Genetic Diversity Analysis of Sweet Potato and Its Wild Species Using SCoT Molecular Markers

doi:10.7668/hbnxb.20191325

Abstract

Abstract: In order to reveal the genetic diversity of sweet potato and its wild species and analyze the genetic relationship between sweet potato and its wild species, SCoT molecular markers were used to analyze the results of PCR amplification, genetic diversity, evolutionary relationship and population structure of 22 germplasm of sweetpotato and its wild species I.trifida and I.triloba in the present study. The results showed that 278 stable bands were detected by 43 primers, 4-12 bands could be detected by each primer, and five primers with rich polymorphism were screened, which were SCoT-8, SCoT-20, SCoT-26, SCoT-36 and SCoT-35. These primers could be used in the study of sweet potato molecular markers in the future. The analysis of genetic diversity based on the results of molecular markers showed that the highest genetic diversity was in I.trifida, followed by I.batatas, and the lowest in I.triloba. According to the results of genetic cluster analysis and population genetic structure analysis, 22 germplasm were divided into three groups, and the classification of each group was basically the same as its species. There was less blood exchange between different species, and the genetic composition was relatively simple. In comparison, the blood exchange between sweet potato and I.trifida was more than that between I.triloba. In conclusion, the results of this study preliminarily proved the potential application of SCoT molecular markers in the study of sweet potato evolution, and revealed the different genetic relationships between sweet potato and its wild relatives, which provided theoretical support for introducing I. trifida and other wild species into sweet potato breeding to improve the genetic diversity of sweet potato in the future.

Key words: Sweet potato, SCoT molecular markers, Genetic diversity, Genetic structure

CLC Number:

S632.03

FENG Junyan, KANG Le, LANG Tao, ZHANG Cong, LI Ming, ZHAO Shan, PU Zhigang. Genetic Diversity Analysis of Sweet Potato and Its Wild Species Using SCoT Molecular Markers[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2021, 36(1): 18-26. doi: 10.7668/hbnxb.20191325.

