基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定

沈朝贵; 赖瑞联; 陈瑾; 冯新; 陈义挺; 韦晓霞; 吴如健

doi:10.19303/j.issn.1008-0384.2024.05.007

基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定

doi: 10.19303/j.issn.1008-0384.2024.05.007

福建省农业科学院果树研究所，福建　福州　350013

基金项目: 福建省科技计划公益类专项（2022R1028005、2022R1028003）；农业农村部物种品种资源保护项目（18230171）

详细信息

作者简介:
沈朝贵（1971 — ），男，助理研究员，主要从事果树种质资源与保鲜加工研究，E-mail：shenchaogui@163.com

通讯作者:
吴如健（1965 — ），男，研究员，主要从事果树种质资源与栽培育种研究，E-mail: wurujian@126.com

中图分类号: S667.5
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出版历程
- 收稿日期: 2022-05-09
- 修回日期: 2023-05-31
- 网络出版日期: 2024-07-10
- 刊出日期: 2024-05-28

SNP Markers Development and Genetic Relationship Identification of Germplasm Resources of Canarium album Based on SLAF-Seq Technology

Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian　350013, China

摘要

摘要: 目的开发橄榄SNP标记并分析其种质资源遗传多样性，为橄榄种质资源保护和利用提供依据。方法基于SLAF-Seq技术进行橄榄SNP标记开发，同时采用系统进化分析、群体聚类分析和主成分分析等研究了橄榄种质资源遗传结构和遗传多样性。结果基于SLAF-Seq技术共挖掘到506 701个SLAF标签，其中多态性SLAF标签27 108个，开发获得361 386个群体SNP标记；基于SNP标记，利用系统进化树和群体聚类分析可分别将橄榄种质资源分为3和6个类群，整体Nei多样性指数和Shanon-Wiener指数分别为0.321和0.472。两种分类方法分析结果均发现，不同地区之间的橄榄种质资源并未严格按照地域分布归类。结论橄榄种质资源遗传多样性相对丰富，且不同地域间存在种质资源交流，而采用SNP标记可有效鉴定橄榄种质资源。
- 橄榄 /
- 种质资源 /
- SNP标记 /
- 遗传结构 /
- 遗传多样性
Abstract: Objective SNP markers development and genetic diversity analysis of Canarium album were perfomed to facilitate the protection and utilization of germplasm resources of C. album. Method SNP markers of C. album were developed based on SLAF-Seq technology, and the genetic structure and genetic diversity were studied by phylogenetic analysis, population cluster analysis and principal component analysis. Result A total of 506 701 SLAF loci were mined, including 27 108 polymorphic SLAF loci, and 361 386 SNP markers were developed. Based on these SNP markers, germplasm resources of C. album were respectively divided into 3 and 6 groups by phylogenetic tree and population cluster analysis. The overall Nei diversity index and Shanon Wiener index were 0.321 and 0.472, respectively. The results of two classification methods showed that germplasm resources of C. album from different regions were not classified strictly according to regional distribution. Conclusion The genetic diversity of germplasm resources of C. album had great genetic diversity which were exchange frequently among different regions, and the developed SNP markers of C. album could effectively identify the germplasm resources.
- Canarium album /
- germplasm resource /
- SNP marker /
- genetic structure /
- genetic diversity

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图 1 基于邻接法的系统发育树

Figure 1. Phylogenetic tree based on neighbor-joining method

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图 2 不同K值对应遗传结构聚类图（A）、交叉验证错误值（B）以及主成分分析（C）

Figure 2. Genetic structure cluster (A), admixture validation error rate (B) of different K values and PCA analysis (C)

