Fusarium crown rot (FCR), caused by the fungal genus Fusarium, is a severe soil-borne disease of wheat (Triticum aestivum) worldwide. In this study, we identified five quantitative trait loci (QTL) associated with FCR resistance on chromosomes 3A, 3B, 4B (two QTL), and 6A using a population of 128 F₇ recombinant inbred lines (RILs) derived from a cross between the two Chinese cultivars 04zhong 36 and Jinxiu 21. Of these QTL, two major QTL, QFcr.cau-3A and QFcr.cau-4B.1, were stably detected across multiple trials and explained 14.06% and 18.09%, respectively, of the phenotypic variance based on best linear unbiased prediction (BLUP) data. The resistance alleles at these two loci were derived from the parental lines 04zhong36 (QFcr.cau-3A) and Jinxiu 21 (QFcr.cau-4B.1), respectively. We confirmed the effects and stability of QFcr.cau-3A and QFcr.cau-4B.1 in an independent RIL population and in a collection of wheat accessions, respectively. Additionally, we detected a major and stable QTL for plant height, QPh.cau-4B, that overlapped with QFcr.cau-4B.1. The allele of QPh.cau-4B conferring tallness was from Jinxiu 21. Conditional QTL mapping indicated that although QFcr.cau-4B.1 and QPh.cau-4B showed significant interactions, the effect of QFcr.cau-4B.1 remained significant after the effects of plant height were removed. Field inoculation experiments with the 60 RILs showing the greatest sensitivity or resistance to FCR at the seedling stage detected a significant and positive correlation between seedling and adult plant resistance (correlation coefficient = 0.71). The confidence intervals for QFcr.cau-3A and QFcr.cau-4B.1 contain 264 and 240 high-confidence genes, respectively. Based on gene annotation, sequence variation, and expression patterns, three genes (TraesCS3A02G373300, TraesCS3A02G376500, and TraesCS4B02G222600) were considered as potential candidates for QFcr.cau-3A and QFcr.cau-4B.1. Our results provide valuable resources for the cloning of FCR resistance loci that can be utilized in FCR resistance breeding programs.

Fusarium crown rot (FCR) is a soilborne disease causing severe yield losses in many wheat-growing areas of the world. Diseased plants show browning and necrosis of roots and stems causing white heads at maturity. Little is known about the molecular processes employed by wheat roots to respond to the disease. We characterized morphological, transcriptional and hormonal changes in wheat seedling roots following challenge with Fusarium pseudograminearum (Fp), the main pathogen of FCR. The pathogen inhibited root development to various extents depending on plants’ resistance level. Many genes responsive to FCR infection in wheat roots were enriched in plant hormone pathways. The contents of compounds involved in biosynthesis and metabolism of jasmonic acid, salicylic acid, cytokinin and auxin were drastically changed in roots at five days post-inoculation. Presoaking seeds in methyl jasmonate for 24 h promoted FCR resistance, whereas presoaking with cytokinin 6-benzylaminopurine made plants more susceptible. Overexpression of TaOPR3, a gene involved in jasmonic acid biosynthesis, enhanced plant resistance as well as root and shoot growth during infection.

Wheat awns contribute to photosynthesis and grain production. In this study, an F₂ population and F_2:3 families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20 (SY20) were used to identify loci associated with awn length. Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL. Five genes were in the interval, including the recently cloned awn inhibitor B1. Although a single copy of the B1 gene was detected in 7D12, SY20 carried five copies of the gene. Increased copy number of B1 in SY20 enhanced gene expression. Based on sequence variation among the promoter regions of five B1 gene copies in SY20, two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions. All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene, whereas 15 randomly selected awned wheats carried only one copy. These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

Fusarium crown rot (FCR), caused by Fusarium spp., is a chronic and severe plant disease worldwide. In the last years, the incidence and severity of FCR in China has increased to the point that it is now considered a threat to local wheat crops. In this study, for the first time, the metabolites and transcripts responsive to FCR infection in the partial resistant wheat cultivar 04 Zhong 36 (04z36) and susceptible cultivar Xinmai 26 (XM) were investigated and compared at 20 and 25 days post inoculation (dpi). A total of 443 metabolites were detected, of which 102 were significantly changed because of pathogen colonization. Most of these 102 metabolites belonged to the flavonoid, phenolic acid, amino acid and derivative classes. Some metabolites, such as proline betaine, lauric acid, ribitol, and arabitol, were stably induced by Fusarium pseudograminearum (Fp) infection at two time points and may have important roles in FCR resistance. In line with the reduced seedling height of 04z36 and XM plants, RNA-seq analysis revealed that FCR infection significantly affected the photosynthesis activities in two cultivars. Furthermore, 15 jasmonate ZIM-domain genes (JAZ) in the significantly enriched ‘regulation of jasmonic acid mediated signaling pathway’ in 04z36 were down-regulated. The down-regulation of these JAZ genes in 04z36 may cause a strong activation of the jasmonate signaling pathway. Based on combined data from gene expression and metabolite profiles, two metabolites, benzoxazolin-2-one (BOA) and 6-methoxy-benzoxazolin-2-one (MBOA), involved in the benzoxazinoid-biosynthesis pathway, were tested for their effects on FCR resistance. Both BOA and MBOA significantly reduced fungal growth in vitro and in vivo, and, thus, a higher content of BOA and MBOA in 04z36 may contribute to FCR resistance. Above all, the current analysis extends our understanding of the molecular mechanisms of FCR resistance/susceptibility in wheat and will benefit further efforts for the genetic improvement of disease resistance.