Soil salinization is the main abiotic stressor faced by crops. An improved understanding of the transcriptional response to salt stress in roots, the organ directly exposed to a high salinity environment, can inform breeding strategies to enhance tolerance and increase crop yield. Here, RNA-sequencing was performed on the roots of salt-tolerant wheat breeding line CH7034 at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on transcriptome data, a weighted gene co-expression network analysis (WGCNA) was constructed, and five gene co-expression modules were obtained, of which the blue module was correlated with the time course of salt stress at 1 and 48 h. Two GO terms containing 249 differentially expressed genes (DEGs) related to osmotic stress response and salt-stress response were enriched in the blue module. These DEGs were subsequently used for association analysis with a set of wheat germplasm resources, and the results showed that four genes, namely a Walls Are Thin 1-related gene (TaWAT), an aquaporin gene (TaAQP), a glutathione S-transfer gene (TaGST), and a zinc finger gene (TaZFP), were associated with the root salt-tolerance phenotype. Using the four candidate genes as hub genes, a co-expression network was constructed with another 20 DEGs with edge weights greater than 0.6. The network showed that TaWAT and TaAQP were mainly co-expressed with fifteen interacting DEGs 1 h after salt treatment, while TaGST and TaZFP were mainly co-expressed with five interacting DEGs 48 h after salt treatment. This study provides key modules and candidate genes for understanding the salt-stress response mechanism in wheat roots.

The leaf is not only the main site of photosynthesis, but also an important organ reflecting plant salt tolerance. Discovery of salt-stress-responding genes in the leaf is of great significance for the molecular improvement of salt tolerance in wheat varieties. In this study, transcriptome sequencing was conducted on the leaves of salt-tolerant wheat germplasm CH7034 seedlings at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on weighted gene correlation network analysis of differentially expressed genes (DEGs) under salt stress, 12 co-expression modules were obtained, of which, 9 modules containing 4029 DEGs were related to the salt stress time-course. These DEGs were submitted to the Wheat Union database, and a total of 904,588 SNPs were retrieved from 114 wheat germplasms, distributed on 21 wheat chromosomes. Using the R language package and GAPIT program, association analysis was performed between 904,588 SNPs and leaf salt injury index of 114 wheat germplasms. The results showed that 30 single nucleotide polymorphisms (SNPs) from 15 DEGs were associated with salt tolerance. Then, nine candidate genes, including four genes (TaBAM, TaPGDH, TaGluTR, and TaAAP) encoding enzymes as well as five genes (TaB12D, TaS40, TaPPR, TaJAZ, and TaWRKY) encoding functional proteins, were identified by converting salt tolerance-related SNPs into Kompetitive Allele-Specifc PCR (KASP) markers for validation. Finally, interaction network prediction was performed on TaBAM and TaAAP, both belonging to the Turquoise module. Our results will contribute to a further understanding of the salt stress response mechanism in plant leaves and provide candidate genes and molecular markers for improving salt-tolerant wheat varieties.

Soil salinization is a major abiotic stressor that significantly reduces wheat yield. Identifying novel salt-tolerance genes and integrating them into wheat breeding programs can enhance wheat productivity in saline soils. Ethylene response factor (ERF) plays an important role in plant response to salt stress, and thus far, four wheat ERF genes have been identified to be involved in salt stress response. To systematically identify salt tolerance-related ERF genes in wheat, in this study, 213 ERF sequences were isolated from the whole genome of common wheat and classified into 54 members based on subgenome homology, named TaERF1 to TaERF54. Transcriptome sequencing results showed different expression patterns of TaERF members in leaves after 1, 6, 24, and 48 h of NaCl treatment. Based on association analysis, nine TaERF genes were correlated with the leaf salt injury index. Among them, five SNPs of TaERF16-B formed two haplotypes: Hap1 and Hap2. RT-qPCR results showed that the expression level of TaERF16-B was significantly higher in Hap2-typed germplasms than that in Hap1-typed germplasms after 1 and 6 h of NaCl treatment. A Kompetitive Allele-Specific PCR marker K52 was developed for genotyping TaERF16-B haplotypes, which further confirmed the significant correlation between TaERF16-B and salt tolerance-related phenotypes in mapping population and wheat germplasms. This study provides new genes and molecular markers for improving salt tolerance in wheat.

The number of spikelets per spike is an important trait that directly affects grain yield in wheat. Three quantitative trait loci (QTLs) associated with spikelet nodes per spike (SNS) were mapped in a population of recombinant inbred lines generated from a cross between two advanced breeding lines of winter wheat based on the phenotypic variation evaluated over six locations/years. Two of the three QTLs are QSns.sxau-2A at the WHEATFRIZZY PANICLE (WFZP) loci and QSns.sxau-7A at the WHEAT ORTHOLOG OF APO1 (WAPO1) loci. The WFZP-A1b allele with a 14-bp deletion at QSns.sxau-2A was associated with increased spikelets per spike. WAPO-A1e, as a novel allele at WAPO1, were regulated at the transcript level that was associated with the SNS trait. The third SNS QTL, QSns.sxau-7D on chromosome 7D, was not associated with homoeologous WAPO-D1 or any other genes known to regulate SNS. The favorable alleles for each of WZFP-A1, WAPO-A1, and QSns.sxau-7D are identified and incorporated to increase up to 3.4 spikelets per spike in the RIL lines. Molecular markers for the alleles were developed. This study has advanced our understanding of the genetic basis of natural variation in spikelet development in wheat.

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.