Genetic Diversity of Germplasm Resources in Job's Tears Revealed by Chloroplast Genome SSR Markers

doi:10.7668/hbnxb.20190745

Abstract

Abstract: For providing a solid base for germplasm protection, discovering and genetic development in Coix L. that collected from China and abroad,whereas genetic diversity and differentiation in Coix L. were assessed. Thirty-three of 38 polymorphic cpSSR primers were amplified in 93 germplasm resources and then their genetic diversity, relationship and structure among different populations were compared. It was reveled that 153 alleles had been amplified from 33 primers, it was observed 3 to 8 alleles with an average of 4.64(Na). The means of Nei's gene diversity index(H) and Shannon's information index(I) were 0.368 8 and 0.720 2, respectively, showing rich diversity in tested materials. It was also revealed that wild and cultivar populations had no obvious genetic divergence, and three ecotype populations of EEMC, EMMCYRR and ELMSC also clustered together that showing closer genetic distance and higher genetic identity, while foreign type(FT) population were more different to other three groups. C. puellarum Balansa and C. stenocarpa Balansa populations divided alone respectively indicating striking genetic divergence; and whereas there were less genetic distance among other four varieties of C. chinensis var. formosana(Ohwi) L. Liu, C. lacryma-jobi var. maxima Makino, C. lacryma-jobi var. lacryma-jobi and C. chinensis var. chinesis Tod.. No absolutely relation between genetic distance and geographic location were observed by clustering analysis, suggesting introgression among different populations.

Key words: cpSSR marker, Genetic diversity, Germplasm, Coix L.

CLC Number:

LI Xiangdong, SHI Ming, LU Xiujuan, PAN Hong, WEI Xinyuan, LU Ping. Genetic Diversity of Germplasm Resources in Job's Tears Revealed by Chloroplast Genome SSR Markers[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(S1): 6-14. doi: 10.7668/hbnxb.20190745.

