Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy 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.

Genetic basis of resistance against powdery mildew in the wheat cultivar "Tabasco".

European winter wheat cultivar "Tabasco" was reported to have resistance to powdery mildew disease caused by Blumeria graminis f. sp. tritici (Bgt) in China. In previous studies, Tabasco was reported to have the resistance gene designated as Pm48 on the short arm of chromosome 5D when a mapping population was phenotyped with pathogen isolate Bgt19 collected in China and was genotyped with simple sequence repeat (SSR) markers. In this study, single-nucleotide polymorphism (SNP) chips were used to rapidly determine the resistance gene by mapping a new F2 population that was developed from Tabasco and a susceptible cultivar "Ningmaizi119" and inoculated with pathogen isolate NCF-D-1-1 that was collected in the USA. The segregation of resistance in the population was found to link with Pm2 which was identified in Tabasco. Therefore, it was concluded that the previously reported Pm48 on chromosome arm 5DS in Tabasco should be the Pm2 gene on the same chromosome. The Pm2 was also found in European cultivars "Mattis" and "Claire" but not in any of the accessions from diploid wheat Aegilops tauschii or modern cultivars such as "Gallagher," "Smith's Gold," and "OK Corral" being used in the Great Plains in the USA. A KASP marker was developed to track the resistance allele Pm2 in wheat breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01402-3.

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL.

KEY MESSAGE: YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55 K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12 Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

Genetic incorporation of genes for the optimal plant architecture in common wheat.

Wheat grain yield is affected by plant height, which is the total length of spike, the uppermost internode, and other elongated internodes. In this study, a population of recombinant inbred lines generated from a cross between two advanced winter wheat breeding lines were phenotyped over four locations/years and genotyped by using markers of genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) for mapping of genes for three traits, including spike length, the uppermost internode length, and plant height. Five genomic regions or quantitative trait loci (QTLs) were associated with candidate genes for these traits. A major QTL was associated with Q5A, and two novel haplotypes of Q5A were identified, one for a single nucleotide polymorphism (SNP) at position -2,149 in promoter region and the other for copy number variation. Compared with one copy Q5A on chromosome 5A in Chinese Spring, the novel haplotype of Q5A with two copies Q5A was found to generate spikes that are extremely compacted. A major QTL was associated with allelic variation in the recessive vrn-A1 alleles involving in protein sequences, and this QTL was associated with increased uppermost internode length but not with plant height. A major QTL for plant height was associated with Rht-B1b on chromosome 4B, but its effects could be compromised by two new minor QTLs on chromosome 7. Collectively, the favorable alleles from the four loci can be used to establish the optimal plant height in wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01336-2.

Fine mapping of a recessive leaf rust resistance locus on chromosome 2BS in wheat accession CH1539.

Leaf rust (LR), caused by Puccinia triticina (Pt), is one of the most important fungal diseases of wheat worldwide. The wheat accession CH1539 showed a high level of resistance to leaf rust. A mapping population of 184 recombinant inbred lines (RILs) was developed from a cross between the resistant accession CH1539 and the susceptible cultivar SY95-71. The RILs showed segregating infection responses to Puccinia triticina Eriks. (Pt) race THK at the seedling stage. Genetic analysis showed that leaf rust resistance was controlled by a monogenic gene, and the potential locus was temporarily named LrCH1539. Bulked segregant analysis (BSA) using a 35 K DArTseq array located LrCH1539 on the short arm of chromosome 2B. Subsequently, a genetic linkage map of LrCH1539 was constructed using the developed 2BS chromosome-specific markers, and its flanking markers were sxau-2BS136 and sxau-2BS81. An F2 subpopulation with 3619 lines was constructed by crossing the resistant and susceptible lines selected from the RIL population. The inoculation identification results showed that LrCH1539 was recessively inherited and was fine-mapped to a 779.4-kb region between markers sxau-2BS47 and sxau-2BS255 at the end of 2BS. The linkage marker analysis showed that the positions of LrCH1539 and Lr16 were the same, but the identification results of the resistance spectrum indicated that the causal genes of the two might be different. The resistant materials reported in this study and the cosegregation marker can be used for marker-assisted selection breeding of leaf rust-resistant wheat cultivars. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01318-4.

Identification of a novel ERF gene, TaERF8, associated with plant height and yield in wheat.