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References

[1] Woolfe J A. Sweet potato:an untapped food resource[M].Cambridge:Cambridge University Press,1992:15-40.
[2] 谢一芝,郭小丁,贾赵东,马佩勇,边小峰,禹阳. 中国食用甘薯育种现状及展望[J]. 江苏农业学报,2018,34(6):1419-1424. doi:10.3969/j.issn.1000-4440.2018.06.030.
Xie Y Z,Guo X D,Jia Z D,Ma P Y,Bian X F,Yu Y. Progresses and prospects on edible sweetpotato breeding in China[J]. Jiangsu Journal of Agricultural Sciences,2018,34(6):1419-1424.
[3] Austin D F. The taxonomy,evolution and genetic diversity of sweet potatoes and related wild species[C]//CIP.Exploration,maintenance and utilization of sweetpotato genetic resources:Report 1st sweet potato planning conference. Lima:International Potato Center,1988:27-60.
[4] Zhang D P,Cervantes J,Huamán Z,Carey E,Ghislain M. Assessing genetic diversity of sweet potato(Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP[J]. Genetic Resources and Crop Evolution,2000,47:659-665. doi:10.1023/A:1026520507223.
[5] Takagi H. Sweetpotato collections in Papua New Guinea[C]//CIP.Exploration,maintenance and utilization of sweetpotato genetic resources:Report 1^st sweet potato planning conference. Lima:International Potato Center, 1988:233-246.
[6] Rao V R,Debouck T,Iwanaga M. The role of international organizations in root and tuber crop conservation[C]//International workshop on genetic resources-root and tubercrops. Tsukuba:1st Ministry of Agriculture, Forestry and Fisheries, 1994:7-22.
[7] Komaki K. Breeding value of wild species closely related to sweetpotato[C].Korea:Proceedings of international workshop on production, utilization and development of sweetpotato, 2004:164-172.
[8] Kriegner A,Cervantes J C,Burg K,Mwanga R O M,Zhang D P. A genetic linkage map of sweetpotato(Ipomoea batatas (L.) Lam.) based on AFLP markers[J]. Molecular Breeding,2003,11:169-185. doi:10.1023/A:1022870917230.
[9] Cervantes-Flores J C,Yencho G C,Kriegner A,Pecota K V,Faulk M A,Mwanga R O M,Sosinski B R. Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers[J]. Molecular Breeding,2008,21:511-532. doi:10.1007/s11032-007-9150-6.
[10] Li H,Zhao N,Yu X X,Liu Y X,Zhai H,He S Z,Li Q,Ma D F,Liu Q C. Identification of QTLs for storage root yield in sweetpotato[J]. Scientia Horticultural,2014,170:182-188. doi:10.1016/j.scienta.2014.03.017.
[11] Monden Y,Hara T,Okada Y,Jahana O,Kobaysahi A,Tabuchi H,Onaga S,Tahara M. Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing[J]. Breeding Science,2015,65(2):145-153. doi:10.1270/jsbbs.65.145.
[12] Shirasawa K,Tanaka M,Takahata Y,Ma D F,Cao Q H,Liu Q C,Zhai H,Kwak S S,Jeong J C,Yoon U H,Lee H U,Hirakawa H,Isobe S. A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato(Ipomoea batatas)[J]. Scientific Reports,2018,7:44207. doi:10.1038/srep44207.
[13] Feng J Y,Li M,Zhao S,Zhang C,Yang S T,Qiao S,Tan W F,Qu H J,Wang D Y,Pu Z G. Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I.trifida using RAD-seq[J]. BMC Plant Biology,2018,18:181. doi:10.1186/s12870-018-1399-x.
[14] Feng J Y,Zhao S,Li M,Zhang C,Qu H J,Li Q,Li J W,Lin Y,Pu Z G. Genome-wide genetic diversity detection and population structure analysis in sweetpotato(Ipomoea batatas) using RAD-seq[J]. Genomics,2020,112(2):1978-1987. doi:10.1016/j.ygeno.2019.11.010.
[15] Yang X S,Su W J,Wang L J,Lei J,Chai S S,Liu Q C. Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers[J]. Journal of Integrative Agriculture, 2015,14(4):633-641.doi:10.1016/S2095-3119(14) 60794-2.
[16] Collard B C Y,Mackill D J. Start Codon Targeted(SCoT) polymorphism:a simple,novel DNA marker technique for generating gene-targeted markers in plants[J]. Plant Molecular Biology Reporter,2009,27(1):86-93. doi:10.1007/s11105-008-0060-5.
[17] 冯俊彦,赵珊,李明,张聪,屈会娟,杨松涛,乔帅,谭文芳,王大一,蒲志刚.四种分子标记技术在甘薯及 I. trifida 遗传多样性研究中的应用[J]. 分子植物育种,2018,16(17):5667-5674. doi:10.13271/j.mpb.016.005667.
Feng J Y,Zhao S,Li M,Zhang C,Qu H J,Yang S Y,Qiao S,Tan W F,Wang D Y,Pu Z G. The application of four molecular marking techniques in the genetic diversity of sweetpotato and I. trifida[J]. Molecular Plant Breeding,2018,16(17):5667-5674.
[18] Murray M G,Thompson W F. Rapid isolation of high molecular weight plant DNA[J]. Nnucleic Acids Research, 1980,8(19):4321-4326. doi:10.1093/nar/8.19.4321.
[19] Hubisz M J,Falush D,Stephens M,Pritchard J K. Inferring weak population structure with the assistance of sample group information[J]. Molecular Ecology Resources,2009,9(5):1322-1332. doi:10.1111/j.1755-0998.2009.02591.x.
[20] Earl D A,Vonholdt B M. STRUCTURE HAVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method[J]. Conservation Genetics Resources,2012,4(2):359-361. doi:10.1007/s12686-011-9548-7.
[21] Yeh F C,Boyle T B J. Population genetic analysis of co-dominant and dominant markers and quantitative traits[J]. Belgian Journal of Botany,1997,129:157-163.
