Identification of Novel Quantitative Trait Loci Linked to Crown Rot Resistance in Spring Wheat

Genome-Wide Association Studies on Chinese Wheat Cultivars Reveal a Novel Fusarium Crown Rot Resistance Quantitative Trait Locus on Chromosome 3BL

Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum, has emerged as a new threat to wheat production and quality in North China. Genetic enhancement of wheat resistance to FCR remains the most effective approach for disease control. In this study, we phenotyped 435 Chinese wheat cultivars through FCR inoculation at the seedling stage in a greenhouse. Our findings revealed that only approximately 10.8% of the wheat germplasms displayed moderate or high resistance to FCR. A genome-wide association study (GWAS) using high-density 660K SNP led to the discovery of a novel quantitative trait locus on the long arm of chromosome 3B, designated as Qfcr.hebau-3BL. A total of 12 significantly associated SNPs were closely clustered within a 1.05 Mb physical interval. SNP-based molecular markers were developed to facilitate the practical application of Qfcr.hebau-3BL. Among the five candidate FCR resistance genes within the Qfcr.hebau-3BL, we focused on TraesCS3B02G307700, which encodes a protein kinase, due to its expression pattern. Functional validation revealed two transcripts, TaSTK1.1 and TaSTK1.2, with opposing roles in plant resistance to fungal disease. These findings provide insights into the genetic basis of FCR resistance in wheat and offer valuable resources for breeding resistant varieties.

Dissecting the genetic basis of Fusarium crown rot resistance in wheat by genome wide association study

KEY MESSAGE

A locus conferring Fusarium crown rot resistance was identified on chromosome arm 3DL through genome wide association study and further validated in two recombinant inbred lines populations. Fusarium crown rot (FCR) is a severe soil borne disease in many wheat growing regions of the world. In this study, we attempted to detect loci conferring FCR resistance through a new seedling inoculation assay. A total of 223 wheat accessions from different geography origins were used to assemble an association panel for GWAS analysis. Four genotypes including Heng 4332, Luwanmai, Pingan 998 and Yannong 24 showed stable resistance to FCR. A total of 54 SNPs associated with FCR resistance were identified. Among the 10 putative QTLs represented by these SNPs, seven QTLs on chromosome 2B, 3A, 3D, 4A, 7A and 7B were novel and were consistently detected in at least two of the three trials conducted. Qfcr.cau.3D-3, which was targeted by 38 SNPs clustered within a genomic region of approximately 5.57 Mb (609.12-614.69 Mb) on chromosome arm 3DL, was consistently detected in all the three trials. The effects of Qfcr.cau.3D-3 were further validated in two recombinant inbred line populations. The presence of this locus reduced FCR severity up to 21.55%. Interestingly, the collinear positions of sequences containing the four SNPs associated with two FCR loci (Qfcr.cau.3A and Qfcr.cau.3B) were within the regions of Qfcr.cau.3D-3, suggesting that genes underlying these three loci may be homologous. Our results provide useful information for improving FCR resistance in wheat.

Screening and Resistance Locus Identification of the Mutant fcrZ22 Resistant to Crown Rot Caused by Fusarium pseudograminearum

Crown rot caused by Fusarium pseudograminearum is a devastating wheat disease worldwide. In addition to yield losses, the fungi causing Fusarium crown rot (FCR) also deteriorate the quality and safety of food because of the production of mycotoxins. Planting resistant cultivars is an effective way to control FCR. However, most wheat cultivars are susceptible to FCR. Therefore, development of new sources and detection of loci for FCR resistance are necessary. In the present study, a resistant mutant, fcrZ22, was identified from an ethyl methane sulfonate (EMS)-mutagenized population of the cultivar Zhoumai 22, and then fcrZ22 was crossed with the wild type to produce an F2 population. Genetic analysis of the F2 population was carried out by the mixed inheritance model of major genes plus polygenes, and 20 resistant and 20 susceptible plants were selected to assemble mixed pools. Combining 660K SNP arrays, the resistance loci were detected by bulked segregant analysis. The resistance to FCR caused by F. pseudograminearum in the F2 population was in accordance with the "mixed model with two major genes of additive-epistasis effect + additive-dominant polygenes," and the heritability of the major gene was 0.92. Twenty-one loci were detected, which were located on 10 chromosomes, namely, 1B (1), 1D (1), 2A (3), 1B (1), 3A (3), 3B (3), 4A (2), 5A (2), 7A (3), and 7B (2). Among the 21 loci, eight were new loci for FCR resistance. This is the first report of detecting loci for FCR resistance from a mutant. The results of the present study provided excellent germplasm resources for breeding wheat cultivars with FCR resistance and laid the foundation for fine mapping of FCR resistance loci.

