基于BSA-seq技术的块茎芽眼深度QTL定位分析

doi:10.3724/SP.J.1006.2025.44201

作物学报 ›› 2025, Vol. 51 ›› Issue (7): 1725-1735.doi: 10.3724/SP.J.1006.2025.44201

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于BSA-seq技术的块茎芽眼深度QTL定位分析

邵顺伟¹^,²(), 陈卓¹, 兰振东¹^,², 蔡兴奎², 邹华芬¹, 李晨曦², 唐景华¹, 朱熙¹, 张彧¹, 董建科², 金辉¹^,^*(), 宋波涛²^,^*()

¹中国热带农业科学院南亚热带作物研究所 / 农业农村部热带果树生物学重点实验室 / 海南省热带园艺产品采后生理与保鲜重点实验室, 广东湛江 524091
²果蔬园艺作物种质创新与利用全国重点实验室 / 农村农业部马铃薯生物学与生物技术重点实验室 / 华中农业大学, 湖北武汉 430070

收稿日期:2024-12-03 接受日期:2025-04-27 出版日期:2025-07-12 网络出版日期:2025-05-07
通讯作者: *金辉, E-mail: jh3635315@sina.com; 宋波涛, E-mail: songbotao@mail.hzau.edu.cn
作者简介:E-mail: m19287560227@163.com
基金资助:
广东省重点领域研发计划项目(2022B0202060001);中央级公益性科研院所基本科研业务费专项(1630062024011);海南省自然科学基金青年基金项目(323QN296);海南省自然科学基金青年基金项目(323QN328);国家自然科学基金地区基金项目(32360459)

QTL mapping of tuber eye depth based on BSA-seq technique

SHAO Shun-Wei¹^,²(), CHEN Zhuo¹, LAN Zhen-Dong¹^,², CAI Xing-Kui², ZOU Hua-Fen¹, LI Chen-Xi², TANG Jing-Hua¹, ZHU Xi¹, ZHANG Yu¹, DONG Jian-Ke², JIN Hui¹^,^*(), SONG Bo-Tao²^,^*()

¹Institute of South Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences / Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs / Key Laboratory for Post-harvest Physiology and Preservation of Tropical Horticultural Products of Hainan, Zhanjiang 524091, Guangdong, China
²National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops / Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs / Huazhong Agricultural University, Wuhan 430070, Hubei, China

Received:2024-12-03 Accepted:2025-04-27 Published:2025-07-12 Published online:2025-05-07
Contact: *E-mail: jh3635315@sina.com; E-mail: songbotao@mail.hzau.edu.cn
Supported by:
Guangdong Provincial Key Areas Research and Development Program(2022B0202060001);Special Fund for Basic Scientific Research Operating Expenses of Central-level Public Welfare Research Institutes(1630062024011);Hainan Provincial Natural Science Foundation Youth Fund(323QN296);Hainan Provincial Natural Science Foundation Youth Fund(323QN328);Regional Fund of the National Natural Science Foundation of China(32360459)

摘要/Abstract

摘要：

芽眼深度是马铃薯块茎的重要性状之一, 对马铃薯的外观品质及加工适宜性具有重要影响。为挖掘控制马铃薯芽眼深度的数量性状位点, 本研究以四倍体深芽眼品种“华薯12”为母本、浅芽眼高代品系“天2002-4-5”为父本, 杂交获得F₁代分离群体, 共255份无性系。基于连续2年田间表型观测数据, 分别选取20个深芽眼和20个浅芽眼个体构建混合池, 利用BSA-seq技术进行芽眼深度相关性状的QTL定位, 并结合传统QTL定位方法, 采用完备区间作图法构建遗传连锁图谱, 成功定位到2个与芽眼深度相关的QTL位点。2年表型相关性分析结果表明, 马铃薯块茎芽眼深度主要受遗传因素的控制。10号染色体上qEyd10.1位点的LOD值为4.96, 表型贡献率为14.49%; 3号染色体上qEyd3.1位点的LOD值为3.29, 表型贡献率为10.18%。其中, qEyd3.1与此前报道的芽眼深度调控位点一致, 而qEyd10.1为新发现的QTL。2个位点的加性效应均为负值, 表明降低芽眼深度的等位基因来源于浅芽眼亲本“天2002-4-5”。通过对定位区间内候选基因注释结合芽眼深浅材料基因结构变异分析, 推测Soltu.DM.10G029390.1、Soltu.DM.03G036540.1、Soltu.DM.03G036140.1和Soltu.DM.03G036580.1可能为与芽眼深度相关的候选基因。本研究通过BSA-seq与传统QTL定位相结合的方式, 快速完成了同源四倍体马铃薯中芽眼深度这一数量性状的调控位点定位工作, 并初步确定了4个候选基因, 为进一步完成芽眼深度调控基因的克隆及其遗传机制解析奠定了重要基础, 也为培育具有浅芽眼块茎的四倍体马铃薯新品种提供了参考。

