甘薯抗茎线虫病的QTL定位与分析

doi:10.3864/j.issn.0578-1752.2025.17.003

摘要/Abstract

摘要：

【目的】分析甘薯（Ipomoea batatas (L.) Lam.）抗茎线虫病相关的QTL，为甘薯抗茎线虫病基因的精细定位、克隆及功能研究奠定基础，同时也为甘薯抗茎线虫病遗传机理研究和培育抗性品种提供支持。【方法】以抗茎线虫病品种豫薯10号和高感病品系新24为亲本构建包含212个子代的F₁群体为试验材料，对其进行田间自然诱发甘薯茎线虫病抗性鉴定，基于前期构建的遗传图谱，采用复合区间作图法（composite interval mapping，CIM）对甘薯抗茎线虫病进行QTL定位与分析，并对QTL置信区间内的候选基因进行预测。同时，采用rMVP（a memory-efficient、visualization-enhanced、parallel-accelerated R package）软件对甘薯抗茎线虫病进行全基因组关联分析（genome-wide association studies，GWAS）。对抗病品种郑红22进行室内接种甘薯茎线虫，在接种线虫后的不同时期进行取样，采用qRT-PCR对筛选的5个候选基因（itf02g19880、itf02g20080、itf02g20100、itf13g18480和itf13g18550）进行定量表达分析。【结果】共定位到3个与甘薯抗茎线虫病相关的QTL——qSNR02-1、qSNR02-2和qSNR13-1，分布于第2和第13染色体。单个QTL表型变异解释率为9.6%—11.7%。经GWAS分析，在第6染色体关联到1个与甘薯抗茎线虫病显著相关的位点。根据基因组注释信息，对QTL置信区间内的候选基因进行预测，筛选出36个与抗茎线虫病相关的候选基因。候选基因功能注释表明，防御机制相关的ABC转运蛋白家族、多药及毒性外排转运蛋白（MATE）外排蛋白家族，以及翻译后修饰、蛋白质周转相关的E3泛素连接酶和谷胱甘肽S转移酶等参与抗病胁迫。qRT-PCR结果表明，5个候选基因的表达模式呈显著性差异，itf02g20100在接种3 d时表达量达到峰值，是对照的6.2倍；itf02g19880在接种0.5 d后表达量急剧上升至最高达到对照的43.2倍；itf13g18480和itf13g18550的表达模式相似，均在接种7 d时达到峰值。表明不同候选基因在甘薯茎线虫侵染后的防御响应中可能发挥不同的调控作用。【结论】定位到3个与甘薯抗茎线虫病相关的QTL，筛选出36个相关候选基因。

关键词: 甘薯, F₁群体, 抗茎线虫病, QTL定位, 候选基因

Abstract:

【Objective】The purpose of this study was to analyze the quantitative trait loci (QTLs) related to stem nematode resistance in sweetpotato (Ipomoea batatas (L.) Lam.), lay a foundation for the fine mapping, cloning, and functional analysis of stem nematode resistance genes in sweetpotato. It also aimed to provide support for the study of the genetic mechanisms of stem nematode resistance, as well as the breeding of resistant varieties in sweetpotato.【Method】An F₁ population of 212 progenies derived from a cross between the highly resistant cultivar Yushu 10 and the susceptible line Xin 24 was used. In this study, field-based natural infection assays were conducted to evaluate stem nematode resistance. QTL mapping was performed using composite interval mapping (CIM), and candidate genes within QTL confidence intervals were predicted. Additionally, genome-wide association studies (GWAS) were carried out using the rMVP software (a memory-efficient, visualization-enhanced, and parallel-accelerated R package). For further validation, the resistant cultivar Zhenghong 22 was artificially inoculated with D. destructor, and samples were collected at different post-inoculation time points. The expression patterns of five candidate genes (itf02g19880, itf02g20080, itf02g20100, itf13g18480 and itf13g18550) were analyzed via qRT-PCR.【Result】Three QTLs (qSNR02-1, qSNR02-2, and qSNR13-1) were identified, distributed on chromosomes 2 and 13. The phenotypic contribution rate of the individual QTL related to stem nematode resistance ranged from 9.6% to 11.7%. GWAS revealed one significantly associated locus with stem nematode resistance on chromosome 6. Based on the genomic annotation information, 36 candidate genes related to stem nematode resistance were predicted within the QTL confidence intervals, including members of the ABC transporter family, multidrug and toxic compound extrusion (MATE) efflux proteins, E3 ubiquitin ligases, and glutathione S-transferases, which are involved in defense mechanisms, post-translational modification, and stress response. qRT-PCR results showed that the expression patterns of the five candidate genes were significantly different. The expression level of itf02g20100 reached a peak at 3 days after inoculation, which was 6.2 times that of the control; the expression level of itf02g19880 increased sharply and reached the highest level at 0.5 days after inoculation, which was 43.2 times that of the control; the expression patterns of itf13g18480 and itf13g18550 were similar, and both reached a peak at 7 days after inoculation. This indicates that different candidate genes may play different regulatory roles in the defense response after Ditylenchus destructor infection.【Conclusion】Three QTLs related to stem nematode resistance in sweetpotato were identified, and 36 related candidate genes were screened out, which can be used for the subsequent cloning and functional study of genes related to stem nematode resistance in sweetpotato.

Key words: sweetpotato, F₁population, resistance to stem nematode, QTL mapping, candidate gene

赵冬兰, 马居奎, 肖世卓, 周志林, 赵凌霄, 王洁, 戴习彬, 孙厚俊, 曹清河. 甘薯抗茎线虫病的QTL定位与分析[J]. 中国农业科学, 2025, 58(17): 3389-3399.