BACKGROUND: Ethylene Responsive Factor (ERF) is involved in various processes of plant development and stress responses. In wheat, several ERFs have been identified and their roles in mediating biotic or abiotic stresses have been elucidated. However, their effects on wheat plant architecture and yield-related traits remain poorly studied. RESULTS: In this study, TaERF8, a new member of the ERF family, was isolated in wheat (Triticum aestivum L.). Three homoeologous TaERF8 genes, TaERF8-2A, TaERF8-2B and TaERF8-2D (named according to sub-genomic origin), were cloned from the common wheat cultivar Chinese Spring. The three homoeologs showed highly similar protein sequences, with identical AP2 domain. Whereas homoeologs sequence polymorphism analysis allowed the establishment of ten, two and three haplotypes, respectively. Expression analysis revealed that TaERF8s were constitutively expressed through entire wheat developmental stages. Analysis of related agronomic traits of TaERF8-2B overexpressing transgenic lines showed that TaERF8-2B plays a role in regulating plant architecture and yield-related traits. Association analysis between TaERF8-2B haplotypes (Hap-2B-1 and Hap-2B-2) and agronomic traits showed that TaERF8-2B was associated with plant height, heading date and 1000 kernel weight (TKW). The TaERF8-2B haplotypes distribution analysis revealed that Hap-2B-2 frequency increased in domesticated emmer wheat and modern varieties, being predominant in five major China wheat producing zones. CONCLUSION: These results indicated that TaERF8s are differentially involved in the regulation of wheat growth and development. Haplotype Hap-2B-2 was favored during domestication and in Chinese wheat breeding. Unveiling that the here described molecular marker TaERF8-2B-InDel could be used for marker-assisted selection, plant architecture and TKW improvement in wheat breeding.

The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat.

Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.

Identification, Characterization, and Evaluation of Novel Stripe Rust-Resistant Wheat-Thinopyrum intermedium Chromosome Translocation Lines.

Stripe rust is an important disease in wheat, and development of genetic resistance in cultivars is an effective approach to control the disease. Wild species of wheat, such as Thinopyrum intermedium, are an excellent gene source for wheat improvement. In this study, two stripe rust-resistant wheat-Th. intermedium chromosome translocation lines, CH4131 and CH4132, were characterized by cytogenetic and pathological methods. The introgressed chromosome fragment was tagged using amplified fragment-length polymorphism-derived sequence-characterized amplified region (SCAR) markers and intron targeting markers, indicating that CH4131 and CH4132 both possess a homologous group 3 chromatin of Th. intermedium. Genomic in situ hybridization results suggested that a very small Th. intermedium chromosome segment was translocated to the terminal region of wheat 1BS for both lines, forming a configuration of T3Ai-1BS.1BL. The two translocation lines were resistant to stripe rust, and the resistance gene, temporarily designated YrCH-1BS, was likely derived from Th. intermedium. The translocated chromosome fragments have no genetic linkage drag to agronomic performance. The grain quality indexes of these two translocations were higher than local wheat varieties. Therefore, CH4131 and CH4132 could be used as potential gene sources in wheat improvement programs. The SCAR markers are useful to select stripe rust resistance from Th. intermedium.

Genome-wide characterization of JASMONATE-ZIM DOMAIN transcription repressors in wheat (Triticum aestivum L.).

BACKGROUND: The JASMONATE-ZIM DOMAIN (JAZ) repressor family proteins are jasmonate co-receptors and transcriptional repressor in jasmonic acid (JA) signaling pathway, and they play important roles in regulating the growth and development of plants. Recently, more and more researches on JAZ gene family are reported in many plants. Although the genome sequencing of common wheat (Triticum aestivum L.) and its relatives is complete, our knowledge about this gene family remains vacant. RESULTS: Fourteen JAZ genes were identified in the wheat genome. Structural analysis revealed that the TaJAZ proteins in wheat were as conserved as those in other plants, but had structural characteristics. By phylogenetic analysis, all JAZ proteins from wheat and other plants were clustered into 11 sub-groups (G1-G11), and TaJAZ proteins shared a high degree of similarity with some JAZ proteins from Aegliops tauschii, Brachypodium distachyon and Oryza sativa. The Ka/Ks ratios of TaJAZ genes ranged from 0.0016 to 0.6973, suggesting that the TaJAZ family had undergone purifying selection in wheat. Gene expression patterns obtained by quantitative real-time PCR (qRT-PCR) revealed differential temporal and spatial regulation of TaJAZ genes under multifarious abiotic stress treatments of high salinity, drought, cold and phytohormone. Among these, TaJAZ7, 8 and 12 were specifically expressed in the anther tissues of the thermosensitive genic male sterile (TGMS) wheat line BS366 and normal control wheat line Jing411. Compared with the gene expression patterns in the normal wheat line Jing411, TaJAZ7, 8 and 12 had different expression patterns in abnormally dehiscent anthers of BS366 at the heading stage 6, suggesting that specific up- or down-regulation of these genes might be associated with the abnormal anther dehiscence in TGMS wheat line. CONCLUSION: This study analyzed the size and composition of the JAZ gene family in wheat, and investigated stress responsive and differential tissue-specific expression profiles of each TaJAZ gene in TGMS wheat line BS366. In addition, we isolated 3 TaJAZ genes that would be more likely to be involved in the regulation of abnormal anther dehiscence in TGMS wheat line. In conclusion, the results of this study contributed some novel and detailed information about JAZ gene family in wheat, and also provided 3 potential candidate genes for improving the TGMS wheat line.