关键词: 马铃薯, 芽眼深度, QTL定位, BSA-seq, 遗传连锁图谱

Abstract:

Eye depth is an important trait of potato tubers, significantly affecting both their appearance and processing quality. To identify quantitative trait loci (QTLs) associated with eye depth, a cross was made between the tetraploid deep-eyed variety “Hua Shu 12” (female) and the shallow-eyed advanced line “Tian 2002-4-5” (male), generating 255 clonal F₁ progeny. Based on field phenotypic data collected over two consecutive years, 20 deep-eyed and 20 shallow-eyed individuals were selected to construct bulks for QTL mapping. The BSA-seq approach was employed to detect QTLs related to eye depth, and combined with traditional QTL mapping methods, a complete interval mapping analysis was conducted to construct a genetic linkage map. Two QTLs associated with eye depth were successfully identified. Phenotypic correlation analysis across both years suggested that tuber eye depth is primarily controlled by genetic factors. The LOD score for locus qEyd10.1 on chromosome 10 was 4.96, with a phenotypic variance explained (PVE) of 14.49%, while qEyd3.1 on chromosome 3 had a LOD score of 3.29 and a PVE of 10.18%. Notably, qEyd3.1 corresponds to a previously reported eye depth locus, whereas qEyd10.1 represents a novel QTL. Both loci exhibited negative additive effects, indicating that the allele responsible for reduced eye depth was inherited from the shallow-eyed parent “Tian 2002-4-5”. Through candidate gene annotation within the mapped intervals and analysis of gene structural variation between deep- and shallow-eyed materials, four candidate genes: Soltu.DM.10G029390.1, Soltu.DM.03G036540.1, Soltu.DM.03G036140.1, and Soltu.DM.03G036580.1 were preliminarily identified as potentially associated with eye depth. This study, by integrating BSA-seq with conventional QTL mapping in autotetraploid potato, provides a preliminary identification of candidate genes regulating tuber eye depth. These findings lay a foundation for future gene cloning and genetic mechanism studies, and offer a valuable reference for breeding new tetraploid potato varieties with shallower eyes.

Key words: potato, eye depth, QTL mapping, bulked segregant analysis sequencing, genetic linkage map

邵顺伟, 陈卓, 兰振东, 蔡兴奎, 邹华芬, 李晨曦, 唐景华, 朱熙, 张彧, 董建科, 金辉, 宋波涛. 基于BSA-seq技术的块茎芽眼深度QTL定位分析[J]. 作物学报, 2025, 51(7): 1725-1735.

SHAO Shun-Wei, CHEN Zhuo, LAN Zhen-Dong, CAI Xing-Kui, ZOU Hua-Fen, LI Chen-Xi, TANG Jing-Hua, ZHU Xi, ZHANG Yu, DONG Jian-Ke, JIN Hui, SONG Bo-Tao. QTL mapping of tuber eye depth based on BSA-seq technique[J]. Acta Agronomica Sinica, 2025, 51(7): 1725-1735.

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年份Year	平均值Mean	标准差SD	变异系数CV (%)	峰度Kurt	偏度Skew
2023	2.40	1.05	43.75	-0.24	0.54
2024	2.44	1.02	41.80	-0.03	0.59

年份 Year	2023ZJ	2024ZJ
2023ZJ	1.00	0.85^**
2024ZJ	0.85^**	1.00

样本名 Sample name	总碱基数 Total bases (bp)	Q20碱基占比 Q20 base (%)	Q30碱基占比 Q30 base (%)	比对率 Mapping rate (%)	GC含量 GC content (%)
深芽眼混池Deep-eyed DNA pool	14,939,252,950	97.36	92.64	98.92	37.13
浅芽眼混池Shallow-eyed DNA pool	16,436,302,586	97.40	92.72	99.00	37.39

