厚皮甜瓜心部果肉蔗糖含量QTL定位及候选基因分析

doi:10.6048/j.issn.1001-4330.2022.10.013

新疆农业科学 ›› 2022, Vol. 59 ›› Issue (10): 2446-2455.DOI: 10.6048/j.issn.1001-4330.2022.10.013

• 园艺特产·林业·农产品加工工程 • 上一篇下一篇

厚皮甜瓜心部果肉蔗糖含量QTL定位及候选基因分析

杨永¹(), 范蓉¹, 张学军¹, 李寐华¹, 凌悦铭¹, 张红¹, 杨文莉¹, 姜雪², 张永兵¹(), 伊鸿平¹()

1.新疆农业科学院哈密瓜研究中心,乌鲁木齐 830091
2.伊犁师范大学生物与地理科学学院,新疆伊宁 835000

收稿日期:2021-11-24 出版日期:2022-10-20 发布日期:2022-12-21
通信作者: 张永兵,伊鸿平
作者简介:杨永(1986-),男,山东人,副研究员,研究方向为甜瓜分子遗传育种,(E-mail)yangyongsj062@163.com
基金资助:
国家自然科学基金(31860567);国家西甜瓜产业技术体系厚皮甜瓜改良岗位和特色甜瓜品种改良岗位(CARS-25);新疆维吾尔自治区重点研发项目(2022B02002-3);天山创新团队(2022D14015);海南省院士创新平台

QTL Mapping and Candidate Gene Analysis of Sucrose Content in the Center Flesh of Muskmelon

YANG Yong¹(), FAN Rong¹, ZHANG Xuejun¹, LI Meihua¹, LING Yueming¹, ZHANG Hong¹, YANG Wenli¹, JIANG Xue², ZHANG Yongbing¹(), YI Hongping¹()

1. Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091,China
2. Colloge of Biology and Geography Sciences,Yili Normal University,Yining Xinjiang 835000,China

Received:2021-11-24 Online:2022-10-20 Published:2022-12-21
Correspondence author: ZHANG Yongbing, YI Hongping
Supported by:
National Natural Science Foundation of China(31860567);China Agriculture Research System of watermelon and melon(CARS-25);Key Research and Development Program of Xinjiang Uygur Autonomas Region(2022B02002-3);Tianshan Innovation Team Project(2022D14015);The Specific Research Fund of the Innovation Platform for Academicians of Hainan Province

摘要/Abstract

摘要：

【目的】运用QTL分析厚皮甜瓜心部果肉蔗糖含量,挖掘影响该性状的候选基因,为厚皮甜瓜甜味性状的遗传改良奠定理论基础。【方法】以高糖材料VZX(V醉仙)为母本和低糖材料HP(高代自交系)为父本杂交衍生的F₂群体为研究对象,利用高效液相色谱仪测定果实赤道位置心部果肉蔗糖含量,从F₂群体中挑选蔗糖含量极端高和极端低的单株各20个,分别构建高蔗糖池和低蔗糖池,对双亲及混合池均进行全基因组重测序(约20×覆盖深度),定位蔗糖性状的关联区间,并结合生物信息学分析候选基因。【结果】厚皮甜瓜心部果肉蔗糖含量在F₂群体中基本呈正态分布,符合典型的数量性状遗传特征;对双亲及混池进行全基因组重测序,共获得有效数据32.62 G,Q20在95%以上,平均覆盖深度为17.76,比对到参考基因组上的总reads数目比例在98.72%~99.02%,测序数据质量高,参考基因组选择合理有效;在8号染色体定位到1个3.29 Mb的区间,共注释到108个基因;在初定位区间内获得1个参与糖酵解和糖异生生化过程的候选基因EVM0000647,在高糖和低糖亲本间编码区无非同义突变,但启动子区域具有大量差异位点,且表达量具有明显差异。【结论】极端混池测序(BSA)方法,在8号染色体上定位到1个影响厚皮甜瓜心部果肉蔗糖含量的QTL,大小为3.29 Mb,共注释到108个基因,其中候选基因EVM0000647,通过差异表达负调控厚皮甜瓜心部果肉蔗糖的积累。

关键词: 厚皮甜瓜; 蔗糖; QTL; 候选基因; 遗传改良; 转录组

Abstract:

【Objective】 This project aims to analyze the content of sucrose in the center flesh of muskmelon by QTL mapping and find out the candidate genes, thus laying a genetic foundation for the genetic improvement of muskmelon with high sucrose content.【Method】 The F₂ population was derived from a cross between VZX with high sucrose content as the female parent and HP (high generation inbred lines) with low sucrose content as the male parent. The sucrose content determination was based on high performance liquid chromatography (HPLC). QTL for the sucrose content in the center flesh of muskmelon were detected by bulked segregant analysis (BSA) method and candidate genes were analyzed combined with bioinformatics. 【Results】 The sucrose content in the center flesh of muskmelon was approximately normal distribution in the F₂ population, which was consistent with the genetic characteristics of quantitative traits. A total of 32.62 G (average 8.16 G) of valid data were obtained by whole-genome resequencing of the parents and two bulked pools, and a 3.29 Mb interval was located on chromosome 8. A total of 108 genes were annotated. After that, further GO enrichment analysis and KEGG pathway analysis were carried out. A candidate gene EVM0000647 involved in glycolysis and gluconeogenesis in the initial localization interval was obtained by combining transcription data. There were no synonymous mutations in the coding region of EVM0000647 between the high-glucose and low-glucose parents, but there were a lot of different sites in its promoter region, and the expression levels were obviously different between parents. 【Conclusion】 One QTL with 3.29 Mb interval is located on chromosome 8 based on BSA method. EVM0000647gene involved in glycolysis and gluconeogenesis pathway is identified by bioinformatics analysis. There are distinct differences in the expression levels between high-glucose and low-glucose parents, which may play a significant role in the sucrose accumulation in the center flesh of muskmelon.

Key words: muskmelon; sucrose; QTL; candidate gene; genetic improvement; RNA-seq

中图分类号:

S652

杨永, 范蓉, 张学军, 李寐华, 凌悦铭, 张红, 杨文莉, 姜雪, 张永兵, 伊鸿平. 厚皮甜瓜心部果肉蔗糖含量QTL定位及候选基因分析[J]. 新疆农业科学, 2022, 59(10): 2446-2455.

YANG Yong, FAN Rong, ZHANG Xuejun, LI Meihua, LING Yueming, ZHANG Hong, YANG Wenli, JIANG Xue, ZHANG Yongbing, YI Hongping. QTL Mapping and Candidate Gene Analysis of Sucrose Content in the Center Flesh of Muskmelon[J]. Xinjiang Agricultural Sciences, 2022, 59(10): 2446-2455.