Evolution of the Aux/IAA Gene Family in Hexaploid Wheat.

The Aux/IAA (IAA) gene family, involved in the auxin signalling pathway, acts as an important regulator in plant growth and development. In this study, we explored the evolutionary trajectory of the IAA family in common wheat. The results showed ten pairs of paralogs among 34 TaIAA family members. Seven of the pairs might have undergone segmental duplication, and the other three pairs appear to have experienced tandem duplication. Except for TaIAA15-16, these duplication events occurred in the ancestral genomes before the divergence of Triticeae. After that point, two polyploidization events shaped the current TaIAA family consisting of three subgenomic copies. The structure or expression pattern of the TaIAA family begins to differentiate in the hexaploid genome, where TaIAAs in the D genome lost more genes (eight) and protein secondary structures (α1, α3 and ß5) than did the other two genomes. Expression analysis showed that six members of the TaIAA family were not expressed, and members such as TaIAA8, 15, 16, 28 and 33 exhibited tissue-specific expression patterns. In addition, three of the ten pairs of paralogs (TaIAA5-12, TaIAA15-16 and TaIAA29-30) showed similar expression patterns, and another five paralog pairs displayed differential expression patterns. Phylogenetic analysis showed that paralog pairs with high rates of evolution (ω > ω 0), particularly TaIAA15-16 and TaIAA29-30, experienced greater motif loss, with only zero to two interacting IAA proteins. In contrast, most paralogous genes with low ω, such as TaIAA5-12, had more complete motifs and higher degrees of interaction with other family members.

Molecular Mapping of the Stripe Rust Resistance Gene Yr69 on Wheat Chromosome 2AS.

Wheat is one of the major food crops in the world. Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an economically important disease that affects wheat worldwide. The discovery of novel resistance genes and the deployment of effectively resistant cultivars are important for the ongoing control of wheat stripe rust and the maintenance of the agricultural productivity of wheat. CH7086, a new stripe rust-resistant wheat introgression line, was selected by crossing susceptible cultivars with the resistant Thinopyrum ponticum-derived partial amphiploid Xiaoyan 7430. The resistance of CH7086 is effective against all current Chinese P. striiformis f. sp. tritici races. CH7086 was crossed with the stripe rust-susceptible cultivars to develop F1, F2, F3, and BC1 populations for genetic analysis. Segregation in the F2 and BC1 populations and F2:3 lines were tested for resistance against the P. striiformis f. sp. tritici race CYR32. This test showed that CH7086 carries a single dominant gene for stripe rust resistance, which was temporarily designated YrCH86. The closest of the eight simple sequence repeat (SSR) and expressed sequence tag-SSR markers flanking the locus were X2AS33, which is 1.9 cM distal, and Xmag3807, which is 3.1 cM proximal. The resistance gene and its polymorphic markers were placed in deletion bin 2AS-0.78-1.00 using the 'Chinese Spring' nullisomic-tetrasomic, ditelosomic, and deletion lines. The tests of both allelism and resistance specificity suggested that the resistance gene found in CH7086 was not Yr17, which was the only current formally named Yr gene on chromosome 2AS. Thus, YrCH86 appeared to be a new locus and was permanently designated Yr69.

Genome-wide identification and expression analysis of SBP-box gene family in Sorghum bicolor L.

