Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

BMC Genomics

Tae-Jin Yang³  Kyounggu Ahn¹  Beom-Seok Park⁴  Mina Jin⁴  Sampath Perumal³  Murukarthick Jayakodi³  Jonghoon Lee³  Nur Kholilatul Izzah² 

[1] Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, Goesan-Gu, Chungcheongbuk-Do 367-833, Korea;Present Address: Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia;Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea;National Institute of Agricultural Biotechnology, Rural development Administration, Suwon 441-707, Korea

关键词: Transcriptome sequencing;    SNP;    SSR;    Genetic linkage map;    EST;    Cabbage;   

Others  :  1217847
DOI  :  10.1186/1471-2164-15-149

 received in 2013-10-28, accepted in 2014-02-17,  发布年份 2014

【 摘 要 】

Background

Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction.

Results

Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F₂ population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility.

Conclusions

This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.

【 授权许可】

   
2014 Izzah et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]UN: Genome-analysis in Brassica with special reference to the experimental formation of Brassica napus and its peculiar mode of fertilization. Jpn J Bot 1935, 7:389-452.
• [2]Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP: Genic microsatellite markers in brassica Rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 2011, 18:305-320.
• [3]Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bembem LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380.
• [4]Morozova O, Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92:255-264.
• [5]Rudd S: Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 2003, 8:321-329.
• [6]Zhou Y, Gao F, Liu R, Feng J, Li H: De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics 2012, 13:266.
• [7]Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EM, Chen S: De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262.
• [8]Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB: Sampling the arabidopsis transcriptome with massive parallel pyrosequencing. Plant Physiol 2007, 144:32-42.
• [9]Vega-Arreguin JC, Ibarra-Laclette E, Jimenez-Moraila B, Martinez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A: Deep sampling of the palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 2009, 10:299.
• [10]Alagna F, D’Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G: Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009, 10:399.
• [11]Edwards CE, Parchman TL, Weekley CW: Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (rhamnaceae), a highly endangered, Florida endemic plant. DNA Res 2012, 19:1-9.
• [12]Hendre PS, Aggarwal RK: DNA markers: development and application for genetic improvement of coffee. In Genomics Assisted Crop Improvement. Genomics Applications in Crops. Volume 2 edition. Edited by Varshney RK, Tuberosa R. Netherlands: Springer; 2007:399-434.
• [13]Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Reyes S, Wo C, Van Deynze A: De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in discovery of SNPs, SSRs and candidate silico genes. BMC Genomics 