图/表 11

参考文献 17

[1]	杨永, 翟文强, 张学军, 等. 新疆厚皮甜瓜果实可溶性糖积累规律及其差异分析[J]. 新疆农业科学, 2021, 58(1):1-8. DOI
	YANG Yong, ZHAI Wenqiang, ZHANG Xuejun, et al. A Comparative Analysis of the Difference and Soluble Sugar Accumulation Rule of Xinjiang Muskmelon Fruit[J]. Xinjiang Agricultural Sciences, 2021, 58(1):1-8. DOI
[2]	乔永旭, 刘栓桃, 赵智中, 等. 甜瓜果实发育过程中糖积累与蔗糖代谢相关酶的关系[J]. 果树学报, 2004, 21(5):447-450.
	QIAO Yongxu, LIU Shuantao, ZHAO Zhizhong, et al. Study on the correlation of sugar accumulation and sucrose-metabolizing enzymes during the developing period of muskmelon (Cucumis melo)[J]. Journal of Fruit Science, 2004, 21(5):447-450.
[3]	Dai N, Cohen S, Portnoy V, et al. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation[J]. Plant Molecular Biology, 2011, 76(1-2):1-18. DOI PMID
[4]	张明方, 李志凌, 陈昆松, 等. 网纹甜瓜发育果实糖分积累与蔗糖代谢参与酶的关系[J]. 植物生理与分子生物学学报, 2003, 29(5):455-462.
	ZHANG Mingfang, LI Zhiling, CHEN Kunshong, et al. The Relationship Between Sugar Accumulation and Enzymes Related to Sucrose Metabolism in Developing Fruits of Muskmelon[J]. Journal of Plant Physiology and Molecular Biology, 2003, 29(5):455-462.
[5]	李慧慧, 张鲁燕, 王建康. 数量性状基因定位研究中若干常见问题的分析与解答[J]. 作物学报, 2010, 36(6):918-931
	LI Huihui, ZHANG Luyan, WANG Jiankang. Analysis and Answers to Frequently Asked Questions in Quantitative Trait Locus Mapping[J]. Acta Agronomica Sinica, 2010, 36(6): 918-931 DOI URL
[6]	张宁, 张显, 张勇, 等. 甜瓜远缘群体果实糖含量相关性状遗传分析[J]. 植物遗传资源学报, 2014, 15(5):932-939.
	ZHANG Ning, ZHANG Xian, ZHANG Yong, et al. Genetic Analysis of Fruit sugar content correlated Traits in Interspecific Population of Melon[J]. Journal of Plant Genetic Resources, 2014, 15(5):932-939.
[7]	吕律. 甜瓜果实含糖量遗传分析及糖分积累与蔗糖代谢酶关系的研究[D]. 杭州: 浙江大学, 2018.
	LV Lv. Genetic Analysis of Sugar Content and the Relationship between Sugar Accumulation and Its Metabolism related Enzymes in Melon (Cucumis melo L.)[D]. Hangzhou: Zhejiang University, 2018.
[8]	张宁, 张显, 张勇, 等. 甜瓜果实糖含量相关性状QTL分析[J]. 西北植物学报, 2015, 35(2):252-257.
	ZHANG Ning, ZHANG Xian, ZHANG Yong, et al. QTL Analysis of Fruit Sugar Content Correlated Traits in Melon[J]. Acta Botanica Boreali-Occidentalia Sinica, 2015, 35(2): 252-257.
[9]	Harel-Beja R, Tzuri G, Portnoy V, et al. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes[J]. Theoretical and Applied Genetics, 2010, 121(3):511-533. DOI PMID
[10]	Argyris J M, Díaz A, Ruggieri V, et al. QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon ( Cucumis melo L.)[J]. Frontiers in Plant Science, 2017,(8):1679.
[11]	邓冠聪. 薄皮甜瓜基因组组装与果实糖分积累主效基因的挖掘[D]. 杭州: 浙江大学, 2021.
	DENG Guancong. Melon genome assembly and mining of major genes associated with fruit sugar[D]. Hangzhou: Zhejiang University, 2021.
[12]	Elad Oren, Asaf Dafna, Galil Tzuri, et al. Melon pangenome and multi-parental framework for high-resolution trait dissection[J]. bioRxiv preprint doi: https://doi.org/10.1101/2022.08.09.503186.
[13]	朱勇, 臧全宇, 吴茜茜, 等. 甜瓜中糖的高效液相色谱测定与分析[J]. 浙江农业科学, 2012,(7):1014-1016,1028.
	ZHU Yong, ZANG Quanyu, WU Qianqian, et al. Determination and analysis of sugar in Melon by high Performance liquid chromatography[J]. Zhejiang Agricultural Sciences, 2012,(7):1014-1016,1028.
[14]	新疆甜瓜西瓜资源调查组. 新疆甜瓜西瓜志[M]. 乌鲁木齐: 新疆人民出版社, 1985.
	The Melon and Watermelon Resources Survey Group of Xinjiang. The Melon and Watermelon in Xinjiang[M]. Urumqi: Xinjiang Renmin Press, 1985.
[15]	张永兵, 李寐华, 吴海波, 等. 新疆甜瓜地方品种资源的表型遗传多样性[J]. 园艺学报, 2012, 39(2):305-314.
	ZHANG Yongbing, LI Meihua, WU Haibo, et al. Genetic Diversity of Melon Landraces(Cucumis melo L.)in Xinjiang Based on Phenotypic Characters[J]. Acta Horticulturae Sinica, 2012, 39(2):305-314.
[16]	Li Z, Chen X, Shi S, et al. Deep BSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits[J]. Mol Plant, 2022.
[17]	Ren Y, Li M, Guo S, et al. Evolutionary gain of oligosaccharide hydrolysis forbid sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits[J]. The Plant Cell, 2021,(1)1-20.