Identification of Genetic Resistance to the Crown and Root Rot Caused by Fusarium culmorum and Cereal Cyst Nematode (Heterodera filipjevi) in the Turkish Cereal Varieties

Soilborne pathogens associated with cereals cause significant yield losses throughout the world. Among soilborne pathogens Heterodera filipjevi and Fusarium culmorum are two main destructive causal agents that attack the roots and crowns of cereals and have been reported as the most prevalent species in Türkiye. A total of 245 Turkish cereal varieties consisting of wheat, oat, triticale and rye which were registered between 1931 to 2013; were tested for their resistance to Fusarium culmorum and Heterodera filipjevi. The varieties were screened under controlled and/or field conditions for two successive growing seasons. The bread wheat ‘Murat-1’ was the most resistant variety for both pathogens. The durum wheats ‘Yelken 2000’ and ‘Yılmaz 98’ were found the most promising varieties for resistance to F. culmorum and H. filipjevi, respectively. The triticale ‘Umranhanim’ ranked moderately resistant at adult plant stage while ‘Presto’ and ‘Melez 2001’ were ranked moderately resistant at seedling stage for Fusarium culmorum. The findings of this study are important for the global wheat breeding programs as those genotypes are still being used in crosses for new genotype development.

Genome-Wide Association Study of Root-Lesion Nematodes Pratylenchus Species and Crown Rot Fusarium culmorum in Bread Wheat

Triticum aestivum L., also known as common wheat, is affected by many biotic stresses. Root diseases are the most difficult to tackle due to the complexity of phenotypic evaluation and the lack of resistant sources compared to other biotic stress factors. Soil-borne pathogens such as the root-lesion nematodes caused by the Pratylenchus species and crown rot caused by various Fusarium species are major wheat root diseases, causing substantial yield losses globally. A set of 189 advanced spring bread wheat lines obtained from the International Maize and Wheat Improvement Center (CIMMYT) were genotyped with 4056 single nucleotide polymorphisms (SNP) markers and screened for root-lesion nematodes and crown rot resistance. Population structure revealed that the genotypes could be divided into five subpopulations. Genome-Wide Association Studies were carried out for both resistances to Pratylenchus and Fusarium species. Based on our results, 11 different SNPs on chromosomes 1A, 1B, 2A, 3A, 4A, 5B, and 5D were significantly associated with root-lesion nematode resistance. Seven markers demonstrated association with P. neglectus, while the remaining four were linked to P. thornei resistance. In the case of crown rot, eight different markers on chromosomes 1A, 2B, 3A, 4B, 5B, and 7D were associated with Fusarium crown rot resistance. Identification and screening of root diseases is a challenging task; therefore, the newly identified resistant sources/genotypes could be exploited by breeders to be incorporated in breeding programs. The use of the identified markers in marker-assisted selection could enhance the selection process and cultivar development with root-lesion nematode and crown rot resistance.

