基于cpInDel标记和cpSSR标记的柑橘属及近缘属植物亲缘关系

doi:10.3864/j.issn.0578-1752.2022.16.012

Abstract

Abstract:

【Objective】The genetic diversity analysis of the chloroplast genome was performed to reveal the genetic evolution of citrus from the cytoplasmic level, so as to provide a reference for the collection, evaluation and utilization of citrus germplasm resources. 【Method】Taking the hypervariable region of Citrus sinensis chloroplast genome as reference, De Novo assemblies were carried out with next-generation sequencing data of representative Citrus and its related genera materials. The assembled sequences were aligned to discover site-variations, and cpInDel markers were designed on the basis of variation sites. SSR sites composed of two or more nucleotide repeats were located in the chloroplast genome of sweet orange, and SSR sites with length variations were adopted to design cpSSR markers. The newly developed markers and reported cpSSR markers were used to detect genetic diversity in 48 samples of Citrus and its relatives that are representative in taxonomy and/or origin through band typing and clustering analysis. 【Result】4 cpInDel markers and 13 cpSSR markers were developed successfully and they could produce clear polymorphic bands in all tested samples. The band pattern of cpIndel was relatively simple. Single marker could distinguish a specific genus or several genera. At species and/or above taxa level, the cpInDel markers gave more convenient and accurate discrimination effect. Similar clustering results were obtained with cpInDel and cpSSR markers, and minor differences were found in the relationship between the lower-rank taxa and the classification of a few genotypes. The cytoplasmic origins of P. trifoliate hybrids were found to be different from P. trifoliata, and those of lemon, limonia and lime hybrid were different from C. medica by both markers. Wangcang zhoupigan, a representative variety of C. speciosa, had a different cytoplasmic origin from other mandarin varieties. Ziyang xiangcheng and Korean xiangcheng, both classified as C. junos, might have different cytoplasmic origin. cpSSR markers classify mandarin, sweet orange and sour orange, ichang papeda and honghe papeda into three clusters, representing C. reticulata, C. sinensis and Papeda, while cpInDel markers showed that they were closely related and classified into one cluster. Indian wild mandarin were clustered into C. medica by cpInDel, and were put into a single cluster by cpSSR. 【Conclusion】Molecular marker analysis of chloroplast genome could reveal the genetic relationship of Citrus and its related genera and discover a different relationship from the view of nuclear genome. However, if combined with markers from nuclear genome, more comprehensive and accurate indentification and phylogenetic relationship revealing should be obtained for the citrus germplasm resources.

Key words: Citrus, chloroplast genome InDel, chloroplast genome SSR, genetic evolution, germplasm

YANG Cheng,GONG GuiZhi,PENG ZhuChun,CHANG ZhenZhen,YI Xuan,HONG QiBin. Genetic Relationship Among Citrus and Its Relatives as Revealed by cpInDel and cpSSR Marker[J].Scientia Agricultura Sinica, 2022, 55(16): 3210-3223.

Figures/Tables 7

Table 1

Forty-eight genotypes used in this study"

