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Key Message: Key message This study identified stable QTL, promising candidate genes and developed novel KASP markers for heat tolerance, providing genomic resources to assist breeding for the development of high-yielding and heat-tolerant wheat germplasm and varieties. To understand the genetic architecture of eleven agronomic traits under heat stress, we used a doubled-haploid population (177 lines) derived from a heat-sensitive cultivar (PBW343) and a heat-tolerant genotype (KSG1203). This population was evaluated under timely, late and very late sown conditions over locations and years comprising fifteen environments. Best linear unbiased estimates and a genetic map (5,710 SNPs) developed using sequencing-based genotyping were used for QTL mapping. The identified 66 QTL (20 novel) were integrated into wheat physical map (14,263.4 Mb). These QTL explained 5.3% (QDth.ccsu-4A for days to heading and QDtm.ccsu-5B for days to maturity) to 24.9% (QGfd.ccsu-7D for grain filling duration) phenotypic variation. Thirteen stable QTL explaining high phenotypic variation were recommended for marker-assisted recurrent selection (MARS) for optimum/heat stress environments. Selected QTL were validated by their presence in high-yielding doubled-haploid lines. Some QTL for 1000-grain weight (TaERF3-3B, TaFER-5B, and TaZIM-A1), grain yield (TaCol-B5), and developmental traits (TaVRT-2) were co-localized with known genes. Specific known genes for traits like abiotic/biotic stress, grain quality and yield were co-located with 26 other QTL. Furthermore, 209 differentially expressed candidate genes for heat tolerance in plants that encode 28 different proteins were identified. KASP markers for three major/stable QTL, namely QGfd.ccsu-7A for grain filling duration on chromosome 7A (timely sown), QNgs.ccsu-3A for number of grains per spike on 3A, and QDth.ccsu-7A for days to heading on 7A (late and very late sown) environments were developed for MARS focusing on the development of heat-tolerant wheat varieties/germplasm., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

With every 1°C rise in temperature, yields are predicted to decrease by 5%-6% for both cool and warm season crops, threatening food production, which should double by 2050 to meet the global demand. While high night-time temperature (HNT) stress is expected to increase due to climate change, limited information is available on the genetic control of the trait, especially in wheat (Triticum aestivum L.). To identify genes controlling the HNT trait, we evaluated a doubled haploid (DH) population developed from a cross between an HNT tolerant line KSG1203 and KSG0057, a selection out of a mega variety PBW343 from South East Asia that turned out to be HNT susceptible. The population, along with the parents, were evaluated under 30°C night-time (HNT stress) keeping the daytime temperature to normal 22°C. The same daytime and 16°C night-time temperature were used as a control. The HNT treatment negatively impacted all agronomic traits under evaluation, with a percentage reduction of 0.5%-35% for the tolerant parent, 8%-75% for the susceptible parent, and 8%-50% for the DH population. Performed using sequencing-based genotyping, quantitative trait locus (QTL) mapping identified 19 QTLs on 13 wheat chromosomes explaining 9.72%-28.81% of cumulative phenotypic variance for HNT stress tolerance, along with 13 that were for traits under normal growing conditions. The size of QTL intervals ranged between 0.021 and 97.48 Mb, with the number of genes ranging between 2 and 867. A candidate gene analysis for the smallest six QTL intervals identified eight putative candidates for night-time heat stress tolerance., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Global chickpea production is restricted by Ascochyta blight caused by the necrotrophic fungi Ascochyta rabiei . Developing locally adapted disease-resistant cultivars is an economically and environmentally sustainable approach to combat this disease. However, the lack of genetic variability in cultivated chickpeas and breeder-friendly markers poses a significant challenge to Ascochyta blight-resistant breeding efforts in chickpeas. In this study, we screened the mini-core germplasm of Cicer reticulatum against a local pathotype of A. rabiei . A modified mini-dome screening approach resulted in the identification of five accessions showing a high level of resistance. The mean disease score of resistant accessions ranged between 1.75 ± 0.3 and 2.88 ± 0.4 compared to susceptible accessions, where the mean disease score ranged between 3.59 ± 0.62 and 8.86 ± 0.14. Genome-wide association study revealed a strong association on chromosome 5 , explaining ∼58% of the phenotypic variance. The underlying region contained two candidate genes ( Cr_14190.1_v2 and Cr_14189.1_v2 ), the characterization of which showed the presence of a DNA-binding domain (cl28899 and cd18793) in Cr_14190.1_v2 and its orthologs in C. arietinum , whereas Cr_14190.1_v2 carried an additional N-terminal domain (cl31759). qPCR expression analysis in resistant and susceptible accessions revealed ∼3- and ∼110-fold higher transcript abundance for Cr_14189.1 and Cr_14190.1 , respectively., Competing Interests: One of the co-authors (K. S. Gill) is the CEO and co-owner of the company where the work was performed.

Development of nutrient efficient cultivars depends on effective identification and utilization of genetic variation. We characterized a set of 276 pre-breeding lines (PBLs) for several traits at different levels of nitrogen application. These PBLs originate from synthetic wheats and landraces. We witnessed significant variation in various traits among PBLs to different nitrogen doses. There was ~ 4-18% variation range in different agronomic traits in response to nitrogen application, with the highest variation for the biological yield (BY) and the harvest index. Among various agronomic traits measured, plant height, tiller number, and BY showed a positive correlation with nitrogen applications. GWAS analysis detected 182 marker-trait associations (MTAs) (at p-value < 0.001), out of which 8 MTAs on chromosomes 5D, 4A, 6A, 1B, and 5B explained more than 10% phenotypic variance. Out of all, 40 MTAs observed for differential nitrogen application response were contributed by the synthetic derivatives. Moreover, 20 PBLs exhibited significantly higher grain yield than checks and can be selected as potential donors for improved plant nitrogen use efficiency (pNUE)., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The Ph1 gene is the principal regulator of homoeologous chromosome pairing control (HECP) that ensures the diploid-like meiotic chromosome pairing behavior of polyploid wheat. The HECP control was speculated to have evolved after the first event of polyploidization. With the objective to accurately understand the evolution of the HECP control, wild emmer wheat accessions previously known to differ for HECP control were characterized for the structure and expression of the candidate Ph1 gene, C-Ph1. The C-TdPh1-5A and 5B gene copies of emmer wheat showed 98 and 99% DNA sequence similarity respectively with the corresponding hexaploid wheat copies. Further, the C-TdPh1-5B carried the C-Ph1-5B specific structural changes and transcribed three splice variants as observed in the hexaploid wheat. Further, single nucleotide changes differentiating accessions varying for HECP control were identified. Analyzed by quantitative expression analysis, the wild emmer accessions with HECP control showed ~ 10,000-fold higher transcript abundance of the C-TdPh1-5B copy during prophase-I compared to accessions lacking the control. Differential transcriptional regulation of C-TdPh1-5B splice variants further revealed that C-Ph1-5B alt1 variant is mainly responsible for differential accumulation of C-Ph1-5B copy in accessions with HECP control. Taken together, these results showed that the HECP control evolved via transcriptional regulation of splice variants during meiosis.