基于基因组学的栎树生物学研究进展

doi:10.12302/j.issn.1000-2006.202208025

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (6): 64-72.doi: 10.12302/j.issn.1000-2006.202208025

所属专题：南京林业大学120周年校庆特刊

基于基因组学的栎树生物学研究进展

方炎明(), 朱福远, 李垚, 李璇

南京林业大学,南方现代林业协同创新中心,国家林业和草原局亚热带森林生物多样性保护重点实验室,南京林业大学生物与环境学院,江苏南京 210037

收稿日期:2022-08-22 修回日期:2022-09-14 出版日期:2022-11-30 发布日期:2022-11-24
基金资助:
国家自然科学基金项目(31770699);国家自然科学基金项目(32201375);国家自然科学基金项目(31370666);江苏省林业三新工程项目(LYSX[2016]49)

Advances and prospects of oak biology based on genomics

FANG Yanming(), ZHU Fuyuan, LI Yao, LI Xuan

Co-Innovation Center for Sustainable Forestry in Southern China,Key Laboratory of state Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation,College of Biology and the Environment, Nanjing Forestry University,Nanjing 210037,China

Received:2022-08-22 Revised:2022-09-14 Online:2022-11-30 Published:2022-11-24

摘要/Abstract

摘要：

栎树(Quercus spp.)是北半球重要的经济与生态树种。夏栎(Q. robur)、加州白栎(Q. lobata)、麻栎(Q. acutissima)等树种基因组的公布,对栎树生物学研究产生了深刻的影响。近5年来,栎树生物学出现了包括系统进化与物种鉴定、基因渐渗与适应进化、景观基因组学与生态保育、生物共存与互作机制、次生代谢与生长发育、DNA甲基化与表观遗传调控及基因与长寿机制等方面的研究热点。虽然基于基因组学的栎树生物学若干研究前沿已经形成,但尚处于起步阶段,笔者预期未来会向4个方面深入:①强调栎树基因组资源的深度应用。应用景观基因组学途径,探究栎树的杂交渐渗与适应进化;联合基因组、转录组、蛋白组等多组学技术,探究栎树生长发育与胁迫响应过程中的基因调控网络与信号通路;优化体细胞发生和遗传转化体系,攻克栎树遗传改良和基因资源开发技术瓶颈。②促进栎树研究体系的广度拓展。随着壳斗科其他树种全基因组序列的公布,基于从分子到群落的不同生物层次的模式系统,将对欧亚大陆和北美不同区域的栎树,包括白栎组、红栎组、冬青栎组、麻栎组等不同栎树类群,以及壳斗科其他属树种基因组生物学研究产生深远影响。③关注栎树资源利用的遗传与发育主题。用栎树基因组资源对其结构的、代谢的和农艺性状的差异及其优化加以解析,全基因组关联研究(GWAS)也将应用于栎树,从而为阐释木材发育和木栓形成的机制奠定基础。④聚焦栎林保育的生态与进化主题。在全球气候变化背景下,通过增加耐受胁迫的基因型,以缓解气候变化对森林生态系统的影响。同时维持和保护栎树在自然生态系统中的生态与进化过程,阐明栎树多样性、迁移与适应、趋异与趋同生态适应等方面进化成功的机制。

关键词: 栎树, 基因组, 基因渐渗, 景观基因组学, 资源保育

Abstract:

Oaks are important economic and ecological tree species in the northern Hemisphere, and are colloquially known as the “tree of life” or the “frame of civilization”. The publication of several oak genomes, such as those of Quercus robur, Q. lobata and Q. acutissima, has a profound impact on oak biology. In the past five years,numerous topics in oak biology have been investigated, including the systematic evolution and species identification, gene introgression and adaptive evolution, landscape genomics and ecological conservation, biological coexistence and interaction mechanism, secondary metabolism and growth and development, DNA methylation and epigenetic regulation, genes and longevity mechanisms. The expected development trends include four aspects: highlighting the in-depth application of oak genome resources, promoting extension of oak study systems, emphasizing topics in genetics and development for utilization of oak resources, and highlighting themes in ecology and evolution for conservation of oak forests.

Key words: oak, genome, gene introgression, landscape genomics, resource conservation

中图分类号:

S718

方炎明,朱福远,李垚,等. 基于基因组学的栎树生物学研究进展[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 64-72.

FANG Yanming, ZHU Fuyuan, LI Yao, LI Xuan. Advances and prospects of oak biology based on genomics[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(6): 64-72.DOI: 10.12302/j.issn.1000-2006.202208025.

图/表 3

表1

叶绿体全基因组数据已完成测序的栎属植物"

亚属 subgen.	组 Sect.	树种(首次报道的GenBank序列号) tree species(first reported GenBank accession No.)
栎亚属 Quercus	弗吉尼亚栎组 Virentes	弗吉尼亚栎Q. virginiana (MT916773)
	白栎组 Quercus	槲栎Q. aliena (KP301144);锐齿槲栎Q. aliena var. acutiserrata (KU240008);槲树Q. dentata (MG967555);黄山栎Q. dentata subsp. stewardii (MG678022);白栎Q. fabri (MG678031);凤城栎Q. fenchengensis (MN095295);深裂叶栎Q. gambelii (MK105457);大叶栎Q. griffithii (MG678034);大果栎Q. macrocarpa (MK105459);蒙古栎Q. mongolica (MG678033);皱叶栎Q. mongolica subsp. crispula (MK860969);无梗花栎 Q. petraea (LT996899);夏栎Q. robur (LT996900);枹栎Q. serrata (MG678024);短柄枹栎Q. serrata var. brevipetiolata (MG678032);星毛栎Q. stellata (MK105467);辽东栎Q. wutaishanica (MG678027)和云南波罗栎Q. yunnanensis (MG678028)
	红栎组 Lobatae	海滨常绿栎Q. agrifolia (OK634019);猩红栎Q. coccinea (MN308055);加州黑栎Q. kelloggii (OM541584);沼生栎Q. palustris (MK105461);柳叶栎Q. phellos (MZ196210);红槲栎Q. rubra (JX970937)和山地常绿栎Q. wislizeni (OM541583)
麻栎亚属 Cerris	青冈组 Cyclobalanopsis	赤栎Q. acuta (MT742291);细叶青冈Q. ciliaris (MN199024);福建青冈Q. chungii (MW401633);黄毛青冈Q. delavayi (MW450870);华南青冈Q. edithiae (KU382355);饭甑青冈Q. fleuryi (MG678008);赤皮青冈Q. gilva (MG678009);青冈Q. glauca (KX852399);大叶青冈Q. jenseniana (MG678011);木姜叶青冈Q. litseoides (ON598394);多脉青冈Q. multinervis (MG678004);小叶青冈Q. myrsinifolia (MG678005);竹叶青冈Q. neglecta (MG678010);宁冈青冈Q. ningangensis (MG678013);倒卵叶青冈Q. obovatifolia (MG356785);薄叶青冈Q. saravanensis (MW411183);滇青冈Q. schottkyana (=Q.glaucoides, MW450872);云山青冈Q. sessilifolia (MG678012);西畴青冈Q. sichourensis (MF787253)和褐叶青冈Q. stewardiana (MN199023)
	冬青栎组 Ilex	岩栎Q. acrodonta (MG678019);川滇高山栎Q. aquifolioides (KP340971);橿子栎Q. baronii (KT963087);坝王栎Q. bawanglingensis (MK449426);铁橡栎Q. cocciferoides (MG678016);匙叶栎Q. dolicholepis (KU240010);巴东栎Q. engleriana (MG678029);锥连栎Q. franchetii (MG678018);川西栎Q. gilliana (MG678007);帽斗栎Q. guyavifolia (MG678020);矮高山栎Q. monimotricha (MG678006);尖叶栎Q. oxyphylla (MG678021);黄背栎Q. pannosa (MG678025);乌冈栎Q. phillyraeoides (MG678026);毛脉高山栎Q. rehderiana (MG678037);光叶高山栎Q. pseudosemecarpifolia (MG678014);高山栎Q. semecarpifolia (MG678017);灰背栎Q. senescens (MG678023);刺叶高山栎Q. spinosa (KM841421);太鲁阁栎Q. tarokoensis (MF135621);通麦栎Q. tungmaiensis (MF593893)和炭栎Q. utilis (MG678015)
	麻栎组 Cerris	麻栎Q. acutissima (MF593895);小叶栎Q. chenii (MF593894)和栓皮栎Q. variabilis (KU240009)

表1

表2

表3

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组 Sect.	树种 species	遗传标记 genetic markers	文献 reference
麻栎组Cerris	麻栎Q. acutissima、栓皮栎Q. variabilis	nSNPs	[6]
白栎组 Quercus	夏栎Q. robur、无梗花栎Q. petraea	nSNPs、cpSNPs、mtSNPs	[22]
	夏栎Q. robur、无梗花栎Q. petraea	nSNPs	[23]
	槲树Q. dentata、皱叶栎Q. mongolica subsp. crispula	nSNPs	[24]
红栎组 Lobatae	北方针栎Q. ellipsoidalis、红槲栎Q. rubra	EST-SSRs	[25]
红栎组 Lobatae	猩红栎Q. coccinea、北方针栎Q. ellipsoidalis、红槲栎Q. rubra和黑栎Q. velutina	SSRs、EST-SSRs	[26]
中间栎组Protobalanus	金杯栎Q. chrysolepis、岛屿栎Q. tomentella	nSNPs	[27]
麻栎组和冬青栎组 Cerris and Ilex	冬青栎Q. ilex、欧洲栓皮栎Q. suber	nSSRs	[28]
麻栎组和白栎组 Cerris and Quercus	麻栎Q. acutissima、白栎Q. fabri、枹栎Q. serrata和栓皮栎Q. variabilis	nSSRs	[29]

树种 species	个体数 number of individuals	测序方法 sequencing method	SNP数 number of SNPs	参考基因组 reference genome	主要发现 main findings	文献 reference
川滇高山栎 Q. aquifolioides	587	Pool-seq	381	夏栎 Q. robur	RONA分析表明有一个谱系适应能力更强;在长寿广布栎树中检测到自然选择和分子适应相关的遗传印记;物种在异质生境中发生了不同的种内适应过程	[41]
加州白栎 Q. lobata	436	GBS	11 019	加州白栎 Q. lobata	许多位点可能是多空间尺度或多地理环境局域适应的基础,新候选基因与气候适应关联	[42]
网叶栎 Q. rugosa	103	GBS	5 354	加州白栎 Q. lobata	遗传变异的空间模式与降水季节性和地理距离密切相关,预测了种群未来面临风险的区域	[46]
麻栎 Q. acutissima	167	RAD-seq	55 361	加州白栎 Q. lobata	环境对非中性SNP的影响大于中性SNP,环境与表型分化显著相关;同质园试验与景观基因组学数据相结合可验证栎树局域适应假设	[47]
欧洲栓皮栎 Q. suber	95	GBS	1 996	加州白栎 Q. lobata	RONA分析途径可以应用于物种响应气候变化与适应研究	[48]
槲树 Q. dentata	38	WGS	16 654 671	夏栎 Q. robur	发现一个500 kb基因组区域,含12个环境相关单核苷酸多态性位点;单核苷酸多态性密度比基因组背景高160倍;群体遗传分析揭示了该基因组区域的各种选择迹象	[49]

基于基因组学的栎树生物学研究进展

Advances and prospects of oak biology based on genomics

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