编号 Code	材料名称 Common name	学名 Scientific name
1	莽山野柑 Mangshan yegan	C. mangshanensis S. W. He & G.F.Liu
2	贺州姑婆山野柑 Hezhou guposhan yegan	C. spp
3	印度野橘 India wild mandarin	C. indica Tanaka
4	道县野橘 Daoxian yeju	C. daoxianensis S. W. He & G.F.Liu
5	印度酸橘 Cleopatra mandarin	C. reticulata var. austera
6	岑溪酸橘 Cenxi suan ju	C. sunki Hort ex Tanaka
7	茶枝柑 Chazhi gan*	C. chachiensis Hort.
8	安江红橘 Anjiang hongju	C. tangerina Hort. ex Tanaka
9	万州少核红橘 Wanzhou seedfew hongju	C. tangerina Hort. ex Tanaka
10	新生系3号椪柑 New No. 3 penggan	C. reticulata Blanco
编号 Code	材料名称 Common name	学名 Scientific name
11	克里曼丁 Clementina	C. clementina Hort
12	兴津温州蜜柑 Okitsu satsuma mandarin	C. unshiu Marc.
13	砂糖橘 Shatangju*	C. reticulata Blanco
14	永顺冰糖橘 Yongshun bingtangju	C. reticulata Blanco
15	资阳香橙 Ziyang xiangcheng	C. junos Sied. ex Tanaka
16	韩国香橙 Korean xiangcheng	C. junos Sied. ex Tanaka
17	旺苍皱皮柑 Wangcang zhoupigan	C. verrucosa Hort.
18	梨橙2号 Licheng No.2	C. sinensis (L.) Osbeck
19	塔罗科血橙 Tarocco blood orange	C. sinensis (L.) Osbeck
20	小叶酸橙 Lobular sour orange	C. aurantium L.
21	意大利酸橙 Italian sour orange	C. aurantium L.
22	尤力克柠檬 Eureka lemon*	C.limon (L.) Burm
23	里斯本柠檬 Lisbon lemon	C.limon (L.) Burm
24	来檬杂种 Lime hybrid*	C. spp
25	北京柠檬 Meyer lemon	C. meyerii Y. Tan.
26	红藜檬 Hong limeng*	C. limonia Osbeck
27	南川佛手 Nanchuan buddha's hand*	C. medica L.
28	合江佛手 Hejiang buddha's hand	C. medica L.
29	云南大香橼 Yunnan daxiangyuan*	C. medica L.
30	小香橼 Xiao xiangyuan	C. medica var. ethrog Engl.
31	白玉霜 Baiyushuang*	C. grandis (L.) Osbeck
32	红肉琯溪蜜柚 Hongrou guanximiyou*	C. grandis (L.) Osbeck
33	金刀峡宜昌橙 Jindaoxia ichang papeda	C. ichangensis Swingle
34	元江宜昌橙 Yuanjiang ichang papeda	C. ichangensis Swingle
35	宜昌橙2586 Ichang papeda 2586*	C. ichangensis Swingle
36	红河大翼橙 Honghe papeda*	C. hongheensis Y. L. D. L
37	金豆 Jindou kumquat*	F. hindsii Swingle
38	罗纹 Round kumquat	F. japonica Swingle
39	金弹 Meiwa kumquat*	F. crassifolia Swingle
40	罗浮 Nagami kumquat	F. margarita Swingle
41	四季橘 Calamindin	C. madurensis Lour
42	旺苍大叶枳 Wangcang daye trifoliate orange	P. trifoliata
43	飞龙枳 Flying dragon trifoliate orange*	P. trifoliata var. Monstrosa
44	富民枳 Fumin trifoliate orange	Poncirus polyandra S. Q. Ding et al
45	枳杂-3 Trifoliate hybrid 3	P. spp
46	卡里佐枳橙 Carrizo citrange	C. sinensis (L.) Osbeck×P. trifoliata (L.) Raf.
47	澳指檬 Australian finger lime	Microcitrus australasica (F.Muell) Swingle
48	澳沙檬 Austrlian Desert lime	Eremocitrus glauca (Lindl.) Swingle