Detecting Crown Rot Disease in Wheat in Controlled Environment Conditions Using Digital Color Imaging and Machine Learning

Crown rot is one of the major stubble soil fungal diseases that bring significant yield loss to the cereal industry. The most effective crown rot management approach is removal of infected crop residue from fields and rotation of nonhost crops. However, disease screening is challenging as there are no clear visible symptoms on upper stems and leaves at early growth stages. The current manual screening method requires experts to observe the crown and roots of plants to detect disease, which is time-consuming, subjective, labor-intensive, and costly. As digital color imaging has the advantages of low cost and easy use, it has a high potential to be an economical solution for crown rot detection. In this research, a crown rot disease detection method was developed using a smartphone camera and machine learning technologies. Four common wheat varieties were grown in greenhouse conditions with a controlled environment, and all infected group plants were infected with crown rot without the presence of other plant diseases. We used a smartphone to take digital color images of the lower stems of plants. Using imaging processing techniques and a support vector machine algorithm, we successfully distinguished infected and healthy plants as early as 14 days after disease infection. The results provide a vital first step toward developing a digital color imaging phenotyping platform for crown rot detection to enable the management of crown rot disease effectively. As an easy-access phenotyping method, this method could provide support for researchers to develop an efficiency and economic disease screening method in field conditions.

Transgene pyramiding in wheat: Combination of deoxynivalenol detoxification with inhibition of cell wall degrading enzymes to contrast Fusarium Head Blight and Crown Rot

Fusarium Head Blight (FHB) and Crown Rot (FCR) are major diseases of wheat crops, causing extensive damages and mycotoxin contamination. In this work, we investigated the possibility to improve resistance to either or both diseases by combining different resistance mechanisms. To this aim, we stacked in the same wheat genotype transgenes controlling the DON-to-D3G conversion by specific UDP-glucosyltransferases (UGT) and the inhibition of cell wall degrading enzymes (CWDEs) by glycosidase inhibitors. We obtained: i) a durum wheat UGT+PMEI double-transgenic line constitutively expressing the HvUGT13248 and AcPMEI genes, coding for a barley UGT and a kiwi pectin methylesterase inhibitor, respectively; ii) a bread wheat UGT+PGIP line, expressing in floral tissues the HvUGT13248 gene and constitutively the PvPGIP2 gene, coding for a bean polygalacturonase inhibiting protein. We observed that both UGT+PMEI and UGT+PGIP plants exhibited increased resistance against Fusarium graminearum in FHB, further reducing by 10-20 % FHB symptoms as compared to the lines carrying the individual transgenes, and of up to 50 % as compared to wild-type plants. On the other hand, double-transgenic UGT+PMEI seedlings exhibited similar FCR symptoms as the UGT single transgenic line after infection with F. culmorum, indicating no contribution of the PMEI transgene to FCR resistance. This result is also supported by the inability of AcPMEI or PvPGIP2, constitutively expressed in durum wheat transgenic lines, to counteract F. graminearum in FCR. We also verified that F. graminearum produces PG and PME activity on infected wheat crown. We conclude that CWDEs inhibition combined with UGT-based DON detoxification contribute in an additive manner to limiting F. graminearum in FHB. Conversely, UGT-based DON detoxification is the only mechanism contributing to resistance observed against FCR. Indeed, the reinforcement of pectin does not enhance resistance against FCR.

Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.

Lessons from a GWAS study of a wheat pre-breeding program: pyramiding resistance alleles to Fusarium crown rot