样品 Sample	原始 Reads Raw Reads	原始数据量 Raw Bases	有效 Reads Valid Reads	有效数据量 Valid Bases	有效 Reads比 Valid reads(%)	Q20 (%)	Q30 (%)	GC (%)	比对率 Mapped (%)	平均测序深度 Mean Coverage
VZX	54760488	8.21G	54291372	8.05G	99.02	95.63	89.07	36.16	99.02	19.47
HP	54990792	8.25G	54554276	8.09G	98.8	95.59	89.07	37.03	98.8	18.71
HS	57851318	8.68G	56875210	7.91G	98.78	96.81	92.22	44.01	98.72	17.12
LS	61879250	9.28G	60969402	8.57G	98.72	96.75	92.19	43.7	98.78	15.72

样品 Sample	原始 Reads Raw Reads	原始数据量 Raw Bases	有效 Reads Valid Reads	有效数据量 Valid Bases	有效 Reads比 Valid reads(%)	Q20 (%)	Q30 (%)	GC (%)	比对率 Mapped (%)	平均测序深度 Mean Coverage
VZX	54760488	8.21G	54291372	8.05G	99.02	95.63	89.07	36.16	99.02	19.47
HP	54990792	8.25G	54554276	8.09G	98.8	95.59	89.07	37.03	98.8	18.71
HS	57851318	8.68G	56875210	7.91G	98.78	96.81	92.22	44.01	98.72	17.12
LS	61879250	9.28G	60969402	8.57G	98.72	96.75	92.19	43.7	98.78	15.72

样品 Sample	SNP数量 SNPnumber	转换类型 Transition	颠换类型 Transversion	转换颠换比 Ti/Tv	杂合类型 Heterozygosity	纯合类型 Homozygosity	杂合比例 Het-ratio(%)
VZX	1 085 663	715238	370425	1.93	288596	797067	26.58
HP	1 447 738	957173	490565	1.95	334375	1113363	23.09
HS	1 522 875	1040990	481885	2.16	1031661	491214	67.74
LS	1 570 752	1071527	499225	2.14	1084333	486419	69.03

样品 Sample	SNP数量 SNPnumber	转换类型 Transition	颠换类型 Transversion	转换颠换比 Ti/Tv	杂合类型 Heterozygosity	纯合类型 Homozygosity	杂合比例 Het-ratio(%)
VZX	1 085 663	715238	370425	1.93	288596	797067	26.58
HP	1 447 738	957173	490565	1.95	334375	1113363	23.09
HS	1 522 875	1040990	481885	2.16	1031661	491214	67.74
LS	1 570 752	1071527	499225	2.14	1084333	486419	69.03

基因编号 Gene ID	长度 Length	注释 Annotation	KEGG通路 KEGG pathway
EVM0001419	2 466	PREDICTED: LOW QUALITY PROTEIN: beta-galactosidase 7-like [Cucumis melo]	brp00052(Galactose metabolism)
EVM0004758	2 466	PREDICTED: LOW QUALITY PROTEIN: beta-galactosidase 7-like [Cucumis melo]	brp00053(Galactose metabolism)
EVM0005074	2 466	PREDICTED: LOW QUALITY PROTEIN: beta-galactosidase 7-like [Cucumis melo]	brp00054(Galactose metabolism)
EVM0013242	2 466	PREDICTED: LOW QUALITY PROTEIN: beta-galactosidase 7-like [Cucumis melo]	brp00055(Galactose metabolism)
EVM0000647	1 561	PREDICTED: triosephosphate isomerase, cytosolic [Cucumis melo]	cmo00010(Glycolysis /Gluconeogenesis);cmo00051(Fructose and mannose metabolism);cmo00710(Carbon fixation in photosynthetic organisms)
EVM0008701	3 160	PREDICTED: zinc finger CCCH domain-containing protein 36-like [Cucumis melo]	gmx00052(Galactose metabolism);gmx00500(Starch and sucrose metabolism);gmx00520(Amino sugar and nucleotide sugar metabolism)
EVM0019814	2 856	PREDICTED: carbon catabolite repressor protein 4 homolog 1-like [Cucumis melo]	cmo03018(RNA degradation)

厚皮甜瓜心部果肉蔗糖含量QTL定位及候选基因分析

QTL Mapping and Candidate Gene Analysis of Sucrose Content in the Center Flesh of Muskmelon

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参考文献 17

相关文章 15

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数据库 Annotated databases	注释到的基因数 Annotated Gene Number
NR	108
SwissProt	72
GO	88
KEGG	40
COG	101
Total	108

数据库 Annotated databases	注释到的基因数 Annotated Gene Number
NR	108
SwissProt	72
GO	88
KEGG	40
COG	101
Total	108