大花序桉群体适应性相关的SSR位点

doi:10.3969/j.issn.1000-2006.201811018

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南京林业大学学报（自然科学版） ›› 2019, Vol. 43 ›› Issue (5): 59-66.doi: 10.3969/j.issn.1000-2006.201811018

大花序桉群体适应性相关的SSR位点

王莉¹(), 李昌荣²(), 李发根¹, 周长品¹, 翁启杰¹, 吕佳斌¹, 陈健波², 陈剑成³, 甘四明¹^,²^,^*()

1.中国林业科学研究院热带林业研究所, 热带林业研究国家林业局重点实验室,广东广州 510520
2.广西壮族自治区林业科学研究院, 广西优良用材林资源培育重点实验室,中南速生材繁育国家林业局重点实验室,广西南宁 530002
3.玉林市林业科学研究所, 广西容县 537501

收稿日期:2018-11-09 修回日期:2018-12-19 出版日期:2019-10-08 发布日期:2019-10-08
基金资助:
广西创新驱动发展专项(桂科AA17204087-3);“广西主要用材林资源高效培育与利用人才小高地”专项(桂财社函[2018]112号)

SSR loci associated with population adaptation in Eucalyptus cloeziana

WANG Li¹(), LI Changrong²(), LI Fagen¹, ZHOU Changpin¹, WENG Qijie¹, LÜ Jiabin¹, CHEN Jianbo², CHEN Jiancheng³, GAN Siming¹^,²^,^*()

1. Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
2. Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation & Key Laboratory of Central South Fast-growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning 530002, China
3. Yulin Forestry Research Institute, Rongxian 537501, China

Received:2018-11-09 Revised:2018-12-19 Online:2019-10-08 Published:2019-10-08

摘要/Abstract

摘要：

【目的】检测大花序桉群体与环境适应性相关的基因组位点,为种质资源保护和利用提供分子生物学信息。【方法】利用84个SSR标记(包括29个基因组SSR 和55个EST-SSR)分析引种到广西,来源于澳大利亚昆土兰州北部和南部各7个大花序桉群体,通过Mantel 检验确定群体间是否存在地理隔离;检测群体间分化系数(F_st)离群值的受选择位点;并基于空间分析法检测与群体气候因子显著相关的等位片段,将显著相关位点的序列与NCBI数据库比对进行功能注释。【结果】大花序桉北部与南部群体间存在地理隔离,基于19个气候因子的聚类分析将北方与南方群体分为独立的组,这表明气候因子亦驱动了群体的分化。共检测到F_st离群值的受选择SSR位点39个(46.4%),其中,LOSITAN软件检测到12个正向选择位点和17个平衡选择位点。5个F_st离群值位点的6个等位片段与1个或多个气候因子显著相关(P<0.001),其等位频率在北部与南部群体间差异明显,其中,Embra6-118 bp与最冷月最低气温(T_mcm)显著相关,位点DNA序列的功能注释为碱性螺旋-环-螺旋(basic helix-loop-helix, bHLH)转录因子bHLH155;Embra20-121 bp与最暖季度降水量(P_wq)显著相关,位点的功能注释为蔗糖转运蛋白(sucrose transporters);EUCeSSR676-168 bp与T_mcm、P_wq、年均气温(T_ma)和最暖月最高气温(T_mwm)均显著相关,位点的功能注释为光系统Ⅱ稳定性/组装因子HCF136 (photosystem II stability/assembly factor HCF136);另外两个显著相关位点EUCeSSR298和EUCeSSR1009的功能未知。【结论】大花序桉北部与南部群体的显著分化受长期气候的影响,在第四纪大冰期可能存在北部和南部避难所。与气候因子显著相关的SSR位点在北部和南部群体间的等位频率差异为基于正向选择的气候适应性提供了分子证据。

关键词: 大花序桉, SSR标记, 气候因子, 正向选择, 群体适应性, 地理隔离

Abstract:

【Objective】 Genomic loci that are significantly associated with population adaptation were detected inEucalyptus cloeziana F. Muell. populations to obtain useful molecular information for germplasm conservation and utilization. 【Method】 Seven northern and southern populations of E. cloeziana were analyzed using 84 simple sequence repeats (SSR) markers [29 genomic SSRs and 55 expressed sequence tag (EST) derived SSRs]. Isolation by distance (IBD) among populations was determined using Mantel test. Outlier loci ofF-statistics of between-population differentiation (F_st) and their significant allelic associations with habitat climatic variables were investigated for all the SSR loci, with further functional annotation of the significantly associated loci against the NCBI non-redundant protein database. 【Result】 IBD was revealed between the northern and southern populations of E.cloeziana, and the clustering analysis based on 19 climatic variables also resulted in division of the northern and southern populations into independent groups, suggesting the climatic effect on driving the population divergence. A total of 39 F_st outliers (46.4%) were identified as selective loci. Specifically, the software LOSITAN detected 12 positive and 17 balancing selection loci. Six alleles from five outlier loci were identified with spatial analysis methods, each associated significantly with one or more climatic factors (P < 0.001) and showed dramatic difference in allelic frequency between the northern and southern populations. Among the six significant alleles, Embra6-118 bp was associated with the minimum temperature of the coldest month ( T_mcm), with the locus Embra6 functionally annotated as basic helix-loop-helix (bHLH) transcript factor bHLH155. The allele Embra20-121 bp was associated with the precipitation of the warmest quarter (P_wq), with Embra20 functionally annotated as sucrose transporters. EUCeSSR676-168 bp was associated with T_mcm, P_wq, the mean annual temperature (T_ma) and the minimum temperature of the warmest month (T_mwm), with the locus functionally annotated as photosystem II stability/assembly factor HCF136. However, the two other significant markers EUCeSSR298 and EUCeSSR1009 were of unknown function. 【Conclusion】 The divergence between the northern and southern populations of E. cloeziana was strongly related with historical climate, and there might be glacial refugia in the northern and southern zones during the Quaternary. The marked difference in the frequency of climate-associated SSR alleles between the northern and southern populations provides molecular evidence for positive selection oriented climatic adaptation in E. cloeziana.

Key words: Eucalyptus cloeziana, SSR marker, climatic factor, positive selection, population adaptation, isolation by distance (IBD)

中图分类号:

S718.51

王莉,李昌荣,李发根,等. 大花序桉群体适应性相关的SSR位点[J]. 南京林业大学学报（自然科学版）, 2019, 43(5): 59-66.

WANG Li, LI Changrong, LI Fagen, ZHOU Changpin, WENG Qijie, LÜ Jiabin, CHEN Jianbo, CHEN Jiancheng, GAN Siming. SSR loci associated with population adaptation in Eucalyptus cloeziana[J].Journal of Nanjing Forestry University (Natural Science Edition), 2019, 43(5): 59-66.DOI: 10.3969/j.issn.1000-2006.201811018.

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区域 region	群体 popu- lation	海拔/m altitude	气候因子climatic factors							频率/% frequency
区域 region	群体 popu- lation	海拔/m altitude	T_ma/ ℃	T_mcm/ ℃		T_mwm/ ℃		P_wq/ mm		Embra6- 118 bp		Embra20- 121 bp		EUCeSSR 298- 265 bp		EUCeSSR 676- 168 bp		EUCeSSR 1009- 179 bp		EUCeSSR 1009- 189 bp
北部 north	SC	250	24.2		16.8		30.9		932		0.0		50.0		35.7		57.1		7.1		28.6
	Bar	830	20.7		10.9		29.1		809		0.0		0.0		50.0		12.5		12.5		75.0
	Rav	1 000	19.5		8.9		28.5		661		0.0		8.3		50.0		16.7		16.7		25.0
	CarS	20	23.8		13.6		31.6		1097		20.0		5.0		55.0		50.0		10.0		40.0
	Car	6	23.9		13.8		31.6		1124		12.5		0.0		52.5		65.0		2.5		47.5
	PR	300	22.0		10.9		30.6		568		25.0		12.5		0.0		62.5		12.5		25.0
	MP	600	22.5		12.0		31.2		682		20.0		0.0		10.0		70.0		0.0		50.0
	平均 mean	429.4	22.4		12.41		30.50		839.0		11.07		10.83		36.17		47.69		8.76		41.59
南部 south	Nee	70	20.8		9.2		29.9		485		42.9		35.7		7.1		7.1		50.0		0.0
	GV	100	20.4		7.9		30.2		482		50.0		50.0		0.0		0.0		40.0		0.0
	WWP	210	20.3		8.4		29.7		513		40.0		40.0		0.0		10.0		50.0		0.0
	Wol	120	20.3		8.4		29.7		513		62.5		43.8		0.0		0.0		50.0		0.0
	TC	80	20.5		9.0		29.3		567		62.5		50.0		0.0		0.0		50.0		0.0
	Woo	400	19.6		7.9		28.9		567		66.7		44.4		11.1		0.0		33.3		5.6
	Pom	40	20.3		8.8		28.9		623		61.1		50.0		61.1		0.0		50.0		0.0
	平均 mean	145.7	20.30		8.51		29.51		535.7		55.09		44.84		11.34		2.45		46.19		0.79

SSR位点 SSR locus	等位片段/bp allele	T_ma	T_mcm	T_mwm	P_wq
Embra6	118	-	0.537 1^***	-	-
Embra20	121	-	-	-	0.382 6^***
EUCeSSR298	265	-	-	-	0.356 6^***
EUCeSSR676	168	0.662 2^***	0.661 2^***	0.621 5^***	0.496 1^***
EUCeSSR1009	179	0.523 3^***	0.590 1^***	0.457 4^***	0.535 7^***
	189	0.551 0^***	0.617 4^***	0.489 0^***	0.550 3^***

大花序桉群体适应性相关的SSR位点

SSR loci associated with population adaptation in Eucalyptus cloeziana

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[1]	姚俊修, 任飞, 王因花, 李庆华, 燕丽萍, 郑岩, 吴德军. 基于荧光SSR标记的接骨木种质资源遗传多样性分析[J]. 南京林业大学学报（自然科学版）, 2025, 49(2): 75-82.
[2]	韩新宇, 高露双, 秦莉, 庞荣荣, 刘鸣谦, 朱一泓, 田益雨, 张金. 林分密度对兴安落叶松径向生长-气候关系的影响[J]. 南京林业大学学报（自然科学版）, 2024, 48(2): 182-190.
[3]	罗楚滢, 佘济云, 唐子朝. 基于SSPs气候场景的濒危植物银杉潜在分布区预测[J]. 南京林业大学学报（自然科学版）, 2024, 48(1): 161-168.
[4]	高羽, 李静, 刘洋, 乌雅瀚, 巩家星, 辛启睿. 结构方程模型在兴安落叶松林生长中的应用[J]. 南京林业大学学报（自然科学版）, 2023, 47(1): 38-46.
[5]	郭常酉, 郭宏仙, 王宝华. 基于气候因子的杉木单木胸径生长模型构建[J]. 南京林业大学学报（自然科学版）, 2023, 47(1): 47-56.
[6]	王欢利, 严灵君, 黄犀, 王仲伟, 汤诗杰. 南京椴群体遗传多样性和遗传结构分析[J]. 南京林业大学学报（自然科学版）, 2023, 47(1): 145-153.
[7]	冯一宁, 李因刚, 祁铭, 周鹏燕, 周琦, 董乐, 徐立安. 基于SSR标记的福建省闽楠代表性群体遗传多样性分析[J]. 南京林业大学学报（自然科学版）, 2022, 46(4): 102-108.
[8]	李丹丹, 翁启杰, 甘四明, 周长品, 黄世能, 李梅. 基于EST-SSR标记鉴定猴耳环自由授粉的全同胞子代[J]. 南京林业大学学报（自然科学版）, 2022, 46(4): 95-101.
[9]	吴帆, 朱沛煌, 季孔庶. 马尾松分布格局对未来气候变化的响应[J]. 南京林业大学学报（自然科学版）, 2022, 46(2): 196-204.
[10]	何旭东, 郑纪伟, 孙冲, 何开跃, 王保松. 33个杨柳品种指纹图谱构建[J]. 南京林业大学学报（自然科学版）, 2021, 45(2): 35-42.
[11]	刘亚静, 周来, 张博, 陈丽萍, 潘磊, 孙玉军. 不同林龄杉木径向变化及其对气象因子的响应[J]. 南京林业大学学报（自然科学版）, 2021, 45(2): 135-144.
[12]	黄红兰, 钟沃谷, 衣德萍, 蔡军火, 张露. 未来气候变化对我国毛红椿适生区分布格局的影响预测[J]. 南京林业大学学报（自然科学版）, 2020, 44(3): 163-170.
[13]	易敏, 张露, 雷蕾, 程子珊, 孙世武, 赖猛. 湿地松转录组SSR分析及EST-SSR标记开发[J]. 南京林业大学学报（自然科学版）, 2020, 44(2): 75-83.
[14]	孙利娜, 周群, 黄妹平, 周长品, 徐世松, 杨舒婷, 杜铃, 甘四明, 唐庆. 基于SSR标记构建宝巾花品种的分子指纹[J]. 南京林业大学学报（自然科学版）, 2019, 43(6): 60-66.
[15]	李昌荣,陈健波,郭东强,翁启杰,卢翠香,李建凡,周维,甘四明. 锯材大花序桉生长和材性的综合指数选择[J]. 南京林业大学学报（自然科学版）, 2019, 43(01): 1-8.