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References

[1] 黄亨履, 陆平, 朱玉兴, 李英材. 中国薏苡的生态型、多样性及利用价值[J]. 作物品种资源, 1995(4):4-8. doi:10.19462/j.cnki.1671-895x.1995.04.002.
Hang H L, Lu P, Zhu Y X, Li Y C. Ecotype diversity and utility value in Chinese Job's Tears[J].Journal of Crop Variety Resources, 1995(4):4-8.
[2] 梁云涛, 陈成斌, 梁世春, 赖群珍, 黄娟, 徐志健. 中日韩三国薏苡种质资源遗传多样性研究[J]. 广西农业科学, 2006, 37(4):341-344. doi:10.3969/j.issn.2095-1191.2006.04.001.
Lang Y T, Chen C B, Liang S C, Lai Q Z, Huang J, Xu Z J. Research on genetic diversity of Job's Tears(Coix lacryma-jobi L.) germplasm from China Japan and Korea[J]. Guangxi Agricultural Sciences, 2006, 37(4):341-344.
[3] 王硕, 张世鲍, 何金宝, 陆光著, 杨志清. 薏苡资源性状的主成分和聚类分析[J]. 云南农业大学学报, 2013, 28(2):157-162. doi:10.3969/j.issn.1004-390X(n).2013.02.002.
Wng S, Zhang S B, He J B, Lu G Z, Yang Z Q. The principal component analysis and cluster analysis of Coix resource characteristics[J]. Journal of Yunnan Agricultural University, 2013, 28(2):157-162.
[4] 李春花, 王艳青, 卢文洁, 王莉花. 云南薏苡种质资源农艺性状的主成分和聚类分析[J]. 植物遗传资源学报, 2015, 16(2):277-281. doi:10.13430/j.cnki.jpgr.2015.02.010.
L C H, Wang Y Q, Lu W J, Wang L H. The principal component and cluster analysis of agronomic traits of Coix germplasm resources in Yunnan[J]. Journal of Plant Genetic Resources, 2015, 16(2):277-281.
[5] 金关荣, 奚秀洁, 程舟, 陈常理, 洛霞虹, 李珊. 薏苡种子形态性状多样性评价[J]. 植物遗传资源学报, 2017, 18(3):421-428. doi:10.13430/j.cnki.jpgr.2017.03.006.
Jn G R, Xi X J, Cheng Z, Chen C L, Luo X H, Li S. Evaluation of seed morphological characteristics diversity of Job's Tears(Coix lacryma-jobi) germplasm[J]. Journal of Plant Genetic Resources, 2017, 18(3):421-428.
[6] 石明, 李祥栋, 秦礼康. 薏苡种质资源描述规范和数据标准[M]. 北京:中国农业出版社, 2017.
Si M, Li X D, Qin L K. Descriptors and data standard for Job's Tears(Coix lacryma-jobi L.)[M]. Beijing:China Agriculture Press, 2017.
[7] 李祥栋, 潘虹, 陆秀娟, 魏心元, 陆平, 石明, 练启仙. 薏苡属种质资源的主要表型性状多样性研究[J]. 植物遗传资源学报, 2019, 20(1):229-238. doi:10.13430/j.cnki.jpgr.20180604003.
L X D, Pan H, Lu X J, Wei X Y, Lu P, Shi M, Lian Q X. Analysis of main phenotypic characteristics in Coix L. germplasm resources[J]. Journal of Plant Genetic Resources, 2019, 20(1):229-238.
[8] 张立娜, 曹桂兰, 韩龙植. 利用SSR标记揭示中国粳稻地方品种遗传多样性[J]. 中国农业科学, 2012, 45(3):405-413. doi:10.3864/j.issn.0578-1752.2012.03.001.
Zang L N, Cao G L, Han L Z. Analysis of genetic diversity of Japonica rice landrace in China with microsatellite marker[J]. Scientia Agricultura Sinica, 2012, 45(3):405-413.
[9] 连帅, 陆平, 乔治军, 张琦, 张茜, 刘敏轩, 王瑞云. 利用SSR分子标记研究国内外黍稷地方品种和野生资源的遗传多样性[J].中国农业科学, 2016, 49(17):3264-3275. doi:10.3864/j.issn.0578-1752.2016.17.002.
Lan S, Lu P, Qiao Z J, Zhang Q, Zhang Q, Liu M X, Wang R Y. Genetic diversity in Broomcorn Millet(Panicum miliaceum L.)from China and abroad by using SSR markers[J]. Scientia Agricultura Sinica, 2016, 49(17):3264-3275.
[10] 陆徐忠, 倪金龙, 李莉, 汪秀峰, 马卉, 张小娟, 杨剑波. 利用SSR分子指纹和商品信息构建水稻品种身份证[J]. 作物学报, 2014, 40(5):823-829. doi:10.3724/SP.J.1006.2014.00823.
L X Z, Ni J L, Li L, Wang X F, Ma H, Zhang X J, Yang J B. Construction of rice variety indentity using SSR fingerprint and commodity information[J]. ACTA Agronomica Sinica, 2014, 40(5):823-829.
[11] 王瑞, 张福耀, 程庆军, 田承华, 凌亮. 利用SSR荧光标记构建20个高粱品种指纹图谱[J]. 作物学报, 2015, 41(4):658-665. doi:10.3724/SP.J.1006.2015.00658.
Wng R, Zhang F Y, Cheng Q J, Tian C H, Ling L. Establishment of 20 sorghum hybrids fingerprints using SSR fluorescent marker[J]. ACTA Agronomica Sinica, 2015, 41(4):658-665.
[12] 郭建斌, 黄莉, 成良强, 陈伟刚, 任小平, 陈玉宁, 周小静, 沈金雄, 姜慧芳. 利用3个F₂群体整合高密度栽培种花生遗传连锁图[J]. 作物学报, 2016, 42(2):159-169. doi:10.3724/SP.J.1006.2016.00159.
