Phenotypic and genotypic characterization of near-isogenic lines targeting a major 4BL QTL responsible for pre-harvest sprouting in wheat

Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies.

The Expression of Triticum aestivum Cysteine-Rich Receptor-like Protein Kinase Genes during Leaf Rust Fungal Infection

Understanding the role of cysteine-rich receptor-like kinases (CRKs) in plant defense mechanisms is crucial for enhancing wheat resistance to leaf rust fungus infection. Here, we identified and verified 164 members of the CRK gene family using the Triticum aestivum reference version 2 collected from the international wheat genome sequencing consortium (IWGSC). The proteins exhibited characteristic features of CRKs, including the presence of signal peptides, cysteine-rich/stress antifungal/DUF26 domains, transmembrane domains, and Pkinase domains. Phylogenetic analysis revealed extensive diversification within the wheat CRK gene family, indicating the development of distinct specific functional roles to wheat plants. When studying the expression of the CRK gene family in near-isogenic lines (NILs) carrying Lr57- and Lr14a-resistant genes, Puccinia triticina, the causal agent of leaf rust fungus, triggered temporal gene expression dynamics. The upregulation of specific CRK genes in the resistant interaction indicated their potential role in enhancing wheat resistance to leaf rust, while contrasting gene expression patterns in the susceptible interaction highlighted potential susceptibility associated CRK genes. The study uncovered certain CRK genes that exhibited expression upregulation upon leaf rust infection and the Lr14a-resistant gene. The findings suggest that targeting CRKs may present a promising strategy for improving wheat resistance to rust diseases.

Identification of a stable major-effect quantitative trait locus for pre-harvest sprouting in common wheat (Triticum aestivum L.) via high-density SNP-based genotyping

A major and stable QTL cQSGR.sau.3D, which can explain 33.25% of the phenotypic variation in SGR, was mapped and validated, and cQSGR.sau.3D was found to be independent of GI. In this study, a recombinant inbred line (RIL) population containing 304 lines derived from the cross of Chuan-nong17 (CN17) and Chuan-nong11 (CN11) was genotyped using the Wheat55K single-nucleotide polymorphism array. A high-density genetic map consisting of 8329 markers spanning 4131.54 cM and distributed across 21 wheat chromosomes was constructed. QTLs for whole spike germination rate (SGR) were identified in multiple years. Six and fourteen QTLs were identified using the Inclusive Composite Interval Mapping-Biparental Populations and Multi-Environment Trial methods, respectively. A total of 106 digenic epistatic QTLs were also detected in this study. One of the additive QTLs, cQSGR.sau.3D, which was mapped in the region from 3.5 to 4.5 cM from linkage group 3D-2 on chromosome 3D, can explain 33.25% of the phenotypic variation in SGR and be considered a major and stable QTL for SGR. This QTL was independent of the seeds' germination traits, such as germination index. One Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110772653, which is tightly linked to cQSGR.sau.3D, was developed. The genetic effect of cQSGR.sau.3D on SGR in the RIL and natural populations was successfully confirmed. Furthermore, within the interval in which cQSGR.sau.3D is located in Chinese Spring reference genomes, thirty-seven genes were found. cQSGR.sau.3D may provide new resources for pre-harvest sprouting resistance breeding of wheat in the future.

Genomic regions controlling yield-related traits in spring wheat: a mini review and a case study for rainfed environments in Australia and China

A genome-wide association study (GWAS) was performed in six environments to identify major or consistent alleles responsible for wheat yield traits in Australia and North China where rainfed farming system is adopted. A panel of 228 spring wheat varieties were genotyped by double digest restriction-site associated DNA genotyping-by-sequencing. A total of 223 significant marker-trait association (MTAs) and 46 candidate genes for large- or consistent-effect MTAs were identified. The results were compared with previous studies based on a mini-review of 23 GWAS analyses on wheat yield. A phenomenon seldom reported in previous studies was that MTAs responsible for the trait tended to cluster together at certain chromosome segments, and many candidate genes were in the form of gene clusters. Although linkage disequilibrium (LD) might contribute to the co-segregation of the regions, it also suggested that marker-assisted selection (MAS) or transgenic method targeting a single gene might not be as effective as MAS targeting a larger genomic region where all the genes or gene clusters underlying play important roles.

