# Identification of Genomic Regions Associated with Fusarium
## 3 Results
### GWAS for Resistance to FW  
In this study, a total of 29,945 high-quality SNPs were used for association analysis. Given a 620 Mb cowpea genome [18], the marker density in the whole genome reached 48/Mb. Based on the 29,945 SNPs genotype data, PCA analysis showed that 99 accessions were divided into two major clusters (Figure 3). The unrooted phylogenetic tree also showed that the population could be classified into two subgroups (Figure 4). These results were consistent with [PERSON] et al. (2017) [6], which analyzed the entire set of a mini-core collection comprising 299 accessions, indicating that the subgroups differentiation was highly correlated with pod length.  
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline \multirow{2}{*}{**Number**} & \multirow{2}{*}{**Variety**} & \multicolumn{4}{c}{**DI**} \\ \cline{3-5}  & & **2020 LFD** & **2020 VD** & **2021 LFD** & **2021 VD** \\ \hline D406 & G136 & 0.05 & 0.25 & 0.15 & / \\ D501 & X480 & 0.13 & 0.29 & 0.05 & 0.09 \\ D502 & X486 & 0.29 & 0.11 & 0.13 & 0.10 \\ D503 & X487 & 0.04 & 0.17 & 0.07 & 0.11 \\ D506 & X503 & 0.20 & 0.17 & 0.03 & 0.09 \\ D575 & X436 & 0.08 & 0.18 & 0.12 & 0.04 \\ D584 & X450 & 0.25 & 0.20 & 0.00 & 0.08 \\ \hline \hline \end{tabular}
\end{table}
Table 1: The seven accessions with resistance phenotypes at LFD and VD.  
Figure 2: The frequency distributions of LFD and VD.  
Using the 2020 phenotype data, 9 and 15 SNPs significantly associated with LFD and VD were detected, respectively (Figure 5). These SNPs were distributed on chromosomes 3, 4 and 6, explaining 0.20-3.80% of phenotypic variation. Using the 2021 phenotype data, 4 SNPs associated with LFD and 18 SNPs associated with VD were identified, distributed on chromosomes 3, 4, 5 and 9 and accounting for 5.91-13.26% of phenotypic variation. Of the detected SNPs, some formed clusters. For example, nine SNPs significantly associated with 2020 LFD were clustered in a 244.223 kb segment from 20,428,139 to 20,672,362 bp on chromosome 4; there are only 825 bp between the SNPs 2_18465 and 2_48662. Similarly, three SNPs significantly associated with 2021 LFD were located in an interval of 10.838 kb on chromosome 3. Previous studies showed that the LD decay distance of cowpea is about 350 kb [18], indicating that the SNPs in the same LD block may represent a single locus associated with FW resistance. For clarity, a final set of 3 significant SNPs associated with LFD and 7 SNPs associated with VD was reported after retaining only one representative locus with the highest LOD value in a same LD block (Table 2). Among these loci, no locus was detected simultaneously in the two years experiments, indicating that the FW resistance was greatly affected by the environment. Two significant SNPs, 2_01757 for 2021 LFD and 2_19764 for 2021 VD, were found to be apart by a distance of 108.477 kb within a same LD block, indicating that they may represent a same QTL or different alleles for the same gene, which also suggests that LFD and VD may be involved in the same pathway for FW responses. All the SNPs showed minor or moderate effects, which were consistent with [PERSON] et al. (2015) [10], indicating that cowpea FW resistance was controlled by multiple minor genes.  
Figure 4: Phylogenetic tree of 99 accessions.  
Figure 3: PCA plot of 99 materials. Each blue dot represents an accession.