[22] Nei M,Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences of the United States of America, 1979,76(10):5269-5273. doi:10.1073/pnas.76.10.5269.
[23] Evanno G,Regnaunts S,Goudet J. Detecting the number of clusters of individuals using the software structure:A simulation study[J]. Molecular Ecology, 2005,14(8):2611-2620. doi:10.1111/j.1365-294X.2005.02553.x.
[24] 苏一钧,王娇,戴习彬,唐君,赵冬兰,张安,周志林,曹清河. 303份甘薯地方种SSR遗传多样性与群体结构分析[J]. 植物遗传资源学报,2018,19(2):243-251. doi:10.13430/j.cnki.jpgr.2018.02.007.
Su Y J,Wang J,Dai X B,Tang J,Zhao D L,Zhang A,Zhou Z L,Cao Q H. Genetic diversity and population Structure analysis of 303 sweetpotato landraces using SSR markers[J]. Journal of Plant Genetic Resource,2018,19(2):243-251.
[25] Elameen A,Fjellheim S,Larsen A,Rognli O A,Sundheim L,Msolla S,Masumba E,Mtunda K,Klemsdal S S. Analysis of genetic diversity in a sweetpotato(Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP[J]. Genetic Resources and Crop Evolution,2008,55(3):397-408.doi:10.1007/s10722-007-9247-0.
[26] Cervantes-Flores J C,Sosinski B,Pecota K V,Mwanga R O M,Catignani G L,Truong V D,Watkins R H,Yencho G C. Identification of quantitative trait loci for dry-matter,starch,and β-carotene content in sweetpotato[J]. Molecular Breeding,2011,28:201-216. doi:10.1007/s11032-010-9474-5.
[27] Zhao N,Yu X X,Jie Q,Li H,Li H,Hu J,Zhai H,He S Z,Liu Q C. A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato[J]. Molecular Breeding, 2013,32(4):807-820. doi:10.1007/s11032-013-9908-y.
[28] Kim J H,Chung I K,Kim K M. Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweetpotato(Ipomoeabatatas (L.) Lam)[J]. PLoS One,2017,12:e0185073. doi:10.1371/journal.pone.0185073.
[29] Roullier C,Duputié A,Wennekes P,Benoit L,Bringas V M F,Rossel G,Tay D,McKey D,Lebot V. Disentangling the origins of cultivated sweet potato(Ipomoeabatatas (L.) Lam.)[J]. PLoS One, 2013,8:e62707. doi:10.1371/journal.pone.0062707.
[30] Gichuki S T,Berenyi M,Zhang D P,Hermann M,Schmidt J,Glössl J,Burg K. Genetic diversity in sweetpotato[Ipomoea batatas (L.) Lam.]in relationship to geographic sources as assessed with RAPD markers[J]. Genetic Resources and Crop Evolution, 2003,50:429-437. doi:10.1023/A:1023998522845.
[31] Nishiyama I. The origin of the sweetpotato[M]. Honolulu:Tenth Pacific Sci Congr Univ Hawaii,1961:119-128.
[32] 李祥栋,石明,陆秀娟,潘虹,魏心元,陆平.利用叶绿体基因组SSR标记揭示薏苡属种质资源的遗传多样性[J].华北农学报,2019,34(S1):6-14. doi:10.7668/hbnxb.20190745.
Li X D,Shi M,Lu X J,Pan H,Wei X Y,Lu P. 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.
[33] 梁铁军,陈雄辉,崔玉梅,罗方雄,张泽民,彭海峰.影响温敏核不育水稻育性转换的低温敏感度QTL定位[J]. 华北农学报,2020,35(2):29-34. doi:10.7668/hbnxb.20190431.
Liang T J,Chen X H,Cui Y M,Luo F X,Zhang Z M,Peng H F. QTL mapping of low temperature sensitivity affecting the fertility reversibility in thermo-sensitive genic male sterile rice[J]. Acta Agriculturae Boreali-Sinica,2020,35(2):29-34.
[34] 白志元,张瑞军,武国平,连世超,杨玉花,卫保国.基于SSR标记的杂交大豆主要亲本遗传多样性分析[J].华北农学报,2018,33(4):120-125. doi:10.7668/hbnxb.2018.04.017.
Bai Z Y,Zhang R J,Wu G P,Lian S C,Yang Y H,Wei B G. Genetic diversity analysis of main parents for hybrid soybean based on SSR markers[J]. Acta Agriculturae Boreali-Sinica, 2018,33(4):120-125.
[35] Nishiyama I,Fujise K,Teramura T,Miyazaki T. Studies of sweetpotato and its related species:I. Comparative investigationson the chromosome numbers and the main plant characters of Ipomoea species in section Batatas[J]. Japanese Journal of Breeding,1961,11(1):37-43. doi:10.1270/jsbbs1951.11.37.
[36] Kobayashi M,Miyazaki T.Sweetpotato breeding using wild related specie[M]//James C, Reginald M, Michael G. Tropical root and tuber crops:Fourth Triennial Symposium. Columbia:Centro Internacional de Agricultura Tropical, 1976:53-57.
[37] Huang J C,Sun M. Genetic diversity and relationships of sweetpotato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat(ISSR) and restriction analysis of chloroplast DNA[J]. Theoretical and Applied Genetics, 2000,100:1050-1060. doi:10.1007/s001220051386.
[38] Srisuwan S,Sihachakr D,Siljak-Yakovlev S. The origin and evolution of sweetpotato(Ipomoea batatas Lam.) and its wild relatives through the cytogenetic approaches[J]. Plant Science, 2006,171(3):424-433. doi:10.1016/j.plantsci.2006.05.007.
[39] Jarret R L,Austin D F. Genetic diversity and systematic relationships in sweetpotato(Ipomoea batatas (L.) Lam.) and related species as revealed by RAPD analysis[J]. Genetic Resources and Crop Evolution, 1994,41(3):165-173. doi:10.1007/BF00051633.
[40] Kobayashi M. The Ipomoea trifida complex closely related to sweetpotato[C]//Peru:Centro Internacional de la Papua,Proc 6th Symp Int Soc Trop Root Crops,Lima,1984:561-568.

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