Exploring Breakthroughs in Three Traits Belonging to Seed Life

Based on prior knowledge and with the support of new methodology, solid progress in the understanding of seed life has taken place over the few last years. This update reflects recent advances in three key traits of seed life (i.e., preharvest sprouting, genomic imprinting, and stored-mRNA). The first breakthrough refers to cloning of the mitogen-activated protein kinase-kinase 3 (MKK3) gene in barley and wheat. MKK3, in cooperation with ABA signaling, controls seed dormancy. This advance has been determinant in producing improved varieties that are resistant to preharvest sprouting. The second advance concerns to uniparental gene expression (i.e., imprinting). Genomic imprinting primarily occurs in the endosperm. Although great advances have taken place in the last decade, there is still a long way to go to complete the puzzle regarding the role of genomic imprinting in seed development. This trait is probably one of the most important epigenetic facets of developing endosperm. An example of imprinting regulation is polycomb repressive complex 2 (PRC2). The mechanism of PRC2 recruitment to target endosperm with specific genes is, at present, robustly studied. Further progress in the knowledge of recruitment of PRC2 epigenetic machinery is considered in this review. The third breakthrough referred to in this update involves stored mRNA. The role of the population of this mRNA in germination is far from known. Its relations to seed aging, processing bodies (P bodies), and RNA binding proteins (RBPs), and how the stored mRNA is targeted to monosomes, are aspects considered here. Perhaps this third trait is the one that will require greater experimental dedication in the future. In order to make progress, herein are included some questions that are needed to be answered.

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6-18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

Identification of Candidate Genes for Root Traits Using Genotype-Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat (Triticum aestivum L.)

Global wheat (Triticum aestivum L.) production is constrained by different biotic and abiotic stresses, which are increasing with climate change. An improved root system is essential for adaptability and sustainable wheat production. In this study, 10 pairs of near-isogenic lines (NILs)-targeting four genomic regions (GRs) on chromosome arms 4BS, 4BL, 4AS, and 7AL of hexaploid wheat-were used to phenotype root traits in a semi-hydroponic system. Seven of the 10 NIL pairs significantly differed between their isolines for 11 root traits. The NIL pairs targeting qDSI.4B.1 GR varied the most, followed by the NIL pair targeting qDT.4A.1 and QHtscc.ksu-7A GRs. For pairs 5-7 targeting qDT.4A.1 GR, pair 6 significantly differed in the most root traits. Of the 4 NIL pairs targeting qDSI.4B.1 GR, pairs 2 and 4 significantly differed in 3 and 4 root traits, respectively. Pairs 9 and 10 targeting QHtscc.ksu-7A GR significantly differed in 1 and 4 root traits, respectively. Using the wheat 90K Illumina iSelect array, we identified 15 putative candidate genes associated with different root traits in the contrasting isolines, in which two UDP-glycosyltransferase (UGT)-encoding genes, TraesCS4A02G185300 and TraesCS4A02G442700, and a leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene, TraesCS4A02G330900, also showed important functions for root trait control in other crops. This study characterized, for the first time, that these GRs control root traits in wheat, and identified candidate genes, although the candidate genes will need further confirmation and validation for marker-assisted wheat breeding.

Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

BACKGROUND

Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated.

RESULTS

Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines.

CONCLUSIONS

The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

Characterization of near-isogenic lines confirmed QTL and revealed candidate genes for plant height and yield-related traits in common wheat