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表 1 供试橄榄种质资源

Table 1. Germplasm resources of C. album used in this experiment

编号 Number	名称 Germplasm name	来源地 Source	经纬度 Longitude and latitude	简写名 Abbreviated name
1	葡萄	福建福安	119°38′E, 27°08′N	PT
2	大目埕橄榄王	福建闽侯	118°59′E, 26°12′N	DMC
3	七粒尺	福建闽侯	119°00′E, 26°10′N	QLC
4	灵峰	福建闽侯	118°97′E, 26°21′N	LF
5	福榄1号	福建闽侯	118°97′E, 26°21′N	FL1
6	清榄1号	福建闽清	118°54′E, 26°13′N	QL1
7	闽清2号	福建闽清	118°89′E, 26°24′N	MQ2
8	牛榄2号	广西浦北	109°33′E, 22°19′N	NL2
9	合江三白圆	四川合江	105°53′E, 28°46′N	HJSBY
10	平阳3号	浙江平阳	120°30′E, 27°37′N	PY3
11	瑞安2号	浙江瑞安	120°35′E, 27°53′N	RA2
12	瑞安3号	浙江瑞安	120°35′E, 27°53′N	RA3
13	棱尖	广东饶平	116°83′E, 23°99′N	LJ
14	乌榄	广东广州	113°22′E, 23°09′N	WL

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表 2 测序数据统计

Table 2. Summary of sequencing data

样本名称 Sample ID	全部片段数量 Number of total reads	GC含量百分比 GC percentage/%	Q30百分比 Q30 percentage/%
DMC	749 838	40.43	93.28
FL1	894 002	41.03	93.43
HJSBY	7 541 767	37.41	93.43
LF	559 479	39.21	93.54
LJ	1 012 589	38.36	93.61
MQ2	1 139 514	40.38	93.51
NL2	1 071 660	38.80	93.62
PT	876 458	41.65	93.48
PY3	964 858	39.20	93.32
QL1	1 996 699	40.74	93.44
QLC	813 057	41.57	93.61
RA2	1 128 676	39.18	93.76
RA3	873 826	42.05	93.67
WL	901 408	37.88	93.29

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表 3 不同样本中SNP位点数量

Table 3. Number of SNP loci in different samples

样本名称 Sample ID	SNP数量 SNP number	完整度 Hetloci ratio/%	杂合度 Integrity ratio/%
DMC	227 472	13.96	62.94
FL1	239 971	14.73	66.40
HJSBY	297 219	21.86	82.24
LF	209 271	12.95	57.90
LJ	255 598	17.94	70.72
MQ2	249 658	14.61	69.08
NL2	256 355	17.77	70.93
PT	231 235	14.92	63.98
PY3	239 403	15.00	66.24
QL1	290 076	30.22	80.26
QLC	233 083	13.59	64.49
RA2	254 930	16.64	70.54
RA3	236 723	15.11	65.50
WL	165 152	11.72	45.69

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参考文献(30)

[1]	XIANG Z B, WU X L, LIU X Y. Chemical composition and antioxidant activity of petroleum ether extract of Canarium album [J]. Pharmaceutical Chemistry Journal, 2017, 51(7): 606−611. doi: 10.1007/s11094-017-1661-9
[2]	DUAN W J, TAN S Y, CHEN J, et al. Isolation of anti-HIV components from Canarium album fruits by high-speed counter-current chromatography [J]. Analytical Letters, 2013, 46(7): 1057−1068. doi: 10.1080/00032719.2012.749486
[3]	JIA Y L, ZHENG J, YU F, et al. Anti-tyrosinase kinetics and antibacterial process of caffeic acid N-nonyl ester in Chinese olive (Canarium album) postharvest [J]. International Journal of Biological Macromolecules, 2016, 91: 486−495. doi: 10.1016/j.ijbiomac.2016.05.098
[4]	LIU Q P, ZHOU M L, ZHENG M, et al. Canarium album extract restrains lipid excessive accumulation in hepatocarcinoma cells [J]. International Journal of Clinical and Experimental Medicine, 2016, 9(9): 17509−17518.
[5]	赖瑞联, 陈瑾, 韦晓霞, 等. 中国橄榄研究40年 [J]. 热带作物学报, 2020, 41(10):2045−2054. doi: 10.3969/j.issn.1000-2561.2020.10.011 LAI R L, CHEN J, WEI X X, et al. Research of Chinese olive in the past 40 years [J]. Chinese Journal of Tropical Crops, 2020, 41(10): 2045−2054. (in Chinese) doi: 10.3969/j.issn.1000-2561.2020.10.011
[6]	杨培奎. 粤东地区橄榄种质资源遗传多样性ISSR分析及核心种质初步构建[D]. 汕头: 汕头大学, 2010. YANG P K. Analysis of genetic diversity of Canarium album L. germplasm resources from East Guangdong Province using ISSR and construction of core collection[D]. Shantou: Shantou University, 2010. (in Chinese)
[7]	刘天亮. 福建省橄榄(Canavium album Raeusch)种质资源的ISSR分析[D]. 福州: 福建农林大学, 2010. LIU T L. ISSR analysis of germplasm resources of Fujian Canavium album Raeusch[D]. Fuzhou: Fujian Agriculture and Forestry University, 2010. (in Chinese)
[8]	赖瑞联, 陈瑾, 冯新, 等. 橄榄ISSR和RAPD遗传多样性分析和核心种质构建 [J]. 热带亚热带植物学报, 2022, 30(1):41−53. doi: 10.11926/jtsb.4437 LAI R L, CHEN J, FENG X, et al. ISSR and RAPD genetic diversity analysis and core germplasms construction of Canarium album [J]. Journal of Tropical and Subtropical Botany, 2022, 30(1): 41−53. (in Chinese) doi: 10.11926/jtsb.4437
[9]	聂珍素. 福建橄榄(Canarium album L. )资源的RAPD分析[D]. 福州: 福建农林大学, 2005. NIE Z S. RAPD analysis of album(Canarium album) genetic resources in Fujian Province[D]. Fuzhou: Fujian Agriculture and Forestry University, 2005. (in Chinese)
[10]	MEI Z L, ZHANG X Q, LIU X Y, et al. Genetic analysis of Canarium album in different areas of China by improved RAPD and ISSR [J]. Comptes Rendus Biologies, 2017, 340(11/12): 558−564.
[11]	MEI Z Q. Improved RAPD analysis of Canarium album (Lour. ) raeusch from Sichuan Province along Yangtze River in China [J]. Annual Research & Review in Biology, 2014, 4: 51−60.
[12]	CHENG J L, YIN Z C, MEI Z Q, et al. Development and significance of SCAR marker QG12-5 for Canarium album (Lour. ) Raeusch by molecular cloning from improved RAPD amplification [J]. Genetics and Molecular Research, 2016, 15(3): gmr8347.
[13]	张小红, 赵依杰, 林航. 基于SRAP技术的甜橄榄种质资源遗传多样性分析 [J]. 中国南方果树, 2017, 46(6):53−56. ZHANG X H, ZHAO Y J, LIN H. Genetic diversity analysis of sweet olive germplasm resources based on SRAP technology [J]. South China Fruits, 2017, 46(6): 53−56. (in Chinese)
[14]	张平湖, 刘冠明. 橄榄SRAP-PCR体系的建立和优化 [J]. 中国农学通报, 2010, 26(15):86−88. ZHANG P H, LIU G M. Establishment and optimization of SRAP-PCR system in Canarium album reausch [J]. Chinese Agricultural Science Bulletin, 2010, 26(15): 86−88. (in Chinese)
[15]	王燕平, 陈勤, 周志钦, 等. 橄榄基因组AFLP扩增体系的优化 [J]. 果树学报, 2012, 29(3):505−511. WANG Y P, CHEN Q, ZHOU Z Q, et al. Optimization of AFLP reaction system in Canarium album [J]. Journal of Fruit Science, 2012, 29(3): 505−511. (in Chinese)
