Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (05): 641-647.doi: 10.3724/SP.J.1006.2016.00641

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of Interspecific SNPs in Sweetpotato Using a Reduced-Representation Genotyping Technology

SHI Xuan1,WANG Ru-Yuan1,TANG Jun2,LI Zong-Yun1,*,LUO Yong-Hai1,*   

  1. 1 School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; 2 Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences / National Sweetpotato Improvement Centre, Xuzhou 221121, China
  • Received:2015-10-19 Revised:2016-01-11 Online:2016-05-12 Published:2016-02-18
  • Contact: Luo Yonghai, E-mail: yhluo@jsnu.edu.cn; 李宗芸, E-mail: zongyunli@jsnu.edu.cn E-mail:shixuanluck@163.com
  • Supported by:

    This study was supported by the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions, the Project on Crop Conservation Funded by the Ministry of Agriculture of China (2015NWB006), the General Projects Funded by Natural Science Foundation of Jiangsu Province (BK2012579, BK20141146), and the Major Project Funded by Natural Science Foundation of Jiangsu Higher Education Institutions (12KJA180001).

Abstract:

Xushu18 (2x), Nancy Hall (6x), I. trifida (2x) 4597-10, I. trifida (2x) 4597-21, I. trifida (4x), I. trifida (6x), I. temussima (2x), and I. littorallis (2x) were used as experimental materials for sequencing by specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput reduced-representation genotyping technology. In total, 724 589 SLAF tags were obtained and 40 765 SNPs were identified out of 35 310 polymorphic SLAF tags. A total of 40 765 single nucleotide polymorphisms (SNPs) were obtained by sequence analysis. Population structure and phylogenetic relationship of eight germplasm were analyzed using the SNP dataset, which suggests that SLAF-seq can be used to develop large-scale SNPs for population genetic analysis, effectively and economically. Our analysis revealed that the relationship between sweet potato cultivars and the wild species I. trifida is closer. These results provide empirical data for further study of the origin of sweet potato.

Key words: Sweetpotato, SLAF-seq, Molecular marker, SNP, Phylogenetic analysis

[1] Lande R. Neutral theory of quantitative genetic variance in an island model with local extinction and colonization. Evolution, 1992, 46: 381–389
[2] 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. Theor Appl Genet, 2000, 100: 1050–1060
[3] Jarret R L, Gawel N, Whittemore A . Phylogenetic relationships of the sweetpotato [Ipomoea batatas (L.) Lam.]. J Am Soc Hort Sci, 1992, 117: 633–637
[4] Wright S. The genetical structure of populations. Ann Eugen, 1951, 15: 323–354
[5] Buteler M I, Jarret R L, LaBonte D R. Sequence characterization of microsatellites in diploid and polyploid Ipomoea. Theor Appl Genet, 1999, 99: 123–132
[6] Huang J C, Corke H, Sun M. Highly polymorphic AFLP markers as a complementary tool to ITS sequences in assessing genetic diversity and phylogenetic relationships of sweetpotato (Ipomoea batatas (L.) Lam.) and its wild relatives. Genet Resour Crop Evol, 2000, 49: 541–550
[7] Rajapakse S, Nilmalgoda S D, Molnar M, Ballard R E, Austin D F, Bohac J R. Phylogenetic relationships of the sweetpotato in Ipomoea series Batatas (Convolvulaceae) based on nuclear beta-amylase gene sequences. Mol Phylogenet Evol, 2004, 30: 623–632
[8] Srisuwan S, Sihachakr D, Siljak-Yakovlev S. The origin and evolution of sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives through the cytogenetic approaches. Plant Sci, 2006, 171: 424–433
[9] Jarret R L, Austin D F. Genetic diversity and systematic relationship in sweetpotato (Ipomoea batatas) (L.) Lam.) and related species as revealed by RAPD analysis. Gen Resour Crop Evol, 1994, 41: 165–173
[10] 贺学勤, 刘庆昌, 翟红, 王玉萍. 用RAPD、ISSR和AFLP标记分析系谱关系明确的甘薯品种的亲缘关系. 作物学报, 2005, 10: 1300–1304
He X Q, Liu Q C, Zhai H, Wang Y P. The use of RAPD , ISSR and AFLP markers for analyzing genetic relationships among sweetpotato cultivars with known origin. Acta Agron Sin, 2005, 10: 1300–1304 (in Chinese with English abstract)
[11] Kobayashi M. The Ipomoea trifida complex closely related to sweet potato. In: Shideler S F, Rincon H, eds. Proceedings of the 6th Symposium of the International Society of Tropical Root Crop. Lima, Peru: CIP. 1984. pp 561–568
[12] Roullier C, Kambouo R, Paofa J, Mckey D, Lebot V. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary center of diversity. Heredity, 2013, 1–11
[13] Heffelfinger C, Fragoso C A, Moreno M A, Overton J D, Mottinger J P, Zhao H Y, Tohme J, Dellaporta S L. Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genom, 2014, 15: 979–1001
[14] 王洋坤, 胡艳, 张天真. RAD-seq技术在基因组研究中的现状及展望. 遗传, 2014, 36: 41–49
Wang Y K, Hu Y, Zhang T Z. Current status and perspective of RAD-seq in genomic research. Hereditas (Beijing), 2014, 36: 41–49 (in Chinese with English abstract)
[15] Crow J F, Kimura M. Population Genetics. (Book Reviews: An Introduction to Population Genetics Theory). Science, 1971, 171: 666-–667
[16] Sun X, Liu D Y, Zhang X F, Li W B, Liu H, Hong W G, Jiang C B, Guan N, Ma C X, Zeng H P, Xu C H, Song J, Huang L, Wang C M, Shi J J, Wang R, Zheng X H, Lu C Y, Wang X W, Zheng H K. SLAF-seq: an efficient method of large-scale De novo SNP discovery and genotyping using high-throughput sequencing. PloS One, 2013, 8: e58700
[17] Davey J W, Cezard T, Fuentes-Utrila P, Eland C, Gharbi K, Blaxter M L. Special features of RAD Sequencing data: implications for genotyping. Mol Ecol, 2013, 22: 3151–3164
[18] http://potatogenomics.plantbiology.msu.edu
[19] Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 2009, 19: 1655–1664
[20] Hoon M J L D, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics, 2004, 20: 1453–1454
[21] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 2011, 28: 2731–2739
[22] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987, 4: 406–425
[23] 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. Mol Breed, 2003, 11: 169–185
[24] Cervantes 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. Mol Breed, 2008, 21: 511–532
[25] 吴洁, 谭文芳, 何俊蓉, 蒲志刚, 王大一, 阎文昭. 甘薯SRAP连锁图构建淀粉含量QTL检测. 植物分子育种, 2005, 6: 841–845
Wu J, Tan W F, He J R, Pu Z G, Wang D Y, Yan W Z. Construct on of SRAP Linkage Map and QTL Mapping for Starch Content in Sweet Potato. Mol Plant Breed, 2005, 6: 841–845 (in Chinese with English abstract)
[26] 唐茜, 何凤发, 王季春, 王瑞娜. 甘薯SRAP遗传图谱构建及淀粉含量QTL初步定位. 西南大学学报(自然科学版), 2010, 32(6): 40–45
Tang Q, He F F, Wang J C, Wang R N. Construct on of SRAP Genetic Map and QTL Mapping for Starch Content in Sweet Potato. J Southwest Univ (Nat Sci Edn), 2010, 32(6): 40–45 (in Chinese)
[27] 蒲志刚, 王大一, 谭文芳, 吴洁, 阎文昭. 利用AFLP构建甘薯连锁图及淀粉含量QTL定位. 西南农业学报, 2010, 23: 1047–1050
Pu Z G, Wang D Y, Tan W F, Wu J, Yan W Z. AFLP Maps and QTL Analysis of Starch Content of Sweet Potato. Southwest China J Agric Sci, 2010, 23: 1047–1050 (in Chinese with English abstract)
[28] 李爱贤, 刘庆昌, 王庆美, 张立明, 翟红, 刘树震. 利用SRAP标记构建甘薯分子连锁图谱. 作物学报, 2010, 36: 1286–1295
Li A X, Liu Q C, Wang Q M, Zhang L M, Zhai H, Liu S Z. Establishment of Molecular Linkage Maps Using SRAP Markers in Sweet Potato. Acta Agron Sin, 2010, 36: 1286–1295 (in Chinese with English abstract)