Table 1

Table 2

Fig. 1

Table 3

Fig. 2

Fig. 3

Fig. 4

References 39

[1]	PANG X M, HU C G, DENG X X. Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genetic Resources and Crop Evolution, 2007, 54(2): 429-436. doi: 10.1007/ s10722-006-0005-5. doi: 10.1007/ s10722-006-0005-5
[2]	BARKLEY N A, ROOSE M L, KRUEGER R R, FEDERICI C T. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theoretical and Applied Genetics, 2006, 112(8): 1519-1531. doi: 10.1007/s00122-006-0255-9. doi: 10.1007/s00122-006-0255-9
[3]	SHARAFI A A, ABKENAR A A, SHARAFI A, MASAELI M. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers. Physiology and Molecular Biology of Plants, 2016, 22(1): 87-95. doi: 10.1007/s12298-016-0336-4. doi: 10.1007/ s12298-016-0336-4
[4]	UZUN A, YESILOGLU T, POLAT I, AKA-KACAR Y, GULSEN O, YILDIRIM B, TUZCU O, TEPE S, CANAN I, ANIL S. Evaluation of genetic diversity in lemons and some of their relatives based on SRAP and SSR markers. Plant Molecular Biology Reporter, 2011, 29(3): 693-701. doi: 10.1007/s11105-010-0277-y. doi: 10.1007/s11105-010-0277-y
[5]	王炯, 龚桂芝, 彭祝春, 李一兵, 王艳杰, 洪棋斌. 基于COS Marker分析柑橘属及其近缘、远缘属植物的遗传与进化. 中国农业科学, 2017, 50(2): 320-331. doi: 10.3864/j.issn.0578-1752.2017. 02.011. doi: 10.3864/j.issn.0578-1752.2017. 02.011
	WANG J, GONG G Z, PENG Z C, LI Y B, WANG Y J, HONG Q B. Genetic and phylogenetic relationships AmongCitrus and its close and distant relatives based on COS marker. Scientia Agricultura Sinica, 2017, 50(2): 320-331. doi: 10.3864/j.issn.0578-1752.2017.02.011. (in Chinese) doi: 10.3864/j.issn.0578-1752.2017. 02.011
[6]	贾婧婧, 潘小军, 张敏, 胡勇, 何奕昆. 叶绿体的遗传进化. 生物学通报, 2009, 44(11): 7-9. doi: 10.3969/j.issn.0006-3193.2009.11. 003. doi: 10.3969/j.issn.0006-3193.2009.11. 003
	JIA J J, PAN X J, ZHANG M, HU Y, HE Y K. The genetic revolution of Chloroplast. Microbiology China, 2009, 44(11): 7-9. doi: 10.3969/j.issn.0006-3193.2009.11.003. (in Chinese) doi: 10.3969/j.issn.0006-3193.2009.11. 003
[7]	CHENG Y J, GUO W W, DENG X X. cpSSR: A new tool to analyze chloroplast genome of Citrus somatic hybrids. Acta Botanica Sinica, 2003, 45(8): 906-909.
[8]	CHENG Y J, DE VICENTE M C, MENG H J, GUO W W, TAO N G, DENG X X. A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera. Tree Physiology, 2005, 25(6): 661-672. doi: 10.1093/treephys/25.6.661. doi: 10.1093/treephys/25.6.661
[9]	龚桂芝, 洪棋斌, 彭祝春, 江东, 向素琼. 枳属种质遗传多样性及其与近缘属植物亲缘关系的SSR和cpSSR分析. 园艺学报, 2008, 35(12): 1742-1750. doi: 10.16420/j.issn.0513-353x.2008.12.005. doi: 10.16420/j.issn.0513-353x.2008.12.005
	GONG G Z, HONG Q B, PENG Z C, JIANG D, XIANG S Q. Genetic diversity of Poncirus and its phylogenetic relationships with relatives as revealed by nuclear and chloroplast SSR. Acta Horticulturae Sinica, 2008, 35(12): 1742-1750. doi: 10.16420/j.issn.0513-353x.2008.12.005. (in Chinese) doi: 10.16420/j.issn.0513-353x.2008.12.005
[10]	王福生, 江东. 应用cpSSR和EST-SSR标记进行柑橘特异种质资源遗传背景研究. 园艺学报, 2010, 37(3): 465-474. doi: 10.16420/j. issn.0513-353x.2010.03.018. doi: 10.16420/j. issn.0513-353x.2010.03.018
	WANG F S, JIANG D. Studies on genetic background of important germplasm resources among Citrus based on cpSSR and EST-SSR marker. Acta Horticulturae Sinica, 2010, 37(3): 465-474. doi: 10.16420/j.issn.0513-353x.2010.03.018. (in Chinese) doi: 10.16420/j. issn.0513-353x.2010.03.018
[11]	徐静, 谭李梅, 符红艳, 朱志媚, 龙栎冰, 胡哲, 马先锋, 邓子牛. 利用分子标记对14份枸橼种质进行多样性分析. 分子植物育种, 2021, 19(14): 4726-4737. doi: 10.13271/j.mpb.019.004726. doi: 10.13271/j.mpb.019.004726
	XU J, TAN L M, FU H Y, ZHU Z M, LONG L B, HU Z, MA X F, DENG Z N. Genetic diversity analysis of 14 citron genotypes based on molecular markers. Molecular Plant Breeding, 2021, 19(14): 4726-4737. doi: 10.13271/j.mpb.019.004726. (in Chinese) doi: 10.13271/j.mpb.019.004726
[12]	WEBER J L, DAVID D, HEIL J, FAN Y, ZHAO C F, MARTH G. Human diallelic insertion/deletion polymorphisms. American Journal of Human Genetics, 2002, 71(4): 854-862. doi: 10.1086/342727
[13]	江东, 普金安, 赵婉彤, 刘小丰, 高恒锦, 王婷. 基于SSR和InDel标记的大翼橙亚属种质遗传多样性及群体结构分析. 中国南方果树, 2020, 49(5): 1-11. doi: 10.13938/j.issn.1007-1431.20200281. doi: 10.13938/j.issn.1007-1431.20200281
	JIANG D, PU J A, ZHAO W T, LIU X F, GAO H J, WANG T. Genetic diversity and population structure analysis of papeda germplasms using SSR and InDel markers. South China Fruits, 2020, 49(5): 1-11. doi: 10.13938/j.issn.1007-1431.20200281. (in Chinese) doi: 10.13938/j.issn.1007-1431.20200281
[14]	ZHU S P, WANG F S, SHEN W X, JIANG D, HONG Q B, ZHAO X C. Genetic diversity of Poncirus and phylogenetic relationships with its relatives revealed by SSR and SNP/InDel markers. Acta Physiologiae Plantarum, 2015, 37(7): 1-11. doi: 10.1007/s11738-015- 1890-z. doi: 10.1007/s11738-015- 1890-z
[15]	BAUSHER M G, SINGH N D, LEE S B, JANSEN R K, DANIELL H. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ‘Ridge Pineapple’: Organization and phylogenetic relationships to other angiosperms. BMC Plant Biology, 2006, 6: 21. doi: 10.1186/ 1471-2229-6-21. doi: 10.1186/
[16]	LAM D T, ISHIKAWA R. Molecular discrimination of landraces of Citrus species in the Okinawa, Japan. Genetic Resources and Crop Evolution, 2019, 66(2): 321-333. doi: 10.1007/s10722-018-0710-x. doi: 10.1007/s10722-018-0710-x
[17]	侯艳红. 无融合生殖候选基因CitRWP在柑橘及其近缘属的分析评价[D]. 重庆: 西南大学, 2020.
	HOU Y H. The evaluation of apomixes candidate gene CitRWP in Citrus and its close related genus[D]. Chongqing: Southwest University, 2020. (in Chinese)
[18]	CARBONELL-CABALLERO J, ALONSO R, IBAÑEZ V, TEROL J, TALON M, DOPAZO J. A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. Molecular Biology and Evolution, 2015, 32(8): 2015-2035. doi: 10.1093/molbev/msv082. doi: 10.1093/molbev/msv082
[19]	洪棋斌, 龚桂芝. 一种组装叶绿体基因组序列的方法: CN104450682A [P]. 2015-03-25.
