Short RNAs, potential novel molecular markers for higher plants

doi:10.3724/SP.J.1003.2012.08123

Abstract

Abstract:

In recent years, molecular biology techniques, especially molecular markers, have been applied to the study of species similarity and evolutionary relationships in the field of plant systematics. Here, we attempted to find a small fragment of RNA that could be used as a molecular marker for the rapid identification of plant taxa above genus. To do so, total nucleic acids were isolated from 53 species of higher plants using SDS extracting solution containing HAc-NaAc buffer. The isolated nucleic acids were subjected to 7% polyacrylamide gel electrophoresis (PAGE). Results showed: (1) A large number of bands, which were at the length of 100-200 bases and with clear shape. The bands patterns were stable and repeatable. These segments were confirmed to be short RNAs by DNaseI and RNaseA treatment; (2) No obvious differences in band patterns were found among different varieties, organs, sexualities and ploidy of kiwifruit seedlings. A similar case existed in mung bean seedlings after different light treatment periods; (3) Banding patterns of plants in the same family were polymorphic, with differences mainly related to geographic isolation. Higher taxonomic categories had a higher percentage of polymorphic band (PPB) and higher values of polymorphism information content (PIC) than lower taxonomic categories; (4) Three to six clear bands with a length of 100-200 bases, whose band patterns were related to the phylogenic relationship, were found through comparison of short RNAs from 53 species of ferns, gymnosperms and angiosperms. Thus, short RNAs with a length of 100-200 bases showed potential as a molecular marker for determining inter- or intrafamily phylogenic relationships.

Key words: SDS method, total nucleic acid, short RNA, phylogenic relationship, molecular markers

Wen Liu, Hong Liang, Biren Yang, Jiewen Lin, Yanji Hu. Short RNAs, potential novel molecular markers for higher plants[J]. Biodiv Sci, 2012, 20(1): 86-93.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2012.08123

https://www.biodiversity-science.net/EN/Y2012/V20/I1/86

Figures/Tables 7

References 27

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分类阶元 Taxonomic category		中文名 Chinese name	拉丁名 Scientific name
被子植物门 Angiospermae
双子叶植物纲 Dicotyledononeae	猕猴桃科 Actinidiaceae	中华猕猴桃品种红阳♂	A. chinensis ‘Hongyang’♂
		中华猕猴桃品种红阳♀	A. chinensis ‘Hongyang’♀
		中华猕猴桃品种武雄♂	A. chinensis ‘Wuxiong’♂
		中华猕猴桃品种武植3号♀	A. chinensis ‘Wuzhi No.3’♀
		美味猕猴桃品种帮增1号♂	A. chinensis var. deliciosa‘Bangzeng No.1’♂
		美味猕猴桃品种和平1号♀	A. chinensis var. deliciosa ‘Heping No.1’♀
		美味猕猴桃品种米良1号♀	A. chinensis var. deliciosa ‘Miliang No.1’ ♀
	桑科 Moraceae	大叶榕	Ficus altissima Blume
		水同木	Ficus fistulosa Reinw. ex Blume
		垂叶榕	Ficus benjamina L.
		柳叶榕	Ficus variolosa Lindl. ex Benth.
		细叶榕	Ficus microcarpa L. f.
		桂木	Artocarpus nitidus subsp.lingnanensis(Merr.) F. M. Jarrett
		面包树	Artocarpus communis J. R. Forst. et G. Forst.
		树菠萝	Artocarpus heterophyllus Lam.
	豆科 Leguminosae	红花羊蹄甲	Bauhinia blakeanaDunn
		酸豆	Tamarindus indica L.
		紫花苜蓿	Medicago sativa L.
		花生	Arachis hypogaeaL.
		柱花草	Stylosanthes scabra Vogel.
		黄槐	Cassia surattensis Burm. f.
		红绒球	Calliandra haematocephala Hassk.
		绿豆	Vigna radiata (L.) R. Wilczek
	夹竹桃科 Apocynaceae	夹竹桃	Nerium oleander L.
		鸡蛋花	Plumeria rubraL.
		狗牙花	Tabernaemontana divaricata (L.)R. Br. ex Roem. et Schult.
		长春花	Catharanthus roseus (L.) G. Don
		沙漠玫瑰	Adenium obesum (Forsk.) Roem. & Schult.
	木犀科 Oleaceae	茉莉	Jasminum sambac (L.) Aiton
	樟科 Lauraceae	樟树	Cinnamomum camphora (L.) J. Presl.
单子叶植物纲Monocotyledoneae	禾本科 Poaceae	玉米	Zea mays L.
		香根草	Chrysopogon zizanioides (L.) Roberty
		狗尾草	Setaria viridis (L.) P. Beauv.
		小麦	Triticum aestivum L.
		水稻	Oryza sativa L.
		佛肚竹	Bambusa ventricosa McClure
	棕榈科 Arecaceae	鱼尾葵	Caryota ochlandra Hance
	天南星科 Araceae	合果芋	Syngonium podophyllumSchott.
	鸭跖草科 Commeliaceae	鸭跖草	Commelina communisL.
裸子植物门 Gymnospermae	银杏科 Ginkgoaceae	银杏	Ginkgo bilobaL.
	苏铁科 Cycadaceae	华南苏铁	Cycas rumphiiMiq.
	罗汉松科 Podocarpaceae	罗汉松	Podocarpus macrophyllus (Thunb.) Sweet
	松科 Pinaceae	马尾松	Pinus massonianaD. Don
	南洋杉科 Araucariaceae	南洋杉	Araucaria cunninghamii Aiton ex D. Don
	杉科 Taxodiaceae	落羽杉	Taxodium distichum (L.) Rich.
	柏科 Cupressaceae	龙柏	Sabina chinensis(L.) Antoine ‘Kaizuca’
蕨类植物门 Pteridophyta	海金沙科 Lygodiaceae	海金沙	Lygodium japonicum (Thunb.) Sw.
	凤尾蕨科 Pteridaceae	井栏边草	Pteris multifidaPoir.
	铁角蕨科 Aspleniaceae	鸟巢蕨	Neottopteris nidus (L.) J. Sm.
	鹿角蕨科 Polypodiaceae	鹿角蕨	Platycerium wallichiiHook.
	肾蕨科 Davalliaceae	波士顿肾蕨	Nephrolepis exaltata (L.) Schott ‘Bostoniensis’

分类阶元 Taxonomic category		中文名 Chinese name	拉丁名 Scientific name
被子植物门 Angiospermae
双子叶植物纲 Dicotyledononeae	猕猴桃科 Actinidiaceae	中华猕猴桃品种红阳♂	A. chinensis ‘Hongyang’♂
		中华猕猴桃品种红阳♀	A. chinensis ‘Hongyang’♀
		中华猕猴桃品种武雄♂	A. chinensis ‘Wuxiong’♂
		中华猕猴桃品种武植3号♀	A. chinensis ‘Wuzhi No.3’♀
		美味猕猴桃品种帮增1号♂	A. chinensis var. deliciosa‘Bangzeng No.1’♂
		美味猕猴桃品种和平1号♀	A. chinensis var. deliciosa ‘Heping No.1’♀
		美味猕猴桃品种米良1号♀	A. chinensis var. deliciosa ‘Miliang No.1’ ♀
	桑科 Moraceae	大叶榕	Ficus altissima Blume
		水同木	Ficus fistulosa Reinw. ex Blume
		垂叶榕	Ficus benjamina L.
		柳叶榕	Ficus variolosa Lindl. ex Benth.
		细叶榕	Ficus microcarpa L. f.
		桂木	Artocarpus nitidus subsp.lingnanensis(Merr.) F. M. Jarrett
		面包树	Artocarpus communis J. R. Forst. et G. Forst.
		树菠萝	Artocarpus heterophyllus Lam.
	豆科 Leguminosae	红花羊蹄甲	Bauhinia blakeanaDunn
		酸豆	Tamarindus indica L.
		紫花苜蓿	Medicago sativa L.
		花生	Arachis hypogaeaL.
		柱花草	Stylosanthes scabra Vogel.
		黄槐	Cassia surattensis Burm. f.
		红绒球	Calliandra haematocephala Hassk.
		绿豆	Vigna radiata (L.) R. Wilczek
	夹竹桃科 Apocynaceae	夹竹桃	Nerium oleander L.
		鸡蛋花	Plumeria rubraL.
		狗牙花	Tabernaemontana divaricata (L.)R. Br. ex Roem. et Schult.
		长春花	Catharanthus roseus (L.) G. Don
		沙漠玫瑰	Adenium obesum (Forsk.) Roem. & Schult.
	木犀科 Oleaceae	茉莉	Jasminum sambac (L.) Aiton
	樟科 Lauraceae	樟树	Cinnamomum camphora (L.) J. Presl.
单子叶植物纲Monocotyledoneae	禾本科 Poaceae	玉米	Zea mays L.
		香根草	Chrysopogon zizanioides (L.) Roberty
		狗尾草	Setaria viridis (L.) P. Beauv.
		小麦	Triticum aestivum L.
		水稻	Oryza sativa L.
		佛肚竹	Bambusa ventricosa McClure
	棕榈科 Arecaceae	鱼尾葵	Caryota ochlandra Hance
	天南星科 Araceae	合果芋	Syngonium podophyllumSchott.
	鸭跖草科 Commeliaceae	鸭跖草	Commelina communisL.
裸子植物门 Gymnospermae	银杏科 Ginkgoaceae	银杏	Ginkgo bilobaL.
	苏铁科 Cycadaceae	华南苏铁	Cycas rumphiiMiq.
	罗汉松科 Podocarpaceae	罗汉松	Podocarpus macrophyllus (Thunb.) Sweet
	松科 Pinaceae	马尾松	Pinus massonianaD. Don
	南洋杉科 Araucariaceae	南洋杉	Araucaria cunninghamii Aiton ex D. Don
	杉科 Taxodiaceae	落羽杉	Taxodium distichum (L.) Rich.
	柏科 Cupressaceae	龙柏	Sabina chinensis(L.) Antoine ‘Kaizuca’
蕨类植物门 Pteridophyta	海金沙科 Lygodiaceae	海金沙	Lygodium japonicum (Thunb.) Sw.
	凤尾蕨科 Pteridaceae	井栏边草	Pteris multifidaPoir.
	铁角蕨科 Aspleniaceae	鸟巢蕨	Neottopteris nidus (L.) J. Sm.
	鹿角蕨科 Polypodiaceae	鹿角蕨	Platycerium wallichiiHook.
	肾蕨科 Davalliaceae	波士顿肾蕨	Nephrolepis exaltata (L.) Schott ‘Bostoniensis’

分类阶元 Taxonomic category	材料数量 No. of species	同源片段数目 No. of band analogs	多态性位点数 No. of polymorphic loci	总位点数 No. of total loci	多态性百分比 PPB(%)	多态性信息量 PIC
禾本科 Poaceae	6	5-6	9	10	90	0.859
桑科 Moraceae	8	5	4	7	57.1	0.791
夹竹桃科 Apocynaceae	5	5	8	9	88.9	0.840
豆科 Leguminosae	7	5	17	17	100	0.926
蕨类植物门 Pteridophyta	5	3-4	12	12	100	0.889
裸子植物门 Gymnospermae	7	4-6	17	17	100	0.917

分类阶元 Taxonomic category	材料数量 No. of species	同源片段数目 No. of band analogs	多态性位点数 No. of polymorphic loci	总位点数 No. of total loci	多态性百分比 PPB(%)	多态性信息量 PIC
禾本科 Poaceae	6	5-6	9	10	90	0.859
桑科 Moraceae	8	5	4	7	57.1	0.791
夹竹桃科 Apocynaceae	5	5	8	9	88.9	0.840
豆科 Leguminosae	7	5	17	17	100	0.926
蕨类植物门 Pteridophyta	5	3-4	12	12	100	0.889
裸子植物门 Gymnospermae	7	4-6	17	17	100	0.917