[16]	苏睿, 林峻, 陈鲤群, 等. 高通量自动化SNP检测技术研究进展 [J]. 中国细胞生物学学报, 2019, 41(7):1412−1422. doi: 10.11844/cjcb.2019.07.0022 SU R, LIN J, CHEN L Q, et al. Research progress on high-throughput automated SNP detection technology [J]. Chinese Journal of Cell Biology, 2019, 41(7): 1412−1422. (in Chinese) doi: 10.11844/cjcb.2019.07.0022
[17]	ZHU Z S, SUN B M, LEI J J. Specific-locus amplified fragment sequencing (SLAF-seq) as high-throughput SNP genotyping methods [J]. Methods in Molecular Biology, 2021, 2264: 75−87.
[18]	赖瑞联, 徐洋, 赖恭梯, 等. 山枇杷基因组DNA的提取及自然群体内ISSR遗传多样性分析 [J]. 森林与环境学报, 2015, 35(1):53−59. LAI R L, XU Y, LAI G T, et al. Extraction of genomic DNA and analysis of genetic diversity of the natural population by ISSR in Garcinia multiflora [J]. Journal of Forest and Environment, 2015, 35(1): 53−59. (in Chinese)
[19]	SUN X W, LIU D Y, ZHANG X F, et al. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing [J]. PLoS One, 2013, 8(3): e58700. doi: 10.1371/journal.pone.0058700
[20]	XU Q, CHEN L L, RUAN X A, et al. The draft genome of sweet orange (Citrus sinensis) [J]. Nature Genetics, 2013, 45: 59−66. doi: 10.1038/ng.2472
[21]	KOZICH J J, WESTCOTT S L, BAXTER N T, et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform [J]. Applied and Environmental Microbiology, 2013, 79(17): 5112−5120. doi: 10.1128/AEM.01043-13
[22]	TAMURA K, PETERSON D, PETERSON N, et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods [J]. Molecular Biology and Evolution, 2011, 28(10): 2731−2739. doi: 10.1093/molbev/msr121
[23]	ALEXANDER D H, NOVEMBRE J, LANGE K. Fast model-based estimation of ancestry in unrelated individuals [J]. Genome Research, 2009, 19(9): 1655−1664. doi: 10.1101/gr.094052.109
[24]	赵亚琴, 樊丛照, 张际昭, 等. 基于简化基因组技术的啤酒花栽培种和野生种SNP位点开发及遗传结构分析 [J]. 中草药, 2021, 52(20):6365−6372. doi: 10.7501/j.issn.0253-2670.2021.20.027 ZHAO Y Q, FAN C Z, ZHANG J Z, et al. SNP loci development and genetic structure of cultivated and wild individuals of Humulus lupulus using SLAF-seq [J]. Chinese Traditional and Herbal Drugs, 2021, 52(20): 6365−6372. (in Chinese) doi: 10.7501/j.issn.0253-2670.2021.20.027
[25]	田倩, 刘双委, 钮世辉, 等. 基于SLAF-seq技术的白皮松SNP分子标记开发 [J]. 北京林业大学学报, 2021, 43(8):1−8. doi: 10.12171/j.1000-1522.20200211 TIAN Q, LIU S W, NIU S H, et al. Development of SNP molecular markers of Pinus bungeana based on SLAF-seq technology [J]. Journal of Beijing Forestry University, 2021, 43(8): 1−8. (in Chinese) doi: 10.12171/j.1000-1522.20200211
[26]	CHEN Z Y, HE Y C, IQBAL Y, et al. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq [J]. BMC Genomics, 2022, 23(1): 43. doi: 10.1186/s12864-021-08277-8
[27]	WEI Q Z, WANG W H, HU T H, et al. Construction of a SNP-based genetic map using SLAF-seq and QTL analysis of morphological traits in eggplant [J]. Frontiers in Genetics, 2020, 11: 178. doi: 10.3389/fgene.2020.00178
[28]	WANG R J, GAO X F, YANG J, et al. Genome-wide association study to identify favorable SNP allelic variations and candidate genes that control the timing of spring bud flush of tea (Camellia sinensis) using SLAF-seq [J]. Journal of Agricultural and Food Chemistry, 2019, 67(37): 10380−10391. doi: 10.1021/acs.jafc.9b03330
[29]	樊晓静, 于文涛, 蔡春平, 等. 利用SNP标记构建茶树品种资源分子身份证 [J]. 中国农业科学, 2021, 54(8):1751−1772. doi: 10.3864/j.issn.0578-1752.2021.08.014 FAN X J, YU W T, CAI C P, et al. Construction of molecular ID for tea cultivars by using of single-nucleotide polymorphism(SNP) markers [J]. Scientia Agricultura Sinica, 2021, 54(8): 1751−1772. (in Chinese) doi: 10.3864/j.issn.0578-1752.2021.08.014
[30]	魏中艳, 李慧慧, 李骏, 等. 应用SNP精准鉴定大豆种质及构建可扫描身份证 [J]. 作物学报, 2018, 44(3):315−323. doi: 10.3724/SP.J.1006.2018.00315 WEI Z Y, LI H H, LI J, et al. Accurate identification of varieties by nucleotide polymorphisms and establishment of scannable variety IDs for soybean germplasm [J]. Acta Agronomica Sinica, 2018, 44(3): 315−323. (in Chinese) doi: 10.3724/SP.J.1006.2018.00315