[29] 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. Mol Breed, 2013, 32:807–820
[30] Li H, Vikram P, Singh R P, Kilian A, Carling J, Song J, Burgueno-Ferreira J A, Bhavani S, Huerta-Espino J, Payne T, Sehgal D, Wenzl P, Singh S. A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits. BMC Genomics, 2015, 16: 1–15
[31] Srisuwan S, Sihachakr D, Siljak-Yakovlev S. The origin and evolution of sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives through the cytogenetic approaches. Plant Sci, 2006, 171: 424–433
[32] Nishiyama I. Evaluation and domestication of the sweet potato. Bot Mag, 1971, 84: 377–387
[33] Austin D F. The taxonomy, evolution and genetic diversity of sweet potatoes and related wild species. In: Gregory P ed. Exploration, Maintenance, and Utilization of Sweet Potato Genetic Resources. 1988, pp 27–60
[34] Roullier C, Duputié A, Wennekes P, Benoit L, Fernández Bringas V M, Rossel G, Tay D, McKey D, Lebot V. Disentangling the Origins of Cultivated Sweet Potato (Ipomoea batatas (L.) Lam.). PLoS One, 2013, 8: e62707
[35] Otto S P. The evolutionary consequences of polyploidy. Cell, 2007, 131: 452–462
[36] Zohary D. Unconscious selection and the evolution of domesticated plants. Econ Bot, 2004, 58: 5–10
[37] Allaby R G, Fuller D Q, Brown T A. The genetic expectations of a protracted model for the origins of domesticated crops. Proc Natl Acad Sci USA, 2008, 105: 13982–13986
[1] HU Wen-Jing, LI Dong-Sheng, YI Xin, ZHANG Chun-Mei, ZHANG Yong. Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat [J]. Acta Agronomica Sinica, 2022, 48(6): 1346-1356.
[2] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[3] LIU Dan, ZHOU Cai-E, WANG Xiao-Ting, WU Qi-Meng, ZHANG Xu, WANG Qi-Lin, ZENG Qing-Dong, KANG Zhen-Sheng, HAN De-Jun, WU Jian-Hui. Rapid identification of adult plant wheat stripe rust resistance gene YrC271 using high-throughput SNP array-based bulked segregant analysis [J]. Acta Agronomica Sinica, 2022, 48(3): 553-564.
[4] FU Mei-Yu, XIONG Hong-Chun, ZHOU Chun-Yun, GUO Hui-Jun, XIE Yong-Dun, ZHAO Lin-Shu, GU Jia-Yu, ZHAO Shi-Rong, DING Yu-Ping, XU Yan-Hao, LIU Lu-Xiang. Genetic analysis of wheat dwarf mutant je0098 and molecular mapping of dwarfing gene [J]. Acta Agronomica Sinica, 2022, 48(3): 580-589.
[5] JIN Rong, JIANG Wei, LIU Ming, ZHAO Peng, ZHANG Qiang-Qiang, LI Tie-Xin, WANG Dan-Feng, FAN Wen-Jing, ZHANG Ai-Jun, TANG Zhong-Hou. Genome-wide characterization and expression analysis of Dof family genes in sweetpotato [J]. Acta Agronomica Sinica, 2022, 48(3): 608-623.
[6] WANG Juan, ZHANG Yan-Wei, JIAO Zhu-Jin, LIU Pan-Pan, CHANG Wei. Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean [J]. Acta Agronomica Sinica, 2022, 48(3): 635-643.
[7] MA Hong-Bo, LIU Dong-Tao, FENG Guo-Hua, WANG Jing, ZHU Xue-Cheng, ZHANG Hui-Yun, LIU Jing, LIU Li-Wei, YI Yuan. Application of Fhb1 gene in wheat breeding programs for the Yellow-Huai Rivers valley winter wheat zone of China [J]. Acta Agronomica Sinica, 2022, 48(3): 747-758.
[8] ZHAO Mei-Cheng, DIAO Xian-Min. Phylogeny of wild Setaria species and their utilization in foxtail millet breeding [J]. Acta Agronomica Sinica, 2022, 48(2): 267-279.
[9] ZHENG Xiang-Hua, YE Jun-Hua, CHENG Chao-Ping, WEI Xing-Hua, YE Xin-Fu, YANG Yao-Long. Xian-geng identification by SNP markers in Oryza sativa L. [J]. Acta Agronomica Sinica, 2022, 48(2): 342-352.
[10] ZHANG Hai-Yan, XIE Bei-Tao, JIANG Chang-Song, FENG Xiang-Yang, ZHANG Qiao, DONG Shun-Xu, WANG Bao-Qing, ZHANG Li-Ming, QIN Zhen, DUAN Wen-Xue. Screening of leaf physiological characteristics and drought-tolerant indexes of sweetpotato cultivars with drought resistance [J]. Acta Agronomica Sinica, 2022, 48(2): 518-528.
[11] XU De-Rong, SUN Chao, BI Zhen-Zhen, QIN Tian-Yuan, WANG Yi-Hao, LI Cheng-Ju, FAN You-Fang, LIU Yin-Du, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of StDRO1 gene polymorphism and association analysis with root traits in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 76-85.
[12] ZHANG Si-Meng, NI Wen-Rong, LYU Zun-Fu, LIN Yan, LIN Li-Zhuo, ZHONG Zi-Yu, CUI Peng, LU Guo-Quan. Identification and index screening of soft rot resistance at harvest stage in sweetpotato [J]. Acta Agronomica Sinica, 2021, 47(8): 1450-1459.
[13] WANG Yin, FENG Zhi-Wei, GE Chuan, ZHAO Jia-Jia, QIAO Ling, WU Bang-Bang, YAN Su-Xian, ZHENG Jun, ZHENG Xing-Wei. Identification of seedling resistance to stripe rust in wheat-Thinopyrum intermedium translocation line and its potential application in breeding [J]. Acta Agronomica Sinica, 2021, 47(8): 1511-1521.
[14] GENG La, HUANG Ye-Chang, LI Meng-Di, XIE Shang-Geng, YE Ling-Zhen, ZHANG Guo-Ping. Genome-wide association study of β-glucan content in barley grains [J]. Acta Agronomica Sinica, 2021, 47(7): 1205-1214.
[15] YIN Ming, YANG Da-Wei, TANG Hui-Juan, PAN Gen, LI De-Fang, ZHAO Li-Ning, HUANG Si-Qi. Genome-wide identification of GRAS transcription factor and expression analysis in response to cadmium stresses in hemp (Cannabis sativa L.) [J]. Acta Agronomica Sinica, 2021, 47(6): 1054-1069.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!