Weigang Xu

Powdery mildew is a devastating fungal disease of wheat. Aegilops caudata , a wild relative of common wheat, is highly resistant to powdery mildew. However, the presence of chromosomal structural variations and the absence of a reference genome for Ae. caudata have significantly hindered the cloning and breeding application of resistance genes from this species. Here, we report the cloning of powdery mildew resistance gene Pm7C from Ae. caudata by integrating map-based cloning, collinearity and Pm7C -direct donor transcriptome analysis. Pm7C encodes a nucleotide-binding leucine-rich repeat (NLR) protein containing two distinct LRR domains. The resistance function of Pm7C is validated by mutagenesis, gene silencing and transgenic assay. The coiled coil (CC) domain of Pm7C induces cell death and self-associates. Additionally, we develop a set of Pm7C introgression lines and a Pm7C- specific diagnostic molecular marker. Cloning of Pm7C will shed light on NLR protein-mediated disease resistance and accelerate its deployment in wheat breeding.

Breeding wheat varieties with a high nitrogen use efficiency (NUE) reduces both production costs and threats to the ecological environment. Here, using candidate-gene and genome-wide association studies, we identify TaNPF7.6-A1 as a positive regulator of NUE in wheat. A widely conserved polymorphism in the coding region of TaNPF7.6-A1 produces allele TaNPF7.6-A1^mod with a higher transcription level and nitrate transport activity than TaNPF7.6-A1^lan, resulting in a greater NUE. We also reveal the mechanism by which TaEIL3-TaJAZ1-TaNPF7.6-A1 regulates NUE in wheat. TaNPF7.6-A1^mod interacts more strongly with TaJAZ1 than TaNPF7.6-A1^lan and promotes the retention of nuclear-localized TaJAZ1 in the cytoplasm. TaJAZ1 interacts with TaEIL3 and represses TaEIL3, binding to the TaNPF7.6-A1^mod promoter, influencing allele expression and causing phenotypic differences. TaNPF7.6-A1^mod also shows significant geographical distribution aggregation globally and undergoes continuous positive selection during the breeding process. Overall, this study provides molecular and evolutionary insights into the regulation of NUE.

Pre-harvest sprouting (PHS) severely impacts white-grain wheat production. To uncover its genetic basis, we conducted a genome-wide association study (GWAS) across 273 wheat varieties and identified 41 quantitative trait loci (QTLs) for PHS resistance. Among these, a major and stable QTL on chromosome 6A, designated QTL15, was detected across all tested environments and accounted for up to 19.12% of the phenotypic variance. Integrated analysis of RNA-seq data and sequence variation within the QTL15 interval pinpointed TaIAA10-6A, an auxin-responsive Aux/IAA family gene, as the candidate. An elite haplotype, TaIAA10-6A-M, featuring an 18-bp deletion and a 21-bp substitution in its coding sequence, was strongly correlated with enhanced PHS resistance. Intriguingly, overexpressing TaIAA10-6A-M allele significantly increased PHS susceptibility, demonstrating that TaIAA10-6A encodes a dose-dependent PHS-promoting protein. Therefore, the TaIAA10-6A-M haplotype confers resistance by acting as a functionally attenuated allele that reduces PHS-promoting signal. A co-dominant CAPS marker, phs-TaIAA10-6A-M, was also developed and validated for its tight association with PHS resistance. Overall, this study not only elucidates a novel auxin-mediated regulatory mechanism for PHS in wheat but also provides a valuable gene resource for marker-assisted breeding of PHS-resistant white-grain wheat varieties.

小麦（Triticum aestivum L.）是全球最重要的粮食作物之一，为人类提供约20%的膳食能量和25%的蛋白质。普通小麦是异源六倍体（AABBDD, 2n = 6x = 42），由A、B和D三套亚基因组组成，分别来源于三个不同的二倍体祖先物种。小麦起源于西亚新月沃地一个狭小的区域，在短短的一万年间，驯化后迅速从一地区向全世界传播，发展为全球种植面积最广的主粮作物，这其中最关键因素是普通小麦具有多倍体优势、更广的环境适应性与优良的加工品质。多倍体小麦这一特性一直是进化生物学、基因组学、遗传学和作物遗传育种学领域关注的科学问题[1~5]。而在生产实践上，随着全球气候变暖加剧，土地盐碱化、沙漠化及其他自然灾害频发，解析这一科学问题显得更加紧迫和重要。近日，河南大学宋纯鹏教授课题组发表的题为“Horizontally acquired CSP genes contribute to wheat adaptation and improvement”研究论文中[6]，首次报道了主粮作物小麦中来源于细菌的水平基因转移（Horizontal Gene Transfer, HGT）及其生物学功能，为这一重要科学问题研究提供了全新的研究思路。该研究发现，一类来源于原核生物的冷激蛋白CSP（Cold Shock Protein）基因，通过水平基因转移到主粮作物小麦及小麦族之中并在长期的进化、驯化与品种改良过程中被保留下来。该基因在小麦族中不仅具有良好的遗传稳定性，同时显著提升了现代六倍体小麦的环境适应性。同时，超表达该基因可同样提高水稻的抗逆能力和产量，进一步显示其在优化作物环境适应性方面的巨大潜力。该研究不仅深化了学界对六倍体小麦广泛适应性遗传基础的认知，更为未来利用现代转基因工程与合成生物学技术，开展作物育种与改良，提供全新的技术思路和遗传资源。