Much has been published on QTL detection for complex traits using bi-parental and multi-parental crosses (linkage analysis) or diversity panels (GWAS studies). While successful for detection, transferability of results to real applications has proven more difficult. Here, we combined a QTL detection approach using a pre-breeding populations which utilized intensive phenotypic selection for the target trait across multiple plant generations, combined with rapid generation turnover (i.e. "speed breeding") to allow cycling of multiple plant generations each year. The reasoning is that QTL mapping information would complement the selection process by identifying the genome regions under selection within the relevant germplasm. Questions to answer were the location of the genomic regions determining response to selection and the origin of the favourable alleles within the pedigree. We used data from a pre-breeding program that aimed at pyramiding different resistance sources to Fusarium crown rot into elite (but susceptible) wheat backgrounds. The population resulted from a complex backcrossing scheme involving multiple resistance donors and multiple elite backgrounds, akin to a MAGIC population (985 genotypes in total, with founders, and two major offspring layers within the pedigree). A significant increase in the resistance level was observed (i.e. a positive response to selection) after the selection process, and 17 regions significantly associated with that response were identified using a GWAS approach. Those regions included known QTL as well as potentially novel regions contributing resistance to Fusarium crown rot. In addition, we were able to trace back the sources of the favourable alleles for each QTL. We demonstrate that QTL detection using breeding populations under selection for the target trait can identify QTL controlling the target trait and that the frequency of the favourable alleles was increased as a response to selection, thereby validating the QTL detected. This is a valuable opportunistic approach that can provide QTL information that is more easily transferred to breeding applications.

Genome-Wide Association Study of Tan Spot Resistance in a Hexaploid Wheat Collection From Kazakhstan

Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat in Kazakhstan with reported yield losses as high as 50% during epidemic years. Here, we report the evaluation of a collection of 191 hexaploid spring and winter wheat lines for tan spot resistance and its underlying genetic architecture using genome-wide association study (GWAS). Our wheat collection comprised candidate varieties from Kazakhstan, Russia, and CIMMYT. It was genotyped using the DArTseq technology and phenotyped for resistance to tan spot at seedling and adult plant stages in Kazakhstan. DArTseq SNPs revealed high genetic diversity (average polymorphic information content = 0.33) in the panel and genome-wide linkage disequilibrium decay at 22 Mb (threshold r² = 0.1). Principal component analysis revealed a clear separation of Eurasian germplasm from CIMMYT and IWWIP lines. GWAS identified 34 marker-trait associations (MTA) for resistance to tan spot and the amount of phenotypic variation explained by these MTA ranged from 4% to 13.7%. Our results suggest the existence of novel valuable resistant alleles on chromosomes 3BS, and 5DL and 6AL for resistance to Race 1 and Race 5, respectively, in addition to known genes tsn1 and tsc2. On chromosome 6AL, a genomic region spanning 3 Mb was identified conferring resistance to both Race 1 and Race 5. Epistatic interaction of associated loci was revealed on chromosomes 1B, 5B, 7B, 5A, and 6A contributing to additional variation of 3.2–11.7%. Twenty-five lines with the best allele combinations of SNPs associated with resistance to both races have been identified as candidates for future variety release and breeding. The results of the present study will be further validated in other independent genetic backgrounds to be able to use markers in breeding.

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm

This study was initiated to identify genomic regions conferring resistance to Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). A GWAS of 6,382 high-quality DArTseq SNPs revealed 15 significant SNPs (P-value <10^-3) on chromosomes 2D, 3B, 4D and 7B that were associated with KB resistance in individual years. In particular, two SNPs (chromosome 4D) had the maximum R² values: SNP 1114200 | F | 0-63:T > C at 1.571 cM and R² of 12.49% and SNP 1103052 | F | 0-61:C > A at 1.574 cM and R² of 9.02%. These two SNPs displayed strong linkage disequilibrium (LD). An in silico analysis of SNPs on chromosome 4D identified two candidate gene hits, TraesCS4D02G352200 (TaNox8; an NADPH oxidase) and TraesCS4D02G350300 (a rhomboid-like protein belonging to family S54), with SNPs 1103052 | F | 0-61:C > A and 1101835 | F | 0-5:C > A, respectively, both of which function in biotic stress tolerance. The epistatic interaction analysis revealed significant interactions among 4D and 7B loci. A pedigree analysis of confirmed resistant PBLs revealed that Aegilops species is one of the parents and contributed the D genome in these resistant PBLs. These identified lines can be crossed with any elite cultivar across the globe to incorporate novel KB resistance identified on 4B.

Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat

Fusarium crown rot (FCR) is one of the most important diseases of wheat (Triticum aestivum L.). FCR is mainly caused by the fungal pathogens Fusarium culmorum and F. pseudograminearum. In order to identify new sources of resistance to FCR and to dissect the complexity of FCR resistance, a panel of 161 wheat accessions was phenotyped under growth room (GR) and greenhouse conditions (GH). Analysis of variance showed significant differences in crown rot development among wheat accessions and high heritability of genotype-environment interactions for GR (0.96) and GH (0.91). Mixed linear model analysis revealed seven novel quantitative trait loci (QTLs) linked to F. culmorum on chromosomes 2AL, 3AS, 4BS, 5BS, 5DS, 5DL and 6DS for GR and eight QTLs on chromosomes on 3AS, 3BS, 3DL, 4BS (2), 5BS, 6BS and 6BL for GH. Total phenotypic variances (R²) explained by the QTLs linked to GR and GH were 48% and 59%, respectively. In addition, five favorable epistasis interactions among the QTLs were detected for both GR and GH with and without main effects. Epistatic interaction contributed additional variation up to 21% under GR and 7% under GH indicating strong effects of environment on the expression of QTLs. Our results revealed FCR resistance responses in wheat to be complex and controlled by multiple QTLs.

Genome-Wide Association Study for Multiple Biotic Stress Resistance in Synthetic Hexaploid Wheat

Genetic resistance against biotic stress is a major goal in many wheat breeding programs. However, modern wheat cultivars have a limited genetic variation for disease and pest resistance and there is always a possibility of the evolution of new diseases and pests to overcome previously identified resistance genes. A total of 125 synthetic hexaploid wheats (SHWs; 2n = 6x = 42, AABBDD, Triticum aestivum L.) were characterized for resistance to fungal pathogens that cause wheat rusts (leaf; Puccinia triticina, stem; P. graminis f.sp. tritici, and stripe; P. striiformis f.sp. tritici) and crown rot (Fusarium spp.); cereal cyst nematode (Heterodera spp.); and Hessian fly (Mayetiola destructor). A wide range of genetic variation was observed among SHWs for multiple (two to five) biotic stresses and 17 SHWs that were resistant to more than two stresses. The genomic regions and potential candidate genes conferring resistance to these biotic stresses were identified from a genome-wide association study (GWAS). This GWAS study identified 124 significant marker-trait associations (MTAs) for multiple biotic stresses and 33 of these were found within genes. Furthermore, 16 of the 33 MTAs present within genes had annotations suggesting their potential role in disease resistance. These results will be valuable for pyramiding novel genes/genomic regions conferring resistance to multiple biotic stresses from SHWs into elite bread wheat cultivars and providing further insights on a wide range of stress resistance in wheat.

Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat

BACKGROUND

Fusarium crown rot (FCR) is a severe and chronic disease in common wheat and is able to cause serious yield loss and health problems to human and livestock.

RESULTS

Here, 234 Chinese wheat cultivars were evaluated in four greenhouse experiments for FCR resistance and genome-wide association studies (GWAS) were performed using the wheat 660 K genotyping assay. The results indicated that most cultivars evaluated showed FCR disease index (DI) of 40-60, while some cultivars showed stably good FCR resistance (DI < 30). GWAS identified 286 SNPs to be significantly associated with FCR resistance, of which 266, 6 and 8 were distributed on chromosomes 6A, 6B and 6D, respectively. The significant SNPs on 6A were located in a 7.0-Mb region containing 51 annotated genes. On the other hand, QTL mapping using a bi-parental population derived from UC1110 and PI610750 detected three QTLs on chromosomes 6A (explaining 7.77-10.17% of phenotypic variation), 2D (7.15-9.29%) and 2A (5.24-6.92%). The 6A QTL in the UC1110/PI610750 population falls into the same chromosomal region as those detected from GWAS, demonstrating its importance in Chinese materials for FCR resistance.

CONCLUSION

This study could provide useful information for utilization of FCR-resistant wheat germplasm and further understanding of molecular and genetics basis of FCR resistance in common wheat.