Association mapping identifies loci and candidate genes for grain-related traits in spring wheat in response to heat stress

Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.)

BACKGROUND

As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars.

RESULTS

To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage.

CONCLUSIONS

This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.

Identification of candidate regulators of the response to early heat stress in climate-adapted wheat landraces via transcriptomic and co-expression network analyses

Introduction

Climate change is likely to lead to not only increased global temperatures but also a more variable climate where unseasonal periods of heat stress are more prevalent. This has been evidenced by the observation of spring-time temperatures approaching 40°C in some of the main spring-wheat producing countries, such as the USA, in recent years. With an optimum growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. A warming climate with increasingly common fluctuations in temperature therefore threatens wheat crops and subsequently the lives and livelihoods of billions of people who depend on the crop for food. To futureproof wheat against a variable climate, a better understanding of the response to early heat stress is required.

Methods

Here, we utilised DESeq2 to identify 7,827 genes which were differentially expressed in wheat landraces after early heat stress exposure. Candidate hub genes, which may regulate the transcriptional response to early heat stress, were identified via weighted gene co-expression network analysis (WGCNA), and validated by qRT-PCR.

Results

Two of the most promising candidate hub genes (TraesCS3B02G409300 and TraesCS1B02G384900) may downregulate the expression of genes involved in the drought, salinity, and cold responses-genes which are unlikely to be required under heat stress-as well as photosynthesis genes and stress hormone signalling repressors, respectively. We also suggest a role for a poorly characterised sHSP hub gene (TraesCS4D02G212300), as an activator of the heat stress response, potentially inducing the expression of a vast suite of heat shock proteins and transcription factors known to play key roles in the heat stress response.

Discussion

The present work represents an exploratory examination of the heat-induced transcriptional change in wheat landrace seedlings and identifies several candidate hub genes which may act as regulators of this response and, thus, may be targets for breeders in the production of thermotolerant wheat varieties.

Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection

Background

Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season.

Methods

To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F2:3 population.

Results

Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.

Identification of Single-Nucleotide Polymorphisms (SNPs) Associated with Heat Tolerance at the Reproductive Stage in Synthetic Hexaploid Wheats Using GWAS

The projected rise in global ambient temperature by 3-5 °C by the end of this century, along with unpredicted heat waves during critical crop growth stages, can drastically reduce grain yield and will pose a great food security challenge. It is therefore important to identify wheat genetic resources able to withstand high temperatures, discover genes underpinning resilience to higher temperatures, and deploy such genetic resources in wheat breeding to develop heat-tolerant cultivars. In this study, 180 accessions of synthetic hexaploid wheats (SHWs) were evaluated under normal and late wheat growing seasons (to expose them to higher temperatures) at three locations (Islamabad, Bahawalpur, and Tando Jam), and data were collected on 11 morphological and yield-related traits. The diversity panel was genotyped with a 50 K SNP array to conduct genome-wide association studies (GWASs) for heat tolerance in SHW. A known heat-tolerance locus, TaHST1, was profiled to identify different haplotypes of this locus in SHWs and their association with grain yield and related traits in SHWs. There was a 36% decrease in grain yield (GY), a 23% decrease in thousand-grain weight (TKW), and an 18% decrease in grains per spike (GpS) across three locations in the population due to the heat stress conditions. GWASs identified 143 quantitative trait nucleotides (QTNs) distributed over all 21 chromosomes in the SHWs. Out of these, 52 QTNs were associated with morphological and yield-related traits under heat stress, while 15 of them were pleiotropically associated with multiple traits. The heat shock protein (HSP) framework of the wheat genome was then aligned with the QTNs identified in this study. Seventeen QTNs were in proximity to HSPs on chr2B, chr3D, chr5A, chr5B, chr6D, and chr7D. It is likely that QTNs on the D genome and those in proximity to HSPs may carry novel alleles for heat-tolerance genes. The analysis of TaHST1 indicated that 15 haplotypes were present in the SHWs for this locus, while hap1 showed the highest frequency of 25% (33 SHWs). These haplotypes were significantly associated with yield-related traits in the SHWs. New alleles associated with yield-related traits in SHWs could be an excellent reservoir for breeding deployment.