Go J B, Huang L, Cheng L Q, Chen W G, Ren X P, Chen Y N, Zhou X J, Shen J X, Jiang H F. An integrated genetic linkage map from three F₂ populations of cultivated peanut(Arachis hypogaea L.)[J]. ACTA Agronomica Sinica, 2016, 42(2):159-169.
[13] Ma K H, Kim K H, Dixit A, Yu J W, Chung J W, Lee J H, Cho E G, Kim T S, Park Y G. Newly developed polymorphic microsatellite markers in Job's tears(Coix lacryma-jobi L.)[J]. Molecular Ecology Notes, 2006, 6(3):689-691. doi:10.1111/j.1471-8286.2006.01311.x.
[14] Ma K H, Kim K H, Dixit A, Chung I M, Gwag J G, Kim T S, Park Y G. Assessment of genetic diversity and relationships among Coix lacryma-jobi accessions using microsatellite markers[J]. Biologia Plantarum, 2006, 54(2):272-278. doi:10.1007/s10535-010-0047-6.
[15] 郭银萍, 彭忠华, 赵致, 陈志兴, 高翔, 刘胜传, 谢云. 基于SSR标记的贵州薏苡种质资源遗传多样性分析[J].植物遗传资源学报, 2012, 13(2):317-320. doi:10.3969/j.issn.1672-1810.2012.02.027.
Go Y P, Peng Z H, Zhao Z, Chen Z X, Gao X, Liu S C, Xie Y. Genetic diversity analysis of Jobs Tears germplasm resources by SSR markers in Guizhou Province[J]. Journal of Plant Genetic Resources, 2012, 13(2):317-320.
[16] Liu H B, Shi J P, Cai Z X, Huang Y M, Lü M L, Du H L, Gao Q, Zuo Y, Dong Z B, Huang W, Qin R, Liang C Z, Lai J S, Jin W W. Evolution and domestication footprints uncovered from the genomes of coix[J]. Molecular Plant,2019.doi:10.1016/j.molp.2019.11.009.
[17] Guo C, Wang Y N, Yang A G, He J, Xiao C W, Lü S H, Han F M, Yuan Y B, Yuan Y, Dong X L, Guo J, Yang Y W, Liu H L, Zuo N Z, Hu Y X, Zhao K X, Jiang Z B, Wang X, Jiang T T, Shen Y O, Cao M J, Wang Y, Long Z B, Rong T Z, Huang L Q, Zhou S F. The Coix genome provides insights into Panicoideae evolution and papery hull domestication[J]. Molecular Plant,2019.doi:10.1016/j.molp.2019.11.008.
[18] Leseberg C H, Duvall M R. The complete chloroplast genome of Coix lacryma-jobi and a comparative molecular evolutionary analysis of plastomes in cereals[J]. Journal of Molecular Evolution, 2009, 69(4):311-318. doi:10.1007/s00239-009-9275-9.
[19] 李祥栋, 潘虹, 陆秀娟, 魏心元, 陆平, 石明, 秦礼康. 薏苡叶绿体基因组的SSR位点分析及种质亲缘关系鉴定[J]. 贵州农业科学, 2018, 46(8):1-5. doi:10.3969/j.issn.1001-3601.2018.08.002.
L X D, Pan H, Lu X J, Wei X Y, Lu P, Shi M, Qin L K. SSR locus analysis of chloroplast genome and identification of genetic relationships in 14 semen adlay germplasm resoures[J]. Guizhou Agricultural Sciences,2018, 46(8):1-5.
[20] Yeh F, Yang R C, Boyle T. Popgene:Microsoft window-based freeware for population genetic analysis, version1.31[M]. Edmonton:University of Alberta, 1999.
[21] Rohlf F J. NTSYS-pc Numerical taxonomy and multivariate analysis system(Version 2.1)[M]. New York:User Guide. Exeter Software Setauket, 2000.
[22] 杨丽, 赵韩生, 彭镇华, 董丽莉, 高志民. 竹子叶绿体基因组SSR分子标记的开发及其应用[J]. 热带亚热带植物学报, 2014, 22(3):263-269. doi:10.3969/j.issn.1005-3395.2014.03.008.
Yng L, Zhao H S, Peng Z H, Dong L L, Gao Z M. Development and application of SSR molecular markers from the chloroplast genome of bamboo[J]. Journal of Tropical and Subtropical Botany, 2014, 22(3):263-269.
[23] Beyer M, Nazareno A G, Lohmann L G. Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)[J]. Applications in Plant Sciences, 2017, 5(10):1700061. doi:10.3732/apps.1700061.
[24] 朱国忠, 戴伟民, 陈晓锋, 张晶旭, 强盛. 基于基因组数据库的杂草稻叶绿体分子标记开发[J]. 南京农业大学学报, 2015, 38(2):240-247. doi:10.7685/j.issn.1000-2030.2015.02.010.
Zu G Z, Dai W M, Chen X F, Zhang J X, Qiang S. Development of molecular markers in weedy rice chloroplast based on genomic database[J]. Journal of Nanjing Agricultural University, 2015, 38(2):240-247.
[25] 程丽莉, 胡广隆, 苏淑钗, 黄武刚. 板栗及其近缘种叶绿SSR遗传多样性分析[J].华北农学报, 2015, 30(2):145-149. doi:10.7668/hbnxb.2015.02.026.
Ceng L L, Hu G L, Su S C, Huang W G. Diversity of cultivated chestnuts and it's close relative species using chloroplast SSRs[J]. ACTA Agriculturae Boreali-Sinaca, 2015, 30(2):145-149.
[26] 李航, 杨晓明, 丁德宽, 王小丽, 谢宗周, 叶俊丽, 彭抒昂, 邓秀新, 柴利军. 基于cpSSR和nSSR标记的地方柑橘资源‘枳雀’亲本分析[J]. 果树学报, 2018, 359(10):1161-1169. doi:10.13925/j.cnki.gsxb.20180001.
L H, Yang X M, Ding D K, Wang X L, Xie Z Z, Ye J L, Peng S A, Deng X X, Chai L J. Parentage analysis of indigenous citrus ‘ZhiQue’ based on nuclear and chloroplast SSR markers[J]. Journal of Fruit Science, 2018, 35(10):1161-1169.
[27] 曾建敏, 陈学军, 吴兴富, 焦芳婵, 肖炳光, 李永平, 童治军. 基于烟草叶绿体基因组和线粒体基因组SSR标记的烟属植物遗传多样性分析[J]. 中国烟草学报, 2016, 22(4):89-97. doi:10.16472/j.chinatobacco.2016.130.
Zng J M, Chen X J, Wu X F, Jiao F C, Xiao B G, Li Y P. Genetic diversity analysis of genusNicotiana based on SSR markers in chloroplast genome and mitochondria genome[J]. ACTA Tabacaria Sinica, 2016, 22(4):89-97.
[28] 杜久军, 左力辉, 刘易超, 于晓跃, 董研, 王进茂, 杨敏生. 裂叶榆叶绿体基因组及CP-SSR位点分析[J]. 植物遗传资源学报, 2018, 19(6):1187-1196. doi:10.13430/j.cnki.jpgr.20180425001.
D J J, Zuo L H, Liu Y C, Yu X Y, Dong Y, Wang J M, Yang M S. Chloroplast genome and CP-SSR Site analyses of Ulmus laciniata[J]. Journal of Plant Genetic Resources, 2018, 19(6):1187-1196.
[29] Li J, Ge X J, Cao H L, Ye W H. Chloroplast DNA diversity in Castanopsis hystrix populations in South China[J]. Forest Ecology and Management, 2017, 243(1):94-101. doi:10.1016/j.foreco.2007.02.012.
[30] Chen P,Yu C M,Wang Y Z, Chen J K,Lu L X,Xiong H P. Analysis of genetic relationship amongBoehmeria varieties using cpSSR markers[J]. Agricultural Biotechnology 2015, 4(3):24-26. doi:10.19759/j.cnki.2164-4993.2015.03.006.
[31] Wang Q B, Zhang Y Y, Fang Z Y, Liu Y M, Yang L M, Zhuang M. Chloroplast and mitochondrial SSR help to distinguish allo-cytoplasmic male sterile types in cabbage(Brassica oleracea L.var.capitata)[J]. Molocular Breeding, 2012, 30(2):709-716. doi:10.1007/s11032-011-9656-9.
[32] Butorac L, Hančević K, LuksÏić K, Škvorc Ž, Leko M, Maul E, Goran Zdunić. Assessment of wild grapevine(Vitis vinifera ssp. sylvestris) chlorotypes and accompanying woody species in the Eastern Adriatic region[J]. PLoS One, 2018, 13(6):e0199495. doi:10.1371/journal.pone.0199495.
[33] 张靖国, 曹玉芬, 陈启亮, 杨晓平, 范净, 田瑞, 胡红菊. 基于叶绿体DNA变异的湖北梨属种质系统进化及遗传多样性分析[J]. 植物遗传资源学报, 2016, 17(4):766-772. doi:10.13430/j.cnki.jpgr.2016.04.023.
Zang J G, Cao Y F, Chen Q L, Yang X P, Fan J, Tian R, Hu H J. Genetic diversty and phylogenetics of pear(Pyrus L.) germplasm resources from Hubei province revealed by chloroplast DNA variation[J]. Journal of Plant Genetic Resources, 2016, 17(4):766-772.
[34] Xu D, Abe J, Gai J, Shimamoto Y. Diversity of chloroplast DNA SSRs in wild and cultivated soybeans:evidence for multiple origins of cultivated soybean[J]. Theoretical and Applied Genetics, 2002, 105(5):645-653. doi:10.1007/s00122-002-0972-7.
[35] 魏潇, 章秋平, 刘威生, 刘宁, 张玉萍, 徐铭, 刘硕, 张玉君, 马小雪. 基于叶绿体SSR单倍型分析普通杏演化关系[J].植物遗传资源学报, 2018, 19(4):705-712. doi:10.13430/j.cnki.jpgr.20171103001.
Wi X, Zhang Q P, Liu W S, Liu N, Zhang Y P, Xu M. Liu S, Zhang Y J, Ma X X. Phylogenetic relationship analysis of common apricot(Prunus armeniaca L.) revealed by chloroplast SSR haplotypes[J]. Journal of Plant Genetic Resources, 2018, 19(4):705-712.
[36] 陆平, 左志明. 广西水生薏苡种的发现与鉴定[J].广西农业科学,1996(1):18-20.
L P, Zuo Z M. Discovery and identification of C. aduatica Roxb. in Guangxi[J]. Journal of Guangxi Agricultural Sciences, 1996(1):18-20.

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