SNP Markers Development and Genetic Relationship Identification of Germplasm Resources of Canarium album Based on SLAF-Seq Technology
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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。 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. -
Key words:
- Canarium album /
- germplasm resource /
- SNP marker /
- genetic structure /
- genetic diversity
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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
name1 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 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 readsGC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 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 IDSNP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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