ZHAO DongLan, MA JuKui, XIAO ShiZhuo, ZHOU ZhiLin, ZHAO LingXiao, WANG Jie, DAI XiBin, SUN HouJun, CAO QingHe. QTL Analysis for Resistance to Stem Nematode Disease in Sweetpotato[J]. Scientia Agricultura Sinica, 2025, 58(17): 3389-3399.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.17.003

https://www.chinaagrisci.com/CN/Y2025/V58/I17/3389

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候选基因注释"

数量性状位点 QTL	候选基因 Candidate genes	COG注释 COG annotation	GO注释 GO annotation	NR注释 NR annotation
qSNR02-1	itf02g20080 itf02g20090	防御机制 Defense mechanisms	GO:0005524 GO:0006200 GO:0016887	ABC转运蛋白A家族成员7和2 ABC transporter A family member 7 and 2
	itf02g20180 itf02g20100 itf02g19820	翻译后修饰、蛋白质周转、分子伴侣 Posttranslational modification, protein turnover, chaperones	GO:0004842 GO:0006511 GO:0009650	泛素缀合酶E2 Ubiquitin-conjugating enzyme E2 E3泛素蛋白连接酶 E3 ubiquitin-protein ligase
	itf02g20350 itf02g20340 itf02g20320	翻译后修饰、蛋白质周转、分子伴侣 Posttranslational modification, protein turnover, chaperones	GO:0004364 GO:0009072 GO:0016034	谷胱甘肽S转移酶zeta类 Glutathione S-transferase zeta class
	itf02g20520	碳水化合物运输和代谢 Carbohydrate transport and metabolism	—	异胡豆苷合成酶 Strictosidine synthase
	itf02g19900 itf02g19880 itf02g20190	—	—	转录因子bHLH47、TCP14和WRKY61 Transcription factor bHLH47, TCP14 and WRKY61
qSNR02-2	itf02g21100	—	GO:0000234 GO:0032259	磷酸乙醇胺N-甲基转移酶 Phosphoethanolamine N-methyltransferase
	itf02g21980	—	GO:0055085	生长素外排促进因子PIN1b Auxin efflux facilitator PIN1b
	itf02g21450	—	GO:0004185 GO:0006508	丝氨酸羧肽酶45 Serine carboxypeptidase-like 45
	itf02g21820	—	—	锌指蛋白VAR3 Zinc finger protein VAR3
qSNR13-1	itf13g19430 itf13g19700	—	GO:0016772	丝裂原活化蛋白激酶激酶激酶2 Mitogen-activated protein kinase kinase kinase 2-like（MAPKKK2）
	itf13g19030	无机离子运输和代谢 Inorganic ion transport and metabolism	GO:0004784 GO:0009651 GO:0042742	超氧化物歧化酶 Superoxide dismutase
	itf13g18440 itf13g18450 itf13g18920 itf13g18910	—	GO:0016787	果胶酯酶28、29 Pectinesterase 28, 29
	itf13g18480 itf13g18470 itf13g18520 itf13g18490 itf13g18500 itf13g18530 itf13g18510	—	GO:0008152 GO:0016787	环氧化物酶 Epoxide hydrolase
	itf13g18550	防御机制 Defense mechanisms	GO:0006855 GO:0015238 GO:0015297	MATE（多药和毒性化合物外排转运蛋白）外排家族蛋白5 MATE (Multidrug and toxic extrusion transporters) efflux family protein 5-like
	itf13g18640	防御机制 Defense mechanisms	—	ABC转运蛋白C家族成员14异构体X1 ABC transporter C family member 14 like isoform X1
	itf13g19860	氨基酸转运和代谢 Amino acid transport and metabolism	GO:0004124 GO:0006535 GO:0016740	半胱氨酸合成酶 Cysteine synthase
	itf13g19220 itf13g18940 itf13g19630	翻译后修饰、蛋白质周转、分子伴侣 Posttranslational modification, protein turnover, chaperones	GO:0046872 GO:0051716 GO:0050794	E3泛素连接酶 E3 ubiquitin-protein ligase

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基因 Gene	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)	产物大小 Product size (bp)
Itf02g20080	GCTACTCAAGCTTTCCACAGGC	GAAGGAGGAGACTGTTTCGC	107
Itf02g20100	TCAATCTTCACCGTCCACTACA	GGAGTTTCTCATCATCATCAGG	200
Itf02g19880	CACCACCACCACCACCATAA	AGAGAGGAGGAGATTGCGAG	161
Itf13g18480	TCATAGTTGGAGACTTGGACTTG	AGCCACACCTTCAAGAACCA	122
Itf13g18550	GGCTCCACCAAGATGCAAG	TCCATAGCAGTGGCCATGTT	141

数量性状位点 QTL	连锁群 Linkage group	标记区间 Marker interval	标记数 Marker number	物理区间 Physical interval	LOD值 LOD value	表型变异解释率 Explained variance (%)	基因数 Gene number
qSNR02-1	LG02	Marker471299-Marker479577	5	Chr.02 15795792-16767105	3.23	9.6	57
qSNR02-2	LG02	Marker484408-Marker498135	27	Chr.02 17052850-19167216	3.96	11.7	41
qSNR13-1	LG13	Marker3187715-Marker3192541	7	Chr.13 20087827-20975255	3.48	10.3	133