Screening of Resistance Germplasm Resources and Genome-wide Association Study of Fusarium Wilt in Common Bean

doi:10.11983/CBB22149

Abstract

Abstract: Fusarium wilt is one of the main diseases that seriously restrict the yield of common bean in China. In this study, the hypocotyl double hole injection method was used to identify the resistance of 601 common bean germplasm resources to fusarium wilt, and 4 highly resistance materials were screened out. Based on 3 765 456 single nucleotide polymorphisms (SNPs) distributed on the whole genome, the genome-wide association study was conducted with P<1×10^-5 as the threshold. A total of 57 significant SNPs were detected, which are distributed on chromosomes 1, 2, 6, 8, and 11 respectively. A total of 8 significant associated regions were obtained, of which region 1 on chromosome 1 contained up to 48 SNPs and the most significant SNP P value was 2.18E-07. Furthermore, 186 genes were detected in 8 significant association regions, of which 157 were annotated genes, including encoding peroxidase, disease resistance protein, transcription factor and protein kinase genes. Combing KEGG enrichment analysis and homology comparison, 9 candidate genes were identified that might be related to resistance.

Key words: common bean, fusarium wilt, genome-wide association study, resistance gene/germplasm resources

Yuan Li, Yujie Chang, Lanfen Wang, Shumin Wang, Jing Wu. Screening of Resistance Germplasm Resources and Genome-wide Association Study of Fusarium Wilt in Common Bean[J]. Chinese Bulletin of Botany, 2023, 58(1): 51-61.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22149

https://www.chinbullbotany.com/EN/Y2023/V58/I1/51

Figures/Tables 10

Figure 1 Common bean vascular bundle lesions of different grades 0, 1, 3, 5, 7 and 9 represent the criteria for disease classification. Bar=4 cm

Table 1 Disease grading standard of common bean fusarium wilt inoculated by hypocotyl double-hole injection

Rating scale	System description
0	No symptom
1	<20% lesions or discoloration of hypocotyledonary axis
3	20%-50% lesions or some discoloration of hypocotyledonary axis
5	50%-100% lesions or heavy discoloration of hypocotyledonary axis
7	>100% lesions or severe discoloration of hypo- cotyledonary axis
9	Plants wilted and died

Figure 2 Frequency distribution histogram and normal distribution of the lesion degree

Table 2 Phenotype description of fusarium wilt resistance levels in natural populations of common bean

Mean	Max	Min	Standard deviation	Skewness	Kurtosis
0.65	1.00	0.18	0.19	-0.10	-0.62

Figure 3 Distribution of common bean germplasm resources for resistance to fusarium wilt HR: Highly resistant; MR: Medium resistant; I: Intermediate; MS: Medium susceptible; HS: Highly susceptible

Figure 4 Genome-wide association study of fusarium wilt in common bean (A) Manhattan plots; (B) QQ plots; (C) Local Manhattan plot of the Region 1

Table 3 Loci related with common bean fusarium wilt by genome-wide association study

Region	Chr.	Interval location^a	P-value
1	1	2583702-2807552	2.18E-07
2	1	50017907-50231907	4.11E-06
3	2	26253984-26467984	5.72E-06
4	2	29642890-29856890	7.61E-06
5	6	26400983-26614983	8.82E-06
6	8	58863473-59077488	5.40E-06
7	11	46491343-46705343	6.48E-06
8	11	49598097-49814082	7.73E-06

Table 4 Candidate genes and annotation

Gene ID	Chr.	Start base-end base^a (bp)	Predicted function
Phvul.001G240400	1	50026833-50031313	RNI-like superfamily protein
Phvul.001G241500	1	50126351-50130393	Transmembrane amino acid transporter family protein
Phvul.001G242200	1	50180058-50185697	Cytochrome P450 superfamily protein
Phvul.002G133400	2	26437427-26440702	NB-ARC domain-containing disease resistance protein
Phvul.002G133600	2	26447784-26451915	NB-ARC domain-containing disease resistance protein
Phvul.002G154800	2	29644994-29651836	PAS domain-containing protein tyrosine kinase family protein
Phvul.006G150900	6	26403392-26405713	Protein kinase superfamily protein
Phvul.008G285400	8	59055451-59060614	Heat shock protein 89.1
Phvul.011G212100	11	49695779-49697294	Leucine-rich repeat (LRR) family protein

Figure 5 Expression patterns of 9 resistance candidate ge- nes in common bean different tissues Stem_10 is to take samples from the stem 10 days after planting, Stem_19 is to take samples from the stem 19 days after planting, Roots_10 is to take samples from the root 10 days after planting, Roots_19 is to take samples from the root 19 days after planting. Data is from https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1.

Figure 6 Haplotype analysis of Phvul.001G212100 (A) The genome structure and haplotypes of the Phvul.001G212100 (the linear gene structure showing 5'UTR (cyan rectangle), CDS region (black rectangle), 3'UTR (red rectangle); the black dotted line indicate the position of the SNP in the gene); (B) Occurrence frequencies of 4 haplotypes in breeding lines and landraces; (C) Significant differences in the degree of lesions between haplotypes (the numbers above the boxplot are P-values, P<0.05 indicate significant differences. n represent the number of germplasm recourses. The significance was tested with two-tailed T-tests). CDS: Coding sequence; UTR: Untranslated region

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