Plant height (PH) is closely associated with yield-related traits and environmental adaptation. Seven pairs of near-isogenic lines (NILs) targeting four QTL on 3AL, 4BL, 4AS, and 7AL wheat chromosome arms were assessed for PH and four yield-related traits including yield per plant (Y/P), grain number per spike (G/S), thousand kernel weight (TKW), and biomass per plant (B/P). Significant differences were observed in the NIL pairs for the measured traits. NIL pairs targeting the 3AL QTL differed significantly in PH, G/S, and TKW; NILs targeting the 4BL QTL differed significantly in PH, Y/P, and B/P; NIL pairs targeting the 4AS QTL differed significantly in all the traits; and NIL pairs targeting the 7AL QTL differed significantly in PH. A 90 K SNP genotyping assay of the NILs detected nineteen SNPs associated with fourteen functional genes. Among them, eight candidate genes are related to Rht proteins, four genes are related to hormone pathways and two genes are related to carbohydrate synthesis and transport. By searching the interval marker physical positions, it was found that the four targeted QTL in this study overlapped with eight previously reported QTL for PH, TKW, biomass, and yield. Correlation analysis revealed that PH significantly and positively correlated with B/P and G/S. The SNP and candidate gene information is potentially useful for marker-assisted selection in breeding programs, and the four targeted QTL are proved to be critical genomic regions controlling the investigated agronomic traits, which can be further fine mapped to identify the underlying genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-020-01196-8.

Identification of loci for pre-harvest sprouting resistance in the highly dormant spring wheat RL4137

Combination of RL4137 alleles at three QTLs on chromosomes 4A, 6B and 6D, and 'Roblin' allele at a novel QTL on chromosome 1D increases pre-harvest sprouting resistance in 'Roblin'/RL4137 doubled haploid population. Pre-harvest sprouting (PHS) significantly reduces wheat grain yield and quality. Therefore, identifying quantitative trait loci (QTL) for PHS resistance is key to facilitate marker-assisted breeding. To this end, we studied PHS in a population of 330 doubled haploid (DH) lines derived from 'Roblin'/RL4137. The parental and DH lines were examined for their PHS phenotype based on speed of germination index in five environments and genotyped using the wheat Infinium 90 K SNP array. A total of five QTLs were detected on linkage groups 1D, 4A.2, 6B.1, 6D and 7A over the five environments. The QTL QPhs.umb-4A on linkage group 4A.2 was the most consistent across all environments and explained 40-50% of phenotypic variation. The QTL on 1D is a novel QTL and explained 1.99-2.33% of phenotypic variation. The QTLs on 6B.1 and 6D each explained 3.09-4.33% and 1.62-2.45% of phenotypic variation, respectively. A combination of four stable QTLs on linkage groups 1D, 4A.2, 6B.1 and 6D greatly increased PHS resistance. Allelic effects for the QTLs QPhs.umb-4A, QPhs.umb-6B and QPhs.umb-6D were contributed by RL4137, whereas 'Roblin' contributed the resistant allele for QPhs.umb-1D. QPhs.umb-4A was required for strong dormancy in the 'Roblin'/RL4137 DH population, and the presence of QTLs QPhs.umb-1D, QPhs.umb-6B and QPhs.umb-6D incrementally increased dormancy; DH lines carrying all four QTLs are considerably more dormant than those carrying only QPhs.umb-4A or none of the four QTLs. Thus, the QTLs identified in this study have the potential to improve PHS resistance in spring wheat.

Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat

Wheat is one of the most important food crops in the world, but as a cool-season crop, it is more prone to heat stress, which severely affects crop production and grain quality. Heat tolerance in wheat is a quantitative trait, and the genes underlying reported quantitative trait loci (QTL) have rarely been identified. Near-isogenic lines (NILs) with a common genetic background but differing at a particular locus could turn quantitative traits into a Mendelian factor; therefore, they are suitable material for identifying candidate genes for targeted locus/loci. In this study, we developed and characterized NILs from two populations Cascades × Tevere and Cascades × W156 targeting a major 7AL QTL responsible for heat tolerance. Molecular marker screening and phenotyping for SPAD chlorophyll content and grain-yield-related traits confirmed four pairs of wheat NILs that contrasted for heat-stress responses. Genotyping the NILs using a 90K Infinium iSelect SNP array revealed five single nucleotide polymorphism (SNP) markers within the QTL interval that were distinguishable between the isolines. Seven candidate genes linked to the SNPs were identified as related to heat tolerance, and involved in important processes and pathways in response to heat stress. The confirmed multiple pairs of NILs and identified candidate genes in this study are valuable resources and information for further fine-mapping to clone major genes for heat tolerance.