A Novel Method for Molecular Identification of Genetic Diversity of Plant Resources in Abies Mill. and Keteleeria Carrière (Pinaceae) Based on Taxon-Specific Variable Nucleotide Characters from Complete Plastomes
Accurate identification of genetic diversity at species/varietas levels is essential for sustainable utilization of plant resources. The genus Abies Mill. and Keteleeria Carrière are two closely related plant groups in the Pinaceae. In this paper, 107 taxon-specific variable nucleotide characters in the plastomes of species/varietas from Abies and Keteleeria were used as molecular traits to identify the plant genetic resource diversity of these plant genera and to compile a molecular classification key for the first time. There are differences in aspects of amount and base composition of variable nucleotide characters among the species/varietas. The amount of taxon-specific variable nucleotide characters in Keteleeria davidiana (C.E. Bertrand) Beissn. var. davidiana (44) is the highest, higher than that in Keteleeria evelyniana Mast. (34) or Abies sachalinensis (F. Schmidt) Mast. (19) or Abies veitchii Lindl.(10). In Keteleeria davidiana (C.E. Bertrand) Beissn. var. davidiana, the proportion of T(36.36%) ishigher than that of A(29.55%), or G(20.45%), C (13.64%) and is 2.6 times that of C. In Keteleeria evelyniana, the proportion of A (50.00%) is the highest and is 2.7 times that of T or C (17.65%), and 3.4 times that of G (14.71%). In Abies sachalinensis, the proportion of C (31.58%) is the highest, higher than T (26.32%), A (21.05%) or G (21.05%), and is 1.5 times that of A or G. In Abies veitchii, the proportion of C (30.00%) is the highest, 1.5 times that of each of the other three nucleotides. Our results indicated that taxon-specific variable nucleotide characters from the plastomes could be used for distinguishing different species successfully in the genus Abies and Keteleeria. The status of Abies and Keteleeria plant specimens collected in the past over 120 years in China is investigated and problems and possible strategies have been discussed. This study is valuable for taxonomic revision, conservation and utilization of Abies and Keteleeria plant germplasm resources.
Pinaceae
松科是裸子植物中最大的科,利用球果、花粉、胚、苞鳞、种鳞、种子、子叶、叶(形态及生理习性)、染色体核型、气孔类型等的形态特征划分为10属,即松属Pinus L.、云杉属Picea A. Dietr.、银杉属Cathaya Chun & Kuang、黄杉属Pseudotsuga Carrière、落叶松属Larix Mill.、铁杉属Tsuga (Endl.) Carrière、金钱松属Pseudolarix Gordon、冷杉属Abies Mill.、油杉属Keteleeria Carrière和雪松属Cedrus Trew;根据雌球花、球果、种翅、叶、气孔线、柔毛、芽型、树枝(果枝、营养枝、枝的年龄及其表皮)等的形态特征进一步分类,全球约有230种/亚种/变种
由于形态特征存在一定的种间相似性,形态性状的表现受环境条件(不同季节或地区)的影响,不同分类专家对各形态特征在分类学上的重要性的判断存在差异,导致分类观点产生差异。例如,油杉属与冷杉属的物种在形态特征方面相似性较高,油杉属的物种最早被归类在冷杉属内。1866年,以油杉(Keteleeria fortunei (A. Murray bis) Carrière)为模式种,从冷杉属中独立出来,成立了油杉属
油杉属和冷杉属植物具有很高的生态、经济和观赏价值,急需研究、制定高效的保护和可持续利用对策。其物种分类鉴定研究经历了形态学、细胞学、孢粉学、化学成分、RAPD、PCR-RFLP、AP-PCR、SSCP、SSR标记、DNA条形码技术等阶段,上述方法信息量较少、分辨率有限
选取10份样品代表油杉属和冷杉属的4个种/变种。供试样品名称及其质体基因组的序列号如
拉丁学名 Latin name |
中文名称 Chinese name |
序列号 Genbank accession no. |
|
1 |
Abies sachalinensis (F.Schmidt) Mast. |
库页冷杉 |
LC509035.1 |
2 |
Abies sachalinensis (F.Schmidt) Mast. |
库页冷杉 |
LC509036.1 |
3 |
Abies veitchii Lindl. |
白叶冷杉 |
OR459817.1 |
4 |
Abies veitchii Lindl. |
白叶冷杉 |
OR459820.1 |
5 |
Abies veitchii Lindl. |
白叶冷杉 |
OR459821.1 |
6 |
Abies veitchii Lindl. |
白叶冷杉 |
OR459823.1 |
7 |
Keteleeria davidiana (C.E. Bertrand) Beissn. var. davidiana |
铁坚油杉(原变种) |
OQ657007.1 |
8 |
Keteleeria davidiana (C.E. Bertrand) Beissn. var. davidiana |
铁坚油杉(原变种) |
OQ657008.1 |
9 |
Keteleeria evelyniana Mast. |
云南油杉 |
OQ657001.1 |
10 |
Keteleeria evelyniana Mast. |
云南油杉 |
OQ657028.1 |
11 |
Tsuga diversifolia (Maxim.) Mast. |
米铁杉* |
MH171102.1 |
12 |
Tsuga diversifolia (Maxim.) Mast. |
米铁杉* |
OR528870.1 |
注:*外类群。
油杉属和冷杉属供试样品的质体基因组的长度为116,867 (OQ657001.1,云南油杉Keteleeria evelyniana Mast.)~121,412 (OR459817.1,白叶冷杉Abies veitchii Lindl.)个核苷酸。在比对序列中,共检测到4592个核苷酸变异位点,占质体基因组序列全长的约3.93%。其中,具有分类价值的特有核苷酸变异位点数目合计为107个核苷酸,占变异位点总数的2.33%。
铁坚油杉(原变种)Keteleeria davidiana (C.E. Bertrand) var. davidiana (44)的特有变异位点的数量最多,
* |
A (%)** |
T (%)** |
C (%)** |
G (%)** |
Total*** 合计 (%) |
1a |
13 (29.55) |
16 (36.36) |
6 (13.64) |
9 (20.45) |
44 (41.12/0.96) |
1b |
9 (20.45) |
4 (9.09) |
17 (38.64) |
14 (31.82) |
44 (41.12/0.96) |
2a |
17 (50.00) |
6 (17.65) |
6 (17.65) |
5 (14.71) |
34 (31.78/0.74) |
2b |
5 (14.71) |
7 (20.59) |
10 (29.41) |
12 (35.29) |
34 (31.78/0.74) |
3a |
2 (20.00) |
2 (20.00) |
3 (30.00) |
2 (20.00) |
10 (9.35/0.22) |
3b |
1 (11.11) |
2 (22.22) |
3 (33.33) |
3 (33.33) |
9 (8.41/0.20) |
4a |
4 (21.05) |
5 (26.32) |
6 (31.58) |
4 (21.05) |
19 (17.76/0.41) |
4b |
6 (31.58) |
6 (31.58) |
3 (15.79) |
4 (21.05) |
19 (17.76/0.41) |
合计 |
107/4592 |
注:*该列的序号与检索表内的序号对应,1a为铁坚油杉(原变种),2a为云南油杉,3a为白叶冷杉,4a为库页冷杉。**核苷酸变异位点数(在4种碱基中的占比);***此列括号中,前一个数字是在物种特有变异位点总数(107)中所占的比例;后一个数字是在全部核苷酸变异位点总数(4592)中所占的比例。
随后依次为云南油杉Keteleeria evelyniana Mast. (34)、库页冷杉Abies sachalinensis (F. Schmidt) Mast. (19)以及白叶冷杉Abies veitchii Lindl. (10)。铁坚油杉(原变种)的特有变异位点中,T的比例(36.36%)最高,随后依次为A (29.55%)、G (20.45%)和C (13.64%),T的比例约为C的比例的2.6倍。云南油杉的特有变异位点中,A的比例(50.00%)最高,是T或C的比例(17.65%)的约2.8倍,是G的比例(14.71%)的约3.4倍。库页冷杉的特有变异位点中,C的比例(31.58%)最高,随后依次为T (26.32%)、A (21.05%)和G(21.05%),C的比例为A或G的比例的约1.5倍。白叶冷杉的特有变异位点中,C的比例(30.00%)最高,是另外3种碱基比例的1.5倍(
中国数字植物标本库(
(a) |
||||||
种/变种 Species/Varietas |
中文名 Chinese name |
标本份数 Amount of herbarium sheets |
||||
1 |
Keteleeria davidiana (C.E. Bertrand) Beissn. |
铁坚油杉 |
611 |
|||
2 |
Keteleeria davidiana (C.E. Bertrand)var. davidiana |
铁坚油杉(原变种) |
353 |
|||
3 |
Keteleeria davidiana var. formosana (Hayata) Hayata |
台湾油杉 |
4 |
|||
4 |
Keteleeria evelyniana Mast. |
云南油杉 |
520 |
|||
5 |
Keteleeria fortunei (A. Murray bis) Carrière |
油杉 |
577 |
|||
6 |
Keteleeria fortunei var. rhombisquama |
1 |
||||
合计 |
2066 |
|||||
(b) |
||||||
种/亚种/变种 Species/Subspecies/Varietas |
中文名 Chinese name |
标本份数 Amount of herbarium sheets |
||||
1 |
Abies alba Mill. |
欧洲冷杉 |
23 |
|||
2 |
Abies amabilis (Douglas ex. Loudon) J. Forbes |
10 |
||||
3 |
Abies balsamea (L.) Mill. |
胶冷杉 |
28 |
|||
4 |
Abies beshanzuensis M.H. Wu |
百山祖冷杉 |
24 |
|||
5 |
Abies borisii-regis Mattf. |
14 |
||||
6 |
Abies bracteata (D. Don) Poit. |
11 |
||||
7 |
Abies cephalonica Loudon |
希腊冷杉 |
43 |
|||
8 |
Abies chensiensis Tiegh. |
秦岭冷杉 |
163 |
|||
9 |
Abies chensiensis subsp. salouenensis (Bordères & Gaussen) Rushforth |
云南黄果冷杉 |
139 |
|||
10 |
Abies chensiensis subsp. yulongxueshanensis Rushforth |
玉龙雪山冷杉 |
2 |
|||
11 |
Abies cilicica (Antoine & Kotschy) Carrière |
西里西亚冷杉 |
7 |
|||
12 |
Abies concolor (Gordon) Lindl. ex. Hildebr. |
白冷杉 |
10 |
|||
13 |
Abies delavayi Franch. |
大理冷杉 |
302 |
|||
14 |
Abies delavayi subsp. fansipanensis (Q.P. Xiang, L.K.Fu & Nan Li) Rushforth |
越南冷杉 |
2 |
|||
15 |
Abies delavayi var. motuoensis W.C. Cheng & L.K. Fu |
墨脱冷杉 |
45 |
|||
16 |
Abies delavayi var. nukiangensis (W.C. Cheng & L.K. Fu) Farjon & Silba |
怒江冷杉 |
33 |
|||
17 |
Abies densa Griff. |
锡金冷杉 |
42 |
|||
18 |
Abies durangensis Martínez |
杜兰戈冷杉 |
8 |
|||
19 |
Abies durangensis var. coahuilensis (I.M. Johnstone) Martínez |
杜兰戈冷杉科阿韦拉变种 |
1 |
续表
20 |
Abies fabri (Mast.) Craib |
峨眉冷杉 |
584 |
21 |
Abies fabri subsp. minensis (Bordères & Gaussen) Rushforth |
1 |
|
22 |
Abies fanjingshanensis W.L.Huang, Y.L. Tu & S.Z. Fang |
梵净山冷杉 |
46 |
23 |
Abies fargesii Franch. |
巴山冷杉 |
488 |
24 |
Abies fargesii var. faxoniana (Rehder & E.H. Wilson) Tang S.Liu |
岷江冷杉 |
740 |
25 |
Abies fargesii var. sutchuenensis Franch. |
洮河冷杉 |
41 |
26 |
Abies firma Siebold & Zucc. |
日本冷杉 |
167 |
27 |
Abies flinckii Rushforth |
3 |
|
28 |
Abies forrestii Coltm.-Rog. |
长苞冷杉 |
654 |
29 |
Abies forrestii var. ferreana (Bordères & Gaussen) Farjon & Silba |
中甸冷杉 |
138 |
30 |
Abies forrestii var. georgei (Orr) Farjon |
长苞冷杉一变种 |
6 |
31 |
Abies forrestii var. smithii R.Vig. & Gaussen |
急尖长苞冷杉 |
324 |
32 |
Abies fraseri (Pursh) Poir. |
9 |
|
33 |
Abies grandis (Douglas ex. D. Don) Lindl. |
大冷杉 |
8 |
34 |
Abies guatemalensis Rehder |
危地马拉冷杉 |
26 |
35 |
Abies hickelii Flous & Gaussen |
30 |
|
36 |
Abies hidalgensis Debreczy, I.Rácz & Guízar |
4 |
|
37 |
Abies holophylla Maxim. |
臭冷杉 |
137 |
38 |
Abies homolepis Siebold & Zucc. |
日光冷杉 |
24 |
39 |
Abies homolepis var. umbellata (Mayr) E.H. Wilson |
1 |
|
40 |
Abies jaliscana (Martínez) Mantilla, Shalisko & A.Vázquez |
1 |
|
41 |
Abies kawakamii (Hayata) Ito |
台湾冷杉 |
26 |
42 |
Abies koreana E.H. Wilson |
朝鲜冷杉 |
16 |
43 |
Abies lasiocarpa (Hook.) Nutt. |
落基山冷杉 |
18 |
44 |
Abies lasiocarpa var. arizonica (Merriam) Lemmon |
毛果冷杉 |
1 |
45 |
Abies magnifica A. Murray bis |
1 |
|
46 |
Abies mariesii Mast. |
3 |
|
47 |
Abies motuoensis |
3 |
|
48 |
Abies nebrodensis (Lojac.) Mattei |
4 |
|
49 |
Abies nephrolepis (Trautv. ex. Maxim.) Maxim. |
沙松冷杉 |
392 |
50 |
Abies nordmanniana (Steven) Spach |
高加索冷杉 |
15 |
51 |
Abies nordmanniana subsp. equi-trojani (Asch. & Sint. ex. Boiss.) Coode & Cullen |
5 |
|
52 |
Abies numidica de Lannoy ex. Carrière |
阿尔及利亚冷杉 |
15 |
53 |
Abies pindrow (Royle ex. D. Don) Royle |
喜马拉雅冷杉 |
13 |
续表
54 |
Abies pindrow var. brevifolia Dallim. & A.B. Jacks. |
1 |
|
55 |
Abies pinsapo Boiss. |
西班牙冷杉 |
6 |
56 |
Abies pinsapo subsp. marocana (Trab.) Emb. & Maire |
1 |
|
57 |
Abies procera Rehder |
壮丽冷杉 |
3 |
58 |
Abies recurvata Mast. |
188 |
|
59 |
Abies recurvata var. ernestii (Rehder) Rushforth |
黄果冷杉 |
381 |
60 |
Abies religiosa (Kunth) Schltdl. & Cham. |
15 |
|
61 |
Abies sachalinensis (F. Schmidt) Mast. |
北海道冷杉 |
11 |
62 |
Abies sachalinensis var. mayriana Miyabe & Kudô |
1 |
|
63 |
Abies sibirica Ledeb. |
新疆冷杉 |
60 |
64 |
Abies spectabilis (D. Don) Mirb. |
西藏冷杉 |
134 |
65 |
Abies squamata Mast. |
紫果冷杉 |
289 |
66 |
Abies veitchii Lindl. |
白叶冷杉 |
12 |
67 |
Abies veitchii var. sikokiana (Nakai) Kusaka |
1 |
|
68 |
Abies vejarii Martínez |
8 |
|
69 |
Abies vilmorinii Mast. |
1 |
|
70 |
Abies yuanbaoshanensis Y.J. Lu & L.K. Fu |
元宝山冷杉 |
25 |
71 |
Abies ziyuanensis L.K. Fu & S.L. Mo |
华南冷杉 |
47 |
合计 |
6,035 |
铁坚油杉(原变种)(353份)的标本数量较多,台湾油杉(4份)和Keteleeria fortunei var. rhombisquama(1份)的标本数量很少(
冷杉属标本的最早采集记录是1900年,经过120多年的积累,来自国内外的冷杉属植物标本数量共计6035份,71个种/亚种/变种(
有些名称实际上是冷杉属以外的其它属的物种的异名。例如,Abies davidiana (C.E. Bertrand) Franch.及Abies sacra Franch.是铁坚油杉Keteleeria davidiana (C.E. Bertrand) Beissn.的异名;Abies larix J.St.-Hil.是欧洲落叶松Larix decidua (L.) Mill.的异名;Abies gmelinii Rupr.是兴安落叶松Larix gmelinii (Rupr.) Kuzen.的异名;Abies pectinata Gilib.是欧洲云杉Picea abies (L.) H. Karst.的异名;Abies brachytyla Franch.是麦吊云杉Picea brachytyla (Franch.) Pritz.的异名;Abies likiangensis Franch.是丽江云杉Picea likiangensis (Franch.) E. Pritz.的异名;Abies sitchensis (Bong.) Lindl. & Gordon是巨云杉Picea sitchensis (Bong.) Carrière的异名;Abies chinensis Franch.、Abies dumosa var. chinensis (Franch.) Franch.是Tsuga chinensis (Franch.) Pritz.的异名;Abies yunnanensis Franch.是云南铁杉Tsuga dumosa (D. Don) Eichler的异名(
52%以上的冷杉属植物标本的采集日期为50年以前。冷杉属植物标本的121个名称中,异名(50个)的比例占41.32%。岷江冷杉(740份)、长苞冷杉(654份)、峨眉冷杉(584份)以及巴山冷杉(488份)的标本份数最多。大于100份标本的有16个种/亚种/变种。大于3份(含)标本的有58个种/亚种/变种,小于3份标本的有13个种/亚种/变种。相关研究团队应该同时赠送一套供试样品各物种的标本到国家植物标本馆,以便分享准确的物种形态鉴定信息,减少异名对科学发展造成的混乱影响。对21国40个植物标本馆的4500份标本的取样调查结果显示,50%以上的热带植物标本存在名称鉴定错误
由于人工种植历史悠久,油杉属植物的叶绿体单倍型资源的收集保存和研究应该是未来的方向之一,有助于深入研究杂交后代群体的遗传变异及价值。全球范围内探讨科属内全部物种的分类和进化关系,应该是研究的方向和趋势。全球野外调查和样品采集滞后仍然是制约相关研究的重要因素之一。本文报道的新方法从叶绿体基因组序列大数据中提取可用于物种分类的关键特征数据,在应用人工智能管理和利用全球植物资源多样性方面可达到节省算力、提高运算速度的目的。
本研究得到天津市人力资源和社会保障局、天津市人力资源建设服务中心、山东省人力资源和社会保障厅、鲁东大学、上海市人力资源和社会保障局、上海计算技术培训中心、上海海洋大学以及国家专业技术人才知识更新工程项目的大力支持。袁国华、方爱国、崔正、杨智慧、严志宏和田宏进行了有意义的讨论。
国家自然科学基金项目(No. 31770744)。
*通讯作者。