Summary: Heat stress is a major factor limiting crop yield, a challenge intensified by climate change. Initial findings indicate that BES1/BZR1 may use heat shock to regulate plant thermal adaptability independently of BIN2‐mediated brassinosteroid signalling, although the exact molecular mechanism remains unclear. In this study, we identified TaBZR2, a wheat gene whose expression showed a strong positive correlation with heat stress tolerance, based on transcriptome analysis of heat‐tolerant wheat cultivars. Overexpression of TaBZR2 enhanced heat stress tolerance, while RNA interference of TaBZR2 reduced it. Further analysis revealed that TaBZR2 interacts with and is phosphorylated by wheat somatic embryogenesis receptor‐like kinase 2 (TaSERL2). Overexpression of TaSERL2 reduced heat stress tolerance by promoting TaBZR2 degradation and inhibiting its regulation of wheat heat stress response genes. However, heat stress reduced the phosphorylation levels of both TaSERL2 and TaBZR2, lessening TaSERL2's inhibitory effect on TaBZR2 and enhancing the stability of TaBZR2. These results reveal that the TaSERL2‐TaBZR2 module negatively regulates plant heat stress tolerance. This study expands the current model of heat stress responses and provides evidence for the role of BES1/BZR1 in heat stress regulation independent of brassinosteroid signalling.

The PHR gene is the core transcription factor in the phosphorus signaling regulatory system, responsible for initiating the adaptive response of downstream parts to phosphorus starvation. At the early stage, the transgenic OsPHR2 wheat pure lines with high phosphorus efficiency were obtained, but the molecular mechanism of OsPHR2 improving the phosphorus absorption and utilization efficiency of wheat is still unclear. In order to reveal the molecular mechanism of OsPHR2 improving the phosphorus uptake and utilization efficiency in wheat, transgenic OsPHR2 wheat pure line with high phosphorus efficiency earlier as the experimental material in this study. Transgenic OsPHR2 wheat and the control were treated with low phosphorus stress when they grew to 4 leaves and 1 heart in hydroponics experiment. Transgenic OsPHR2 wheat and control under low phosphorus stress for 0, 6, 24, and 72 h were used for transcriptomes analysis by RNA-seq. The differentially expression genes (DEGs) in roots and leaves of transgenic wheat and control were analyzed. There were 22 common DEGs in the roots of transgenic wheat and control under low phosphorus stress for 0, 6, 24, and 72 h, and there were nine common DEGs in the leaves under four treatments. The functional and pathway enrichments of differentially expressed genes in roots and leaves were also performed by GO and KEGG analysis. The result showed that the number of DEGs in the root of transgenic wheat and control was the highest under low phosphorus stress for 0 h, followed by 6 h. GO and KEGG enrichment analysis suggested that DEGs were mainly clustered into biological processes such as glucose metabolism, phenylpropanoid biosynthesis, and molecular functions such as nutrient storage activity, ATPase activity, etc. The number of DEGs in the leaves of transgenic wheat and the control was the highest under low phosphorus stress for 72 h. DEGs were mainly clustered into biological processes such as glucose metabolism, organic acid biosynthesis, as well as molecular functions related to glycosyltransferase activity and cellulose synthase activity. Compared with the control, the key enzyme genes of the defense system such as heme peroxidase and glutathione S-transferase in the root of the transgenic line OsT5-28, as well as the trisphosphate transporter family genes in the leaf were up-regulated before and after low phosphorus stresses. The response of transgenic OsPHR2 wheat to low phosphorus stress was different from that of the control. Transgenic wheat had stronger phosphorus absorption and utilization ability than the control under low phosphorus stress, mainly because OsPHR2 regulated the relative expression level of related genes in wheat.

Background: Nitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study. Results: In this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r² > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses. Conclusions: This study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.

Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat.Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding.Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes.Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.

Fusarium head blight (FHB) is a destructive wheat disease worldwide and significantly affects grain yield and quality in wheat. To understand the genetic basis underlying type II FHB resistance in two elite wheat cultivars—Yangmai 4 (YM4) and Yangmai 5 (YM5)—quantitative trait loci (QTL) mapping was conducted in two recombinant inbred line (RIL) populations derived from the crosses of YM4 and YM5 with susceptible cultivar Yanzhan 1 (YZ1), respectively. A survey with markers linked to Fhb1, Fhb2, Fhb4, and Fhb5 in landrace Wangshuibai indicated the nonexistence of these known FHB resistance genes or QTL in YM4, YM5, and YZ1. One overlapped resistance QTL was identified in both RIL populations (namely, QFhb.Y4.2D/QFhb.Y5.2D) with a large effect on FHB resistance. One novel resistance QTL (QFhb.Y4.5A) mapped on chromosome 5A was detected only in the YM4/YZ1 population. The resistance alleles of both QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A did not increase the plant height and did not significantly affect the heading date and flowering date. Kompetitive allele-specific PCR markers for QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A had been developed to verify in an additional set of 244 geographically diverse cultivars or lines. Pyramiding of the two resistance alleles decreased the percentage of symptomatic spikelets by 51.77% relative to the cultivars or lines without these two resistance alleles. QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A were shown to be useful alternatives in FHB resistance breeding programs. The results will facilitate marker-assisted selection for introgression of the favorable alleles for improving FHB resistance in breeding programs.