Screening and analysis of genome sequence difference in wild rose

doi:10.3969/j.issn.1004-1524.2022.05.18

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (5): 1032-1038.DOI: 10.3969/j.issn.1004-1524.2022.05.18

• Horticultural Science • Previous Articles Next Articles

Screening and analysis of genome sequence difference in wild rose

XU Jianjun(), MA Yan, WU Qichao, WANG Baosheng, ZANG Dekui()

Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River,Forestry College, Shandong Agricultural University, Tai’an 271018, Shandong, China

Received:2021-03-23 Online:2022-05-25 Published:2022-06-06
Contact: ZANG Dekui

Abstract

Abstract:

In order to screen out highly polymorphic cpDNA and ITS sequence primers for studying the molecular pedigree of natural populations of wild rose, 8 wild rose populations were used as test materials, 12 pairs of chloroplast genome primers and 4 pairs of nuclear genome ITS primers were adopted. PCR amplification and PCR product sequencing, four pairs of high polymorphic primers trnL-trnF, rpl20-rps12, rbcl, and ITS1 were screened out. Sequence variation calculation and phylogenetic tree results showed that 8 wild rose populations had low variation and could be divided into 2 branches. Three pairs of highly polymorphic cpDNA primers and 1 pair of ITS primers were screened, which were suitable for studying the phylogeny and pedigree of wild rose, and could further explore the pedigree of endangered species of wild rose.

Key words: wild rose, ITS sequence, sequence screening, phylogenetic tree

CLC Number:

S685.12

XU Jianjun, MA Yan, WU Qichao, WANG Baosheng, ZANG Dekui. Screening and analysis of genome sequence difference in wild rose[J]. Acta Agriculturae Zhejiangensis, 2022, 34(5): 1032-1038.

