Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat

Identification of QTL for reducing loss of grain yield under salt stress conditions in bi-parental populations derived from wheat landrace Hongmangmai

A novel QTL (QSt.nftec-2BL) was mapped to a 0.7 cM interval on chromosome 2B. Plants carrying QSt.nftec-2BL produced higher grain yields by up to 21.4% than otherwise in salinized fields. Wheat yield has been limited by soil salinity in many wheat-growing areas globally. The wheat landrace Hongmangmai (HMM) possesses salt tolerance as it produced higher grain yields than other tested wheat varieties including Early Premium (EP) under salt stresses. To detect QTL underlying this tolerance, wheat cross EP × HMM was chosen to serve as mapping population that was homozygous at Ppd (photoperiod response gene), Rht (reduced plant height gene) and Vrn (vernalization gene); thus, interference with QTL detection by these loci could be minimized. QTL mapping was conducted firstly using 102 recombinant inbred lines (RILs) that were selected from the EP × HMM population (827 RILs) for similarity in grain yield under non-saline condition. Under salt stresses, however, the 102 RILs varied significantly in grain yield. These RILs were genotyped using a 90 K SNP (single nucleotide polymorphism) array; consequently, a QTL (QSt.nftec-2BL) was detected on chromosome 2B. Then, using 827 RILs and new simple sequence repeat (SSR) markers developed according to the reference sequence IWGSC RefSeq v1.0, location of QSt.nftec-2BL was refined to a 0.7 cM (6.9 Mb) interval flanked by SSR markers 2B-557.23 and 2B-564.09. Selection for QSt.nftec-2BL was performed based on the flanking markers using two bi-parental wheat populations. Trials for validating effectiveness of the selection were conducted in salinized fields in two geographical areas and two crop seasons, demonstrating that wheat plants with the salt-tolerant allele in homozygous status at QSt.nftec-2BL produced higher grain yields by up to 21.4% than otherwise.

Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat

The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.

Modulating physiological and transcriptional regulatory mechanisms for enhanced climate resilience in cereal crops

Climate change adversely affects the yield and productivity of cereal crops, which consequently impacts food security. Therefore, studying stress acclimation, particularly transcriptional patterns and morpho-physiological responses of cereal crops to different stresses, will provide insights into the molecular determinants underlying climate resilience. The availability of advanced tools and approaches has enabled the characterization of plants at morphological, physiological, biochemical, and molecular levels, which will lead to the identification of genomic regions regulating the stress responses at these levels. This will further facilitate using transgenic, breeding, or genome editing approaches to manipulate the identified regions (genes, alleles, or QTLs) to enhance stress resilience. Next-generation sequencing approaches have advanced the identification of causal genes and markers in the genomes through forward or reverse genetics. In this context, the review enumerates the progress of dissecting the molecular mechanisms underlying transcriptional and physiological responses of major cereals to climate-induced stresses. The review systematically discusses different tools and approaches available to study the response of plants to various stresses and identify the molecular determinants regulating stress-resilience. Further, the application of genomics-assisted breeding, transgene-, and targeted editing-based approaches for modulating the genetic determinants for enhanced climate resilience has been elaborated.

Comparative transcriptome analysis of synthetic and common wheat in response to salt stress

Salt stress reduces wheat yield. Therefore, improvement for enhanced salt stress tolerance is necessary for stable production. To understand the molecular mechanism of salt tolerance in common wheat and synthetic hexaploid (SH) wheat, RNA sequencing was performed on the roots of three wheat lines salt-tolerant SH wheat, salt-tolerant common wheat, and salt-sensitive common wheat. Differentially expressed genes (DEGs) in response to salt stress were characterized using gene ontology enrichment analysis. Salt tolerance in common wheat has been suggested to be mainly regulated by the activation of transporters. In contrast, salt tolerance in SH wheat is enhanced through up-regulation of the reactive oxygen species signaling pathway, other unknown pathways, and different ERF transcription factors. These results indicate that salt tolerance is differentially controlled between common wheat and SH wheat. Furthermore, QTL analysis was performed using the F₂ population derived from SH and salt-sensitive wheat. No statistically significant QTL was detected, suggesting that numerous QTLs with negligible contributions are involved in salt tolerance in SH wheat. We also identified DEGs specific to each line near one probable QTL. These findings show that SH wheat possesses salt tolerance mechanisms lacking in common wheat and may be potential breeding material for salt tolerance.

Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley

Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant's ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately -log₁₀ (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest -log₁₀ (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties.