SSR loci associated with population adaptation in Eucalyptus cloeziana

doi:10.3969/j.issn.1000-2006.201811018

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2019, Vol. 43 ›› Issue (5): 59-66.doi: 10.3969/j.issn.1000-2006.201811018

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
Contact: GAN Siming E-mail:wangli3hao@126.com;andyharry@126.com;siminggan@caf.ac.cn

Abstract

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)

CLC Number:

S718.51

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, 2019, 43(5): 59-66.

Figures/Tables 7

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Table 1

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References 42

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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^***

SSR loci associated with population adaptation in Eucalyptus cloeziana

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