Figures/Tables 6

References 23

[1]	何雨, 董画, 薛桂新. 野生玫瑰果实外观特性及其变化趋势的研究[J]. 北方果树, 2018(5): 5-9.
	HE Y, DONG H, XUE G X. Study on the appearance characteristics and the changing tendency of Rose rugosa[J]. Northern Fruits, 2018(5): 5-9. (in Chinese with English abstract)
[2]	解静, 李明祥, 高建莉, 等. 玫瑰中化学成分及其美容护肤作用机制[J]. 天然产物研究与开发, 2020, 32(2): 341-349.
	XIE J, LI M X, GAO J L, et al. Chemical compositions and their mechanism in cosmetics of Rosa rugosa Thunb[J]. Natural Product Research and Development, 2020, 32(2): 341-349. (in Chinese with English abstract)
[3]	朱红梅, 丰震, 杨科家, 等. 野生玫瑰抗旱性地理变异的初步研究[J]. 中国农学通报, 2009, 25(12): 172-176.
	ZHU H M, FENG Z, YANG K J, et al. Preliminary study on the provenance variation of drought resistance in Rose rugosa[J]. Chinese Agricultural Science Bulletin, 2009, 25(12): 172-176. (in Chinese with English abstract)
[4]	冯立国, 邵大伟, 生利霞, 等. 野生玫瑰的花粉形态及其起源与演化的探讨[J]. 林业科学, 2007, 43(12): 76-80.
	FENG L G, SHAO D W, SHENG L X, et al. Pollen morphology of wild Rosa rugosa and discussion on its origin and evolution[J]. Scientia Silvae Sinicae, 2007, 43(12): 76-80. (in Chinese with English abstract)
[5]	秦忠时, 胡群, 何兴元, 等. 野生玫瑰分布及其生态群落类型[J]. 生态学杂志, 1994, 13(6): 52-54.
	QIN Z S, HU Q, HE X Y, et al. Distrbution of wild Rosa rugosa and its ecological community type[J]. Chinese Journal of Ecology, 1994, 13(6): 52-54. (in Chinese with English abstract)
[6]	ZHU Z M, GAO X F, DANEZANAC M F. Phylogeny of Rosa sections Chinenses and Synstylae(Rosaceae) based on chloroplast and nuclear markers[J]. Molecular Phylogenetics and Evolution, 2015, 87: 50-64. DOI URL
[7]	MIAO C Y, YANG J, MAO R L, et al. Phylogeography of Achyranthes bidentata(Amaranthaceae) in China’s warm-temperate zone inferred from chloroplast and nuclear DNA: insights into population dynamics in response to climate change during the Pleistocene[J]. Plant Molecular Biology Reporter, 2017, 35(1): 166-176. DOI URL
[8]	ZONG Y, SUN P, LIU J, et al. Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia(Rosaceae) in Northern China[J]. Tree Genetics & Genomes, 2014, 10(3): 739-749.
[9]	CHENG B B, ZHENG Y Q, SUN Q W. Genetic diversity and population structure of Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers[J]. Biochemical Systematics and Ecology, 2015, 63: 157-164. DOI URL
[10]	朱仁斌. 中国特有植物文冠果(Xanthocera ssorbifolium Bunge)的谱系地理研究与应用[D]. 杨凌: 西北农林科技大学, 2016.
	ZHU R B. Phylogeography of Xanthoceras sorbifolium Bunge, an endemic plant to China[D]. Yangling: Northwest A & F University, 2016. (in Chinese with English abstract)
[11]	LEE J H, LEE D H, CHOI B H. Phylogeography and genetic diversity of East Asian Neolitsea sericea(Lauraceae) based on variations in chloroplast DNA sequences[J]. Journal of Plant Research, 2013, 126(2): 193-202. DOI URL
[12]	杨志莹, 赵兰勇, 徐宗大. 野生玫瑰与栽培玫瑰对盐胁迫反应的比较研究[J]. 山东林业科技, 2010, 40(2): 43-44.
	YANG Z Y, ZHAO L Y, XU Z D. Comparison of the resistance to salt stress between wild plants and cultivars of Rosa rugosa[J]. Journal of Shandong Forestry Science and Technology, 2010, 40(2): 43-44. (in Chinese with English abstract)
[13]	夏峰梅. 基于转录组信息的玫瑰SSR标记开发及野生玫瑰遗传多样性分析[D]. 泰安: 山东农业大学, 2016.
	XIA F M. Development of SSR markers based on transcriptom and genetic diversity analysis of wild type Rosa rugosa[D]. Tai’an: Shandong Agricultural University, 2016. (in Chinese with English abstract)
[14]	徐宗大, 赵兰勇, 张玲, 等. 玫瑰SRAP遗传多样性分析与品种指纹图谱构建[J]. 中国农业科学, 2011, 44(8): 1662-1669.
	XU Z D, ZHAO L Y, ZHANG L, et al. Analysis of genetic diversity and construction of fingerprint of Rosa rugosa by SRAP[J]. Scientia Agricultura Sinica, 2011, 44(8): 1662-1669. (in Chinese with English abstract)
[15]	JIANG L Y, ZANG D K. Core-germplasm construction of Rosa rugosa collections by CDDP molecular markers[J]. Open Journal of Applied Sciences, 2017, 7(11): 635-645. DOI URL
[16]	HAMILTON M B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation[J]. Molecular Ecology, 1999, 8(3): 521-523.
[17]	SHAW J, LICKEY E B, SCHILLING E E, et al. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III[J]. American Journal of Botany, 2007, 94(3): 275-288. DOI URL
[18]	TABERLET P, GIELLY L, PAUTOU G, et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Molecular Biology, 1991, 17(5): 1105-1109. DOI URL
[19]	WHITE T J, BRUNS T, LEE S, et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics[M]//PCR Protocols. Amsterdam: Elsevier, 1990: 315-322.
[20]	HEWITT G M. Speciation, hybrid zones and phylogeography-or seeing genes in space and time[J]. Molecular Ecology, 2008, 10(3): 537-549. DOI URL
[21]	JIANG L Y, ZANG D K. Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers[J]. Biotechnology & Biotechnological Equipment, 2018, 32(1): 88-94.
[22]	王仁卿. 山东半岛和辽东半岛植被的比较研究[J]. 植物生态学与地植物学丛刊, 1984, 8(1): 41-50.
	WANG R Q. Comparative study on the vegetation between Shandong and Liaodong peninsulas[J]. Acta Phytoecologica Geobotanica Sinica, 1984, 8(1): 41-50. (in Chinese with English abstract)
[23]	牛树银, 孙爱群, 王孟科, 等. 渤海的形成及其深部动力学机制[J]. 海洋地质与第四纪地质, 2014, 34(6): 63-71.
	NIU S Y, SUN A Q, WANG M K, et al. The formation of Bohai sea and its deep dynamics[J]. Marine Geology & Quaternary Geology, 2014, 34(6): 63-71. (in Chinese with English abstract)

代码 Code	采样地点 Locality	经度 Longitude(E)	纬度 Latitude(N)	数量 Quantity
GEF	山东省烟台市大窑镇Dayao Town, Yantai City, Shandong Province	121.406 0	37.273 2	25
JGC	山东省烟台市酒馆村Tavern Village, Yantai City, Shandong Province	121.522 0	37.277 0	10
CSZ	山东省威海市成山镇Chengshan Town, Weihai City, Shandong Province	122.303 9	37.241 0	25
DWGC	山东省威海市大伟广场Dawei Square, Weihai City, Shandong Province	120.005 8	37.501 2	12
HYK	辽宁省庄河市明阳镇Mingyang Town, Zhuanghe City, Liaoning Province	122.408 4	39.311 4	20
SCD	辽宁省庄河市石城岛Shicheng Island, Zhuanghe City, Liaoning Province	121.563 9	40.060 2	20
JSP	吉林省珲春市九沙坪村Jiushaping Village, Hunchun City, Jilin Province	130.320 8	42.365 7	25
SQGY	吉林省珲春市沙丘公园Shaqiu Park, Hunchun City, Jilin Province	130.345 4	42.275 1	20

代码 Code	采样地点 Locality	经度 Longitude(E)	纬度 Latitude(N)	数量 Quantity
GEF	山东省烟台市大窑镇Dayao Town, Yantai City, Shandong Province	121.406 0	37.273 2	25
JGC	山东省烟台市酒馆村Tavern Village, Yantai City, Shandong Province	121.522 0	37.277 0	10
CSZ	山东省威海市成山镇Chengshan Town, Weihai City, Shandong Province	122.303 9	37.241 0	25
DWGC	山东省威海市大伟广场Dawei Square, Weihai City, Shandong Province	120.005 8	37.501 2	12
HYK	辽宁省庄河市明阳镇Mingyang Town, Zhuanghe City, Liaoning Province	122.408 4	39.311 4	20
SCD	辽宁省庄河市石城岛Shicheng Island, Zhuanghe City, Liaoning Province	121.563 9	40.060 2	20
JSP	吉林省珲春市九沙坪村Jiushaping Village, Hunchun City, Jilin Province	130.320 8	42.365 7	25
SQGY	吉林省珲春市沙丘公园Shaqiu Park, Hunchun City, Jilin Province	130.345 4	42.275 1	20

引物名称 Primers	引物序列 Primer sequences(5'-3')	退火温度 Temperature/ ℃	参考文献 References
psbA-trnH	F:GTTATGCATGAACGTAATGCTC	52	[17]
	R:CGCGCATGGTGGATTCACAATCC
trnL-trnF	F:GGTTCAAGTCCCTCTATCCC	55	[18]
	R:ATTTGAACTGGTGACACGAG
trnS-trnG	F:AGATAGGGATTCGAACCCTCGGT	52	[17]
	R:GTAGCGGGAATCGAACCCGCATC
accD-psal	F:TTATTCGATCCAATCGTACCAC	58	[17]
	R:AGAAGCCATTGCAATTGCCGGAAA
ndhF-rpl32	F:CCAATATCCCTTYYTTTTCCAA	52	[17]
	R:GAAAGGTATKATCCAYGMATATT
rpl20-rps12	F:TTT GTTCTA CGTCTCCGA GC	53	[16]
	R:GTCGAGGAACATGTACTA GG
rpl16	F:GCTATGCTTAGTGTGTGACTCGTTG	56	[17]
	R:CCCTTCATTCTTCCTCTATGTTG
atpF-atpH	F:ACTCGCACACACTCCCTTTCC	59	[16]
	R:GCTTTTATGGAAGCTTTAACAAT
rbcl	F:ATGTCACCACAAACAGAAAC	52	[17]
	R:TCGCATGTACCTGCAGTAGC
psbJ-petA	F:ATAGGTACTGTARCYGGTATT	52	[17]
	R:AACARTTYGARAAGGTTCAATT
psbD-trnT	F:CTCCGTARCCAGTCATCCATA	52	[17]
	R:CCCTTTTAACTCAGTGGTAG
trnV-trnW	F:ACT GCC TTG ATC CAC TTG GC	51	[9]
	R:CGA AGCTCCATCTACAAA TGG
ITS5	F:GGAAGTAAAAGCGTAACAAGC	56	[19]
ITS4	R:TCCTCCGCTATATGATATGC
ITSA	F:T CCTCCGCTTATTGATATGC	53	[19]
	R:GGAAGGAGAAGTCGTAACAAGG
ITS2	F:CGAGTCTTTGAACGCAAGTTGC	56	[19]
	R:TTAAATTCCAGCGGGTAACCCCGC
ITS1	F:GTAGGTGAACCTGCGGAAGGAT	55	[19]
	R:GCCGAGATATCCGTTGCCG

引物名称 Primers	引物序列 Primer sequences(5'-3')	退火温度 Temperature/ ℃	参考文献 References
psbA-trnH	F:GTTATGCATGAACGTAATGCTC	52	[17]
	R:CGCGCATGGTGGATTCACAATCC
trnL-trnF	F:GGTTCAAGTCCCTCTATCCC	55	[18]
	R:ATTTGAACTGGTGACACGAG
trnS-trnG	F:AGATAGGGATTCGAACCCTCGGT	52	[17]
	R:GTAGCGGGAATCGAACCCGCATC
accD-psal	F:TTATTCGATCCAATCGTACCAC	58	[17]
	R:AGAAGCCATTGCAATTGCCGGAAA
ndhF-rpl32	F:CCAATATCCCTTYYTTTTCCAA	52	[17]
	R:GAAAGGTATKATCCAYGMATATT
rpl20-rps12	F:TTT GTTCTA CGTCTCCGA GC	53	[16]
	R:GTCGAGGAACATGTACTA GG
rpl16	F:GCTATGCTTAGTGTGTGACTCGTTG	56	[17]
	R:CCCTTCATTCTTCCTCTATGTTG
atpF-atpH	F:ACTCGCACACACTCCCTTTCC	59	[16]
	R:GCTTTTATGGAAGCTTTAACAAT
rbcl	F:ATGTCACCACAAACAGAAAC	52	[17]
	R:TCGCATGTACCTGCAGTAGC
psbJ-petA	F:ATAGGTACTGTARCYGGTATT	52	[17]
	R:AACARTTYGARAAGGTTCAATT
psbD-trnT	F:CTCCGTARCCAGTCATCCATA	52	[17]
	R:CCCTTTTAACTCAGTGGTAG
trnV-trnW	F:ACT GCC TTG ATC CAC TTG GC	51	[9]
	R:CGA AGCTCCATCTACAAA TGG
ITS5	F:GGAAGTAAAAGCGTAACAAGC	56	[19]
ITS4	R:TCCTCCGCTATATGATATGC
ITSA	F:T CCTCCGCTTATTGATATGC	53	[19]
	R:GGAAGGAGAAGTCGTAACAAGG
ITS2	F:CGAGTCTTTGAACGCAAGTTGC	56	[19]
	R:TTAAATTCCAGCGGGTAACCCCGC
ITS1	F:GTAGGTGAACCTGCGGAAGGAT	55	[19]
	R:GCCGAGATATCCGTTGCCG

种群名称 Name of population	引物及变异位点碱基 Primers and bases at variant sites
种群名称 Name of population	trnL-trnF				rpl20-rps12				rbcl				ITS1
GEF	T	C	A	-	-	C	T	-	T	A	C	T	C
JGC	A	-	A	-	-	C	C	-	T	A	C	T	-
CSZ	A	-	A	-	T	T	T	C	T	A	C	T	-
DWGC	T	C	A	C	-	T	T	-	T	A	C	T	C
HYK	A	-	A	-	-	T	T	-	T	A	C	T	-
SCD	A	-	C	-	-	T	T	-	G	G	T	A	-
JSP	A	-	C	-	-	T	T	-	T	G	T	T	-
SQGY	A	-	A	-	-	T	T	-	T	A	C	T	-
比对长度	1 795												285
Comparative length/bp

Screening and analysis of genome sequence difference in wild rose

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