Gene Mining of Resistance to Powdery Mildew Based on BSA-seq and RNA-seq in Cucumber

doi:10.7668/hbnxb.20195359

Abstract

Abstract:

Cucumber powdery mildew is one of the main diseases that adversely impacts cucumber production,posing a significant challenge to its sustainable cultivation.Identifying genes related to cucumber resistance to powdery mildew can help understand the genetic principles and molecular mechanisms of cucumber resistance to powdery mildew,and provide diverse gene resources for disease resistant breeding.This study constructed F₁ and F₂ populations of QK×QG using cucumber resistant inbred line QK and susceptible inbred line QG as parents.Using the extreme trait mixed pool resequencing (BSA-seq) method,the genomic regions harboring the resistance genes of cucumber powdery mildew were preliminarily located.By integrating transcriptome data with gene annotation information,the association interval of the disease phenotype was narrowed,sequence variations were identified,and key genes were screened.The results showed that the resistance of powdery mildew may be controlled by recessive genes,and the population of F₂ showed a continuous normal distribution from resistant to susceptible.The BSA-seq analysis,combining the SNP-Index method and QTG(quantitative trait genomics)-seq method analysis highlighted the 19—21 Mb region of chromosome 5,where there were 77 annotated genes with SNP differences between samples,including 33 non-synonymous mutations.The transcriptome sequencing (RNA-seq) results showed that there were 309 upregulated genes and 697 downregulated genes in the susceptible material.The expression levels of 13 genes within the candidate segment of chromosome 5 showed significant differences after infection.Through a comprehensive analysis of differentially expressed genes and BSA,the candidate genes in this segment were narrowed to 3,and only SNP mutations were detected in the LOC101207011 gene.The candidate gene LOC101207011 was characterized by a mutation resulting in an amino acid change from Valine at position 656 to Leucine.This gene emerges as the primary focus of our investigation due to its potential role in conferring resistance to powdery mildew.

Key words: Cucumber, BSA-seq, RNA-seq, Powdery mildew, Mapping

QIN Lei, ZHANG Qiaoying, SUN Lei, SHI Haoying, TAN Haibin, SHI Xueping. Gene Mining of Resistance to Powdery Mildew Based on BSA-seq and RNA-seq in Cucumber[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(2): 153-160. doi: 10.7668/hbnxb.20195359.

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References 22

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子代 Generations	合计/株 Total	感病植株/株 Disease-type plants	抗病植株/株 Resistance-type plants	分离率 Segregation ratio	卡方(χ²) Chi-square(χ²)
P₁(QG)	50	50	0
P₂(QK)	50	0	50
F₁(P₁×P₂)	30	30	0
F₁(P₂×P₁)	30	30	0
BC₁(F₁×P₁)	60	60	0
BC₁(F₁×P₂)	90	46	44	1.05:1	0.04
F₂(F₁×F₁)	292	220	72	3.06:1	0.02

子代 Generations	合计/株 Total	感病植株/株 Disease-type plants	抗病植株/株 Resistance-type plants	分离率 Segregation ratio	卡方(χ²) Chi-square(χ²)
P₁(QG)	50	50	0
P₂(QK)	50	0	50
F₁(P₁×P₂)	30	30	0
F₁(P₂×P₁)	30	30	0
BC₁(F₁×P₁)	60	60	0
BC₁(F₁×P₂)	90	46	44	1.05:1	0.04
F₂(F₁×F₁)	292	220	72	3.06:1	0.02

子代 Generations	过滤后序列数/个 Clean reads	比对上数据/ 个 Mapping reads	比对率/ % Mapping rate	平均测序深度/X Average sequencing depth	覆盖度/% Coverage	4× 覆盖度/% Coverage ≥4×	10× 覆盖度/% Coverage ≥10×	20× 覆盖度/% Coverage ≥20×
感病亲本	61 968 587	61 783 729	99.70	33.23	98.74	97.52	92.08	48.84
Disease-susceptible parent (QG)
抗病亲本	57 041 607	56 758 890	99.50	30.38	98.65	97.13	87.18	29.11
Disease-resistant parent (QK)
高感子代池	109 767 621	109 159 849	99.45	55.80	99.10	98.42	96.78	87.57
Highly susceptible pool
高抗子代池	106 036 718	105 574 627	99.56	53.53	99.09	98.38	96.57	85.84
Highly resistant pool

子代 Generations	过滤后序列数/个 Clean reads	比对上数据/ 个 Mapping reads	比对率/ % Mapping rate	平均测序深度/X Average sequencing depth	覆盖度/% Coverage	4× 覆盖度/% Coverage ≥4×	10× 覆盖度/% Coverage ≥10×	20× 覆盖度/% Coverage ≥20×
感病亲本	61 968 587	61 783 729	99.70	33.23	98.74	97.52	92.08	48.84
Disease-susceptible parent (QG)
抗病亲本	57 041 607	56 758 890	99.50	30.38	98.65	97.13	87.18	29.11
Disease-resistant parent (QK)
高感子代池	109 767 621	109 159 849	99.45	55.80	99.10	98.42	96.78	87.57
Highly susceptible pool
高抗子代池	106 036 718	105 574 627	99.56	53.53	99.09	98.38	96.57	85.84
Highly resistant pool

样本 Sample	Reads 总数/ 个 Raw read number	碱基总数/ 个 Raw bases number	原始Q20 比例/% Raw Q20 rate	原始Q30 比例/% Raw Q30 rate
QG_1	44 228 470	6.68E+09	98.56	95.62
QG_2	42 921 534	6.48E+09	98.53	95.47
QG_3	46 708 516	7.05E+09	98.54	95.54
QK_1	45 138 140	6.82E+09	98.52	95.46
QK_2	41 316 264	6.24E+09	98.52	95.47
QK_3	43 105 000	6.51E+09	98.51	95.41

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