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.

Foxtail millet (Setaria italicaL.) is of high nutritious value, which is an important crop in arid and semi-arid regions. The objective of this experiment was to explore the effects of the synthetic auxin naphthalene acetic acid (NAA) on the physiological processes of foxtail millet, and to provide a theoretical basis and technical approaches for its efficient use in millet cultivation. Two foxtail millet varieties (‘Jingu 21’ and ‘Zhangzagu 5’) were treated with six concentrations of NAA from 0-144 mg L^-1at the grain-filling stage in field experiments. The photosynthetic pigment contents, gas exchange parameters, chlorophyll fluorescence parameters, and grain yield were measured in foxtail millet. The results showed that low concentrations of NAA (18-36 mg L^-1) increased the contents of photosynthetic pigments, and increased the activities of antioxidant enzymes, the photosynthetic rate, and the activity of photosystem system II (PS II). At higher NAA concentrations, the facilitation effect of the treatments diminished, showing a clear concentration effect. In this study, yield was significantly and positively correlated with PS II effective quantum yield (Y(II)) and the PSII electron transport rate (ETR), and the net photosynthetic rate (Pn) was significantly and positively correlated with chlorophyll content, stomatal conductance (Gs), Y(II), and ETR. These results also indicated that exogenous NAA application promotes the production of ATP and NADPH by increasing the efficiency of electron transfer within the photosystems and also improved photochemical utilization, which facilitates the fixation and reduction of carbon, ultimately leading to an increase in Pn and increasing grain yield in foxtail millet.

The root is an important organ by which plants directly sense variation in soil moisture. The discovery of drought stress-responsive genes in roots is very important for the improvement of drought tolerance in wheat varieties via molecular approaches. In this study, transcriptome sequencing was conducted on the roots of drought-tolerant wheat cultivar YH1818 seedlings at 0, 2, and 7 days after treatment (DAT). Based on a weighted gene correlation network analysis of differentially expressed genes (DEGs), 14 coexpression modules were identified, of which five modules comprising 3107 DEGs were related to 2 or 7 DAT under drought stress conditions. A total of 223,357 single-nucleotide polymorphisms (SNPs) of these DEGs were retrieved from public databases. Using the R language package and GAPIT program, association analysis was performed between the 223,357 SNPs and the drought tolerance coefficient (DTC) values of six drought resistance-related traits in 114 wheat germplasms. The results revealed that 18 high-confidence SNPs of 10 DEGs, including TaPK, TaRFP, TaMCO, TaPOD, TaC3H-ZF, TaGRP, TaDHODH, TaPPDK, TaLectin, and TaARF7-A, were associated with drought tolerance. The RT–qPCR results confirmed that these genes were significantly upregulated by drought stress at 7 DAT. Among them, TaARF7-A contained three DTC-related SNPs, which presented two haplotypes in the tested wheat germplasms. YH1818 belongs to the Hap1 allele, which is involved in increased drought tolerance. This study revealed key modules and candidate genes for understanding the drought-stress response mechanism in wheat roots.

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.

The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross between CH7034 and non-SG SY95-71 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2159 SNP markers was constructed. Then, the chlorophyll content of flag leaf from each RIL was estimated for mapping, and one QTL for SG on chromosome 7D was identified, temporarily named QSg.sxau-7D, with the maximum phenotypic variance explained of 8.81~11.46%. A PCR-based diagnostic marker 7D-16 for QSg.sxau-7D was developed, and the CH7034 allele of 7D-16 corresponded to the higher flag leaf chlorophyll content, while the 7D-16 SY95-71 allele corresponded to the lower value, which confirmed the genetic effect on SG of QSg.sxau-7D. QSg.sxau-7D located in the 526.4~556.2 Mbp interval is different from all the known SG loci on chromosome 7D, and 69 high-confidence annotated genes within the interval expressed throughout the entire period of flag leaf senescence. Moreover, results of an association analysis based on the diagnostic marker showed that there is a positive correlation between QSg.sxau-7D and thousand-grain weight. Our results revealed a novel QTL QSg.sxau-7D whose CH7034 allele had a strong effect on SG, which can be applied in further wheat molecular breeding.