位置 Position (bp)	引物名称 Primer name	正向引物 Forward sequence (5'-3')	反向引物 Reverse sequence (5'-3')
58,290,035	indel0307	GTCTGAAGCACTGTGGAG	CTAACAGCATTGATGGATGG
58,318,797	indel0309	ACTGGAGATAGAGATATTGC	CAGTGGTCTATCGTATGAAT
58,422,470	indel0314	CACCTTCAGATGTCATTACCT	ACTTACTCCTTGGCAGAATAG
58,585,026	indel0323	CGGGTCAAATTGGGCTAA	GGCAAGTTAGACTCGGTATA
58,660,135	indel0325	GTCACCAATACCTACTGTTAC	CAGAGCAATGTGTAGATGTC
59,039,795	indel0340	CGTGTGTTTATTTGGTTGTG	TAGCAGAGGTGGAGTCAG
59,132,974	indel0345	AGAATAGATTCACGCTCAGT	GACATCCAGTTCCACAATAC
60,152,320	indel0378	ACTCATCAGCTCAAGTAACA	GCTGCTCCTCTATTTCTATG
60,185,141	indel0380	ATCTCAGCGACTAAAGTACA	ATTACGGTCCGATAAGAACA
60,301,220	indel0390	CGTACTTCCGCTCCAATT	CCACCGTTCTCTTCTTCAT
59,921,955	indel1050	ATTACAACGGCAACACTTC	GGAATCCAGATTGAGTAGAGA
60,122,521	indel1059	TTCTATGTCTGCCATTACCA	TTCTCCTCCAATGAACACAA
60,244,293	indel1069	GCTAGAGCAACCGTTCTT	AATTGAAGTCCAAGCCAGTA
60,299,315	indel1077	CCTCGCTATAATAGTCATCCT	GCACAGAAGAAGGTATCAGA
60,526,228	indel1087	TGCCTTGCTTACTCTTCAG	TCGTTCTTTATCAGGTCACA
60,647,541	indel1097	GAATGCTTGATGGTTGCTTA	CCGTATTGTGCTCTCCTC
59,999,462	indel-10-5	TTAACTGTGCCTGGAATGT	GCCTAATAGACTTGCTGTTC
59,253,178	EYD10-31	CGGTTGACATTGAGTTGAAT	TGTGACAAGATGATGGAGG
58,449,862	EYD10-36	GTTGGACATAAGGAAGTTCT	TTGATGACATTGGACACTAC
58,525,040	EYD10-37	CGGATTCTTCGCCTGAAT	AAAGGGAAGGGAATAATTGC
58,636,373	EYD10-39	TCCCATCTGTTTGCCTTAC	CCTGTGAGAGTGGTGTTAC
59,935,156	i-10-6	CACTACTTACCCATCCGCTAG	GTGTGGAATGTGGACTCTCAA
59,959,532	i-10-7	AGAGTTGCAGGCATTAGTAGC	ACCAGTGAGATACCAAGAGGA
59,928,242	I10-6	ACAGATGTACCAGAGGAAGACA	CCACAACAGTTGCGTTACCA
60,136,249	I10-17	GAGCCTTGTAGCCCAATAGTTT	ATCCTCAGACATGGCAACCT
60,296,620	I10-19	GTAGTTCCAGTTCCAGTTCCA	GCATTAGCATTCTTGATTCCAC

性状 Trait	染色体 Chr.	物理位置 Physical position (bp)	图谱位置 Map position (cM)	左侧标记 Left marker	右侧标记 Right marker	LOD 值 LOD value	表型贡献率 PVE (%)	加性效应 Add
Eyd	10	60,122,521-60,136,249	27	I10-17	indel1059	4.96	14.49	-0.69
	3	59,039,795-60,301,220	28	indel0390	indel0340	3.29	10.18	-0.31

基于BSA-seq技术的块茎芽眼深度QTL定位分析

QTL mapping of tuber eye depth based on BSA-seq technique

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QTL	候选基因 Candidate genes	候选基因物理位置 Candidate gene physical site (bp)	基因功能注释 Gene function annotation
qEyd10.1	Soltu.DM.10G029390.1	60,131,627-60,132,517	富含半胱氨酸/组氨酸的C1结构域家族蛋白 Cysteine/histidine-rich C1 domain family protein
qEyd3.1	Soltu.DM.03G036540.1	59,516,183-59,516,315	MYB结构域蛋白; 编码特定的转录因子, DNA结合 MYB domain protein; coding specific transcription factors, DNA binding
	Soltu.DM.03G036140.1	59,187,760-59,195,940	蛋白磷酸酶2A, 调节亚基PR55; 启用蛋白质磷酸酶调节因子活性, 实现蛋白质结合 Protein phosphatase 2A, regulatory subunit PR55; activate the activity of protein phosphatase regulatory factors, enabling protein binding
	Soltu.DM.03G036580.1	59,541,306-59,541,454	蛋白激酶超家族蛋白; 实现蛋白质结合, 启用蛋白质丝氨酸/苏氨酸/酪氨酸激酶活性 Epidermal patterning factor proteins domain containing protein; enable protein binding and activate protein serine/threonine/tyrosine kinase activity

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