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
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:
FANG Yanming(), ZHU Fuyuan, LI Yao, LI Xuan
Received:
2022-08-22
Revised:
2022-09-14
Online:
2022-11-30
Published:
2022-11-24
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。
中图分类号:
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.
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2
栎树杂配群与适应性渐渗研究案例"
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 | [ |
白栎组 Quercus | 夏栎Q. robur、无梗花栎Q. petraea | nSNPs、cpSNPs、mtSNPs | [ |
夏栎Q. robur、无梗花栎Q. petraea | nSNPs | [ | |
槲树Q. dentata、皱叶栎Q. mongolica subsp. crispula | nSNPs | [ | |
红栎组 Lobatae | 北方针栎Q. ellipsoidalis、红槲栎Q. rubra | EST-SSRs | [ |
猩红栎Q. coccinea、北方针栎Q. ellipsoidalis、红槲栎Q. rubra和黑栎Q. velutina | SSRs、EST-SSRs | [ | |
中间栎组Protobalanus | 金杯栎Q. chrysolepis、岛屿栎Q. tomentella | nSNPs | [ |
麻栎组和冬青栎组 Cerris and Ilex | 冬青栎Q. ilex、欧洲栓皮栎Q. suber | nSSRs | [ |
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 | [ |
表3
栎树景观基因组学研究的若干案例"
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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