SQUAMOSA PROMOTER BINDING PROTEIN-box (SBP-box) family genes encoding plant-specific transcription factors are involved in many aspects of crop genetic improvement such as yield, plant-type and stress-resistance. The SBP-box gene family have important practical applications. In this study, 18 SBP-box genes were identified from the reference genome of sorghum (Sorghum bicolor L.) using bioinformatics. These genes distributed on nine chromosomes while eight of them located in the segmental duplication region. Phylogenetic reconstruction resulted in six subfamilies of SBP-box genes, among which SbSBP12, SbSBP3 and SbSBP15 are orthologous to ZmLG1, ZmTGA1 and ZmUB2/3 in corn, respectively. RNA-seq data analysis indicated that SbSBP-box genes show the highest expression level in primordial inflorescences. Moreover, SbSBP9 and SbSBP17 exhibited a tissue specific expression in primordial inflorescences. The expression levels of SbSBP5, SbSBP8 and SbSBP18 were increased in response to exogenous ABA and PEG,indicating that SbSBP-box genes are involved in the defense response against abiotic stresses in sorghum. This research provides references for cloning important genes in SbSBP-box gene family. Genes identified in this study could be considered as candidate genes for genetic improvement of sorghum.

Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

Molecular characterization of a new wheat-Thinopyrum intermedium translocation line with resistance to powdery mildew and stripe rust.

A new wheat-Thinopyrum translocation line CH13-21 was selected from the progenies derived from a cross between wheat-Th. intermedium partial amphiploid TAI7047 and wheat line Mianyang11. CH13-21 was characterized by using genomic in situ hybridization (GISH), multicolor-GISH (mc-GISH), multicolor-fluorescence in situ hybridization (mc-FISH) and chromosome-specific molecular markers. When inoculated with stripe rust and powdery mildew isolates, CH13-21 displayed novel resistance to powdery mildew and stripe rust which inherited from its Thinopyrum parent. The chromosomal counting analyses indicated that CH13-21 has 42 chromosomes, with normal bivalent pairing at metaphase I of meiosis. GISH probed by Th. intermedium genomic DNA showed that CH13-21 contained a pair of wheat-Th. intermedium translocated chromosomes. Sequential mc-FISH analyses probed by pSc119.2 and pAs1 clearly revealed that chromosome arm 6BS of CH13-21 was replaced by Thinopyrum chromatin in the translocation chromosome. The molecular markers analysis further confirmed that the introduced Th. intermedium chromatin in CH13-21 belonged to the long arm of homoeologous group 6 chromosome. Therefore, CH13-21 was a new T6BS.6Ai#1L compensating Robertsonian translocation line. It concludes that CH13-21 is a new genetic resource for wheat breeding programs providing novel variation for disease resistances.

Identification of Salt-Stress-Responding Genes by Weighted Gene Correlation Network Analysis and Association Analysis in Wheat Leaves.

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.

RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots.

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.

Rapid identification and deployment of major genes for flowering time and awn traits in common wheat.

Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F2 population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F2 population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar "Ningmaizi119" and a winter wheat cultivar "Tabasco" with a diverse genetic background. It was found that the dominant Vrn-D1 allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F3 populations. It was also found that the dominant Ali-A1 allele for awnless trait in Tabasco or the recessive ali-A1 allele for awn trait in Ningmaizi119 was segregated in the F2 population. The allelic variation in the ALI-A1 gene relies not only on the DNA polymorphisms in the promoter but also on gene copy number, with one copy ali-A1 in Ningmaizi119 but two copies Ali-A1 in Tabasco based on RT-PCR results. According to wheat genome sequences, cultivar "Mattis" has two copies Ali-A1 and cultivar "Spelta" has four copies Ali-A in a chromosome that was uncharacterized (ChrUN), in addition to one copy on chromosome 5A. This study rapidly characterized the effects of the dominant Vrn-D1 allele and identified the haplotype of Ali-A1 in gene copy number in the F2 segregation population of common wheat will accelerate their deployment in cycling lines in breeding.

Genetic Incorporation of the Favorable Alleles for Three Genes Associated With Spikelet Development 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.

Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances.

It is well known that WRKY transcription factors play essential roles in plants' response to diverse stress responses, especially to drought and salt stresses. However, a full comprehensive analysis of this family in wheat is still missing. Here we used in silico analysis and identified 124 WRKY genes, including 294 homeologous copies from a high-quality reference genome of wheat (Triticum aestivum). We also found that the TaWRKY gene family did not undergo gene duplication rather than gene loss during the evolutionary process. The TaWRKY family members displayed different expression profiles under several abiotic stresses, indicating their unique functions in the mediation of particular responses. Furthermore, TaWRKY75-A was highly induced after polyethylene glycol and salt treatments. The ectopic expression of TaWRKY75-A in Arabidopsis enhanced drought and salt tolerance. A comparative transcriptome analysis demonstrated that TaWRKY75-A integrated jasmonic acid biosynthetic pathway and other potential metabolic pathways to increase drought and salt resistances in transgenic Arabidopsis. Our study provides valuable insights into the WRKY family in wheat and will generate a useful genetic resource for improving wheat breeding.

Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background.

Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.