	HONG Q B, GONG G Z. A method for assembling chloroplast genome sequences: CN104450682A [P]. 2015-03-25. (in Chinese)
[20]	LI Q, QI J J, QIN X J, DOU W F, LEI T G, HU A H, JIA R R, JIANG G J, ZOU X P, LONG Q, XU L Z, PENG A H, YAO L X, CHEN S C, HE Y R. CitGVD: A comprehensive database of citrus genomic variations. Horticulture Research, 2020, 7: 12. doi: 10.1038/s41438- 019-0234-3. doi: 10.1038/s41438- 019-0234-3
[21]	SHEN W, LE S, LI Y, HU F Q, ZOU Q. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE, 2016, 11(10): e0163962. doi: 10.1371/journal.pone.0163962
[22]	BEIER S, THIEL T, MÜNCH T, SCHOLZ U, MASCHER M. MISA-web: A web server for microsatellite prediction. Bioinformatics, 2017, 33(16): 2583-2585. doi: 10.1093/bioinformatics/btx198
[23]	PARKS M, CRONN R, LISTON A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology, 2009, 7: 84. doi: 10.1186/1741- 7007-7-84. doi: 10.1186/1741- 7007-7-84
[24]	SWINGLE W T. A new genus, Fortunella, comprising four species of Kumquat orange. Journal of Washington Academy of Science, 1915, 5: 165-176.
[25]	周开隆, 叶荫民. 中国果树志-柑橘卷. 北京: 中国林业出版社, 2010.
	ZHOU K L, YE Y M. Chinese Fruit Tree·Citrus Roll. Beijing: China Forestry Publishing House, 2010. (in Chinese)
[26]	谢让金, 周志钦, 邓烈. 真正柑橘果树类植物基于AFLP分子标记的分类与进化研究. 植物分类学报, 2008, 46(5): 682-691.
	XIE R J, ZHOU Z Q, DENG L. Taxonomic and dnylogentic relationships among the genera of the True Citrus Fruit Trees Group (Aurantioideae, Rutaceae) based on AFLP markers. Journal of Systematics and Evolution, 2008, 46(5): 682-691. (in Chinese)
[27]	SHEDLOCK A M, OKADA N. SINE insertions: Powerful tools for molecular systematics. BioEssays, 2000, 22(2): 148-160. doi: 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z
[28]	GARCÍA-LOR A, LURO F, NAVARRO L, OLLITRAULT P. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: A perspective for genetic association studies. Molecular Genetics and Genomics, 2012, 287(1): 77-94. doi: 10.1007/s00438-011-0658-4. doi: 10.1007/s00438-011-0658-4
[29]	李小孟. 柑橘及其近缘属植物的分子进化与栽培柑橘的起源研究[D]. 重庆: 西南大学, 2010.
	LI X M. Molecular phylogeny of the true Citrus fruit trees group (Aurantioideae, Rutaceae) and the origin of cultivated Citrus [D]. Chongqing: Southwest University, 2010. (in Chinese)
[30]	丁素琴, 张显努, 暴卓然, 梁明清. 中国枳属一新种. 云南植物研究, 1984, 6(3): 292-293.
	DING S Q, ZHANG X N, BAO Z R, LIANG M Q. A new species of Pocirus from China. Acta Botanica Yunnanica, 1984, 6(3): 292-293. (in Chinese)
[31]	范眸天, 梁明清, 浦卫琼. 富民枳与枳的花粉形态与分类位置探讨. 云南农业大学学报, 1998, 13(3): 298-300. doi: 10.16211/j.issn.1004- 390x(n).1998.03.009. doi: 10.16211/j.issn.1004- 390x(n).1998.03.009
	FAN M T, LIANG M Q, PU W Q. Studies on the pollen morphology and taxonomic position of P trifoliata and P polyandra. Journal of Yunnan Agricultural University, 1998, 13(3): 298-300. doi: 10.16211/j. issn.1004-390x(n).1998.03.009. (in Chinese) doi: 10.16211/j.issn.1004- 390x(n).1998.03.009
[32]	刘利勤, 杨静, 顾志建. 富民枳的核型与分类位置探讨. 云南植物研究, 2007, 29(2): 198-200. doi: 10.3969/j.issn.2095-0845.2007.02.013. doi: 10.3969/j.issn.2095-0845.2007.02.013
	LIU L Q, YANG J, GU Z J. Karyomorphology and taxonomic position of Poncirus polyandra (Rutaceae). Acta Botanica Yunnanica, 2007, 29(2): 198-200. doi: 10.3969/j.issn.2095-0845.2007.02.013. (in Chinese) doi: 10.3969/j.issn.2095-0845.2007.02.013
[33]	FANG D Q. Intra and intergeneric relationships of poncirus polyandra: Investigation by leaf isozymes. 武汉植物学研究, 1993, 11(1): 34-40.
	FANG D Q. Intra and intergeneric relationships of poncirus polyandra: investigation by leaf isozymes. Journal of Wuhan Botanical Research, 1993, 11(1): 34-40. (in Chinese)
[34]	朱世平, 陈传武, 刘兆俊, 齐安民, 薛杨, 赵婉彤, 杨海健, 洪林. 卡里佐枳橙在中国的生产适应性调查与比较研究. 中国南方果树, 2020, 49(3): 1-8. doi: 10.13938/j.issn.1007-1431.20190084. doi: 10.13938/j.issn.1007-1431.20190084
	ZHU S P, CHEN C W, LIU Z J, QI A M, XUE Y, ZHAO W T, YANG H J, HONG L. Investigation and comparison of the performance of carrizo citrange in China. South China Fruits, 2020, 49(3): 1-8. doi: 10.13938/j.issn.1007-1431.20190084. (in Chinese) doi: 10.13938/j.issn.1007-1431.20190084
[35]	MALIK S K, CHAUDHURY R, DHARIWAL O P, KALIA R K. Collection and characterization of Citrus indica Tanaka and C. macroptera Montr.: wild endangered species of northeastern India. Genetic Resources and Crop Evolution, 2006, 53: 1485-1493. doi: 10.1007/s10722-005-7468-7
[36]	廖振坤, 张秋明, 刘卫国, 丁伟平, 张玲. 南岭山脉宽皮柑橘近缘野生种亲缘关系鉴定. 湖南农业大学学报(自然科学版), 2006, 32(4): 385-388. doi: 10.3321/j.issn: 1007-1032.2006.04.010. doi: 10.3321/j.issn: 1007-1032.2006.04.010
	LIAO Z K, ZHANG Q M, LIU W G, DING W P, ZHANG L. Identification of relative relationships of wild relatives of eucitrus originated from nanling mountains by AFLP analysis. Journal of Hunan Agricultural University (Natural Sciences), 2006, 32(4): 385-388. doi: 10.3321/j.issn: 1007-1032.2006.04.010. (in Chinese) doi: 10.3321/j.issn: 1007-1032.2006.04.010
[37]	刘通, 邓崇岭, 程玉芳, 李秋景, 陈传武, 刘冰浩, 伊华林. 利用SSR和SRAP技术分析广西柑橘种质遗传多样性. 华中农业大学学报, 2016, 35(2): 23-29. doi: 10.13300/j.cnki.hnlkxb.2016.02.004. doi: 10.13300/j.cnki.hnlkxb.2016.02.004
	LIU T, DENG C L, CHENG Y F, LI Q J, CHEN C W, LIU B H, YI H L. Analyzing genetic diversity of citrus germplasm in Guangxi Province with SSR and SRAP markers. Journal of Huazhong Agricultural University, 2016, 35(2): 23-29. doi: 10.13300/j.cnki. hnlkxb.2016.02.004. (in Chinese) doi: 10.13300/j.cnki.hnlkxb.2016.02.004
[38]	NICOLOSI E, DENG Z N, GENTILE A, LA MALFA S, CONTINELLA G, TRIBULATO E. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics, 2000, 100(8): 1155-1166. doi: 10.1007/s001220051419. doi: 10.1007/s001220051419
[39]	FEDERICI C T, FANG D Q, SCORA R W, ROOSE M L. Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theoretical and Applied Genetics, 1998, 96(6/7): 812-822. doi: 10.1007/ s001220050807. doi: 10.1007/ s001220050807

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引物名称 Primer name	正/反向引物 Forward/Reverse primer	预期产物大小 Excepted size (bp)	扩增总条带数 Amplified bands	期望杂合度 He	多态信息含量 PIC
HVar-cpINDEL1	AATCCACTCAGCCATCTC	464	8	0. 73	0.69
HVar-cpINDEL1	CCCTTTCTACGGTTYAGY	464	8	0. 73	0.69
HVar-cpINDEL2	GTGCGAACCATACCATAA	273	5	0.64	0.56
HVar-cpINDEL2	GTCAGGAGTCCTCGTAAA	273	5	0.64	0.56
HVar-cpINDEL3	AYGAAATAACTCCTCCTT	178	4	0.26	0.24
HVar-cpINDEL3	TACCACTAAACTATACCC	178	4	0.26	0.24
HVar-cpINDEL4	CSAAAGAATCGGTTAMAT	491	4	0.42	0.37
HVar-cpINDEL4	TDCGAATCCTTTTGTTTA	491	4	0.42	0.37

引物名称 Primer name	正/反向引物 Forward primer/Reverse primer	预期产物大小 Excepted size (bp)	扩增总条带数 Amplified bands	期望杂合度 He	多态信息含量 PIC
cpSSRY1	TATCTCCGTGTCAACCAA	180	9	0.81	0.78
cpSSRY1	GGGCAACCCATTCTTATT	180	9	0.81	0.78
cpSSRY2	CAAATCCTATTGGACGCA	291	6	0.58	0.54
cpSSRY2	TCAGGAACAAAAGGAACG	291	6	0.58	0.54
cpSSRY3	TTCTGAACCGGCCCTTGC	247	2	0.19	0.17
cpSSRY3	ACGGGTCAATAAAGCATAGCAG	247	2	0.19	0.17
cpSSRY4	CCGCTCAATCAACGACTT	227	5	0.73	0.68
cpSSRY4	TAATCGAAAGGCTGCTCT	227	5	0.73	0.68
cpSSRY5	GGTGACACTCGCCGCTAT	170	2	0.48	0.36
cpSSRY5	TGAACCGATGACTTACGC	170	2	0.48	0.36
cpSSRY6	GGGATACACGACAGAAGG	160	6	0.78	0.74
cpSSRY6	AGATGGTGCGATTTGATT	160	6	0.78	0.74
cpSSRY7	GACTCCGCAAATTCACCA	249	4	0.48	0.38
cpSSRY7	TCCGAGCAGAACATCAAACT	249	4	0.48	0.38
cpSSRY8	ATTTGAACCCGTGACATT	349	2	0.04	0.04
cpSSRY8	AGGCCCACTTGTATTTGT	349	2	0.04	0.04
cpSSRY9	TTTTACGAACTGAAGCCCTTAT	278	4	0.30	0.27
cpSSRY9	AGGGATGCGACCCGTTTT	278	4	0.30	0.27
cpSSRY10	AATCTGGGTTCTTCTACTTC	188	4	0.47	0.43
cpSSRY10	TCTATTTCGTACCCTTCG	188	4	0.47	0.43
cpSSRY11	AATAGGTATCTAAGGGTG	229	4	0.33	0.31
cpSSRY11	TAGTTTTACGGTTCATTTCATTATC	229	4	0.33	0.31
cpSSRY12	TTCCCTTTTGTAATGTTTTG	205	9	0.83	0.80
cpSSRY12	GTTTATGGTGGGGTGATG	205	9	0.83	0.80
cpSSRY13	ATCTATTTCGTACCCTTCG	189	7	0.81	0.77
cpSSRY13	AATCTGGGTTCTTCTACTT	189	7	0.81	0.77
cpSSR1	AACGGAAAGAGAGGGATTCG	161	12	0.82	0.80
cpSSR1	ACGGGCTTTTTCAAGCATTA	161	12	0.82	0.80
cpSSR2	TCGTATTCTCGAACCCCTTTT	243	10	0.78	0.75
cpSSR2	ATAAATTGCATGGCCGTACC	243	10	0.78	0.75
cpSSRH4	GCTATCCGCCAAGGTAAA	223	9	0.67	0.63
cpSSRH4	GGTTCAAATCCCGTCTCC	223	9	0.67	0.63
cpSSR5	TGATCCCACAAACAAAGGAA	247	5	0.70	0.63
cpSSR5	TTTGAGTCTGGGGAAAAGGA	247	5	0.70	0.63
cpSSR6	TCAAATGGGTTTGAGGTTGA	197	7	0.77	0.72
cpSSR6	GGCGTCCAAAATGCCTATAA	197	7	0.77	0.72
cpSSR21	CAACGAGTCGCACACTAAGC	228	5	0.76	0.70
cpSSR21	TACGGGGTATTGGGAATCAA	228	5	0.76	0.70

Genetic Relationship Among Citrus and Its Relatives as Revealed by cpInDel and cpSSR Marker

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