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

Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study

BACKGROUND

Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers.

RESULTS

In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill.

CONCLUSION

In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.

A novel QTL conferring Fusarium crown rot resistance on chromosome 2A in a wheat EMS mutant

KEY MESSAGE

A novel QTL on chromosome 2A for Fusarium crown rot resistance was identified and validated in wheat. Fusarium crown rot (FCR) is a fungal disease that causes significant yield losses in many cereal growing regions in the world. In this study, genetic analysis was conducted for a wheat EMS mutant C549 which showed stable resistance to FCR at seedling stage. A total of 10 QTL were detected on chromosomes 1A, 2A, 3B, 4A, 6B, and 7B using a population of 138 F7 recombinant inbred lines (RILs) derived from a cross between C549 and a Chinese germplasm 3642. A novel locus Qfcr.cau-2A, which accounted for up to 24.42% of the phenotypic variation with a LOD value of 12.78, was consistently detected across all six trials conducted. Furthermore, possible effects of heading date (HD) and plant height on FCR severity were also investigated in the mapping population. While plant height had no effects on FCR resistance, a weak and negative association between FCR resistance and HD was observed. A QTL for HD (Qhd.cau-2A.2) was coincident with Qfcr.cau-2A. Conditional QTL mapping indicated that although Qfcr.cau-2A and Qhd.cau-2A.2 had significant interactions, Qfcr.cau-2A remained significant after the effects of HD was removed. It is unlikely that genes underlying these two loci are same. Nevertheless, the stable expression of Qfcr.cau-2A in the validation population of 148 F7 RILs developed between C549 and its wild parent Chuannong 16 demonstrated the potential value of this locus in FCR resistance breeding programs.

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.

GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates

Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C₃ crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature-sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome-wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.

An Improved Inoculation Method to Detect Wheat and Barley Genotypes for Resistance to Fusarium Crown Rot

Fusarium crown rot (FCR), caused by Fusarium species, is a serious soilborne fungal disease in many wheat growing regions in the world. A reliable FCR assessment method is essential for germplasm screening and host resistance studies. Here, we report a new assay in which we inoculated wheat seedlings grown in a glasshouse for FCR by injecting spore suspensions into the seedling stems. The effects of inoculum concentration and injection time points on disease severity were investigated. Of different treatments, the injection of 10⁷ macroconidia/ml suspension at one leaf and one heart stage gave best results. A collection of 92 emmer-derived hexaploid bread wheats, 43 barley germplasms, and four wheat genotypes with known resistance levels to FCR was used to validate this new method. Repeatability of the two trials in the validation experiments was high (r = 0.97, P < 0.01). Two emmer-derived hexaploid bread wheat and three Chinese barley germplasms showed consistent resistance to FCR in multiple rounds of selection. The short timeframe of this assay for phenotypic screening makes it a valuable tool to eliminate germplasms with undesirable susceptibility to FCR at seedling stage before costly field assays.

Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies

Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat

Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.