singh et al., 2015). SB is normally a weak disease that takes advantage of heat stress (Rosyara et al., 2009), nutrient deficiency [5], and water stress [6] to induce significant grain damage. SB is favoured by cloudy and foggy days during the post-heading stage [7,8] and is expanding towards nontraditional cooler regions such as India's North West Plain Zone (NWPZ) [2,4]. Further, this disease is predicted to become more severe due to climate change, nutritional and water deficiencies, and increased heat stress [9].

Terminal heat and spot blotch lead to premature leaf senescence, reduced grain filling, low kernel weight, and yield reductions [1,3]. NDVI has been used as an indirect criterion for stay-green and higher grain yield under drought or heat conditions and spot blotch resistance [10]. NDVI and yield associations have been well recorded [10–12]. Grain yield, controlled by several component traits, is important for overall production and food security. However, component traits are equally important for production and the market value and milling yield of bread wheat [13,14].

Due to their importance in affecting wheat production, breeding for heat stress tolerance and spot blotch resistance are the two critical objectives of wheat improvement programs targeting the EGP of South Asia. Genetic evaluation for heat tolerance and spot blotch in cultivated wheat has been attempted separately, and resistance sources have been identified [3,15–18]. However, limited information is available for the genomic regions providing tolerance to the combined stress of spot blotch and terminal heat stress. Hence, this study was initiated to identify the genomic regions associated with the combined stress of spot blotch and terminal heat, wherein a population derived from the cross of *T. aestivum* and *T. spelta* was utilized.

#### **2. Results**

#### *2.1. Descriptive Statistics for Quantitative Traits Indicate Reductions in Yield Contributing Traits Due to the Combined Stress of SB and Terminal Heat*

The distribution of 185 RILs and the parents for mean values for the nine phenotypic traits under different sowing dates and treatments—control, spot blotch, terminal heat stress, and combined stress spot blotch and terminal heat, is presented in Figure 1. The mean and range of phenotypic traits in the RILs across the environments and treatments are given in Table S1. Under control conditions, the mean TGW was 34.17 ± 2.85, about 12% lower than the mean of 30.05 ± 3.33 g under SB infections. The decrease in grain area was observed from 11.57 ± 056 mm<sup>2</sup> to 7.84 ± 0.53 mm2 (32.23%), which implicated in the reduction of thousand kernel weight from 34.17 ± 2.85 gm to 24.75 ± 2.46 gm (27.56%) (Table 1, Figure 1). The mean maturity duration (115.2 ± 1.19 days) under protected conditions decreased by >5% to 107.32 ± 4.06 days when infected to SB and further to 106.12 ± 1.22 and 103.76 ± 3.57 days under terminal heat stress and combined stress, respectively. The mean CT of the RILs under-protected was 23.11 ± 0.81 ◦C, while 25.73 ± 0.95 ◦C under spot blotch infection. A slight increase was noticed under terminal heat stress (30.23 ± 1.01 ◦C) and combined stress (31.75 ± 0.8 ◦C). The NDVI varied between 0.52–0.72, while after infection mean NDVI ranged between 0.39–0.59. It decreased to 0.42 ± 0.04 and 0.31 ± 0.03 units under terminal heat stress and combined SB + terminal heat stress (Figures S1 and S2).

The mean SPAD values were noted at 48.66 ± 2.4 units under protected conditions. However, this depleted to 43.43 ± 3.25 in response to SB infection. Under terminal heat stress, the SPAD mean was 48.63 ± 3.99, significantly decreasing to 26.1 under combined stress.

The AUDPC ranged between 299.31 and 689.35 with a mean of 504.69 7± 71.97. It was elevated to 731.14 ± 127.64 under combined stress. The decrease in grain area was 11.57 ± 056 mm<sup>2</sup> to 7.84 ± 0.53 mm<sup>2</sup> (32.23%) which was implicated in the reduction of TKW from 34.17 ± 2.85 gm to 24.75 ± 2.46 gm (27.56%) (Table 1).

**Figure 1.** Summary of the effect of biotic and abiotic stresses on nine quantitative traits: (**i**) days to heading, (**ii**) thousand kernel weight, (**iii**) days to maturity, (**iv**) canopy temperature, (**v**) normalized distributed vegetation index (NDVI), (**vi**) soil plant analysis development (SPAD), (**vii**) area under disease progress curve (AUDPC), (**viii**) grain area, and (**ix**) grain perimeter.


**Table 1.** Effect of biotic and abiotic stress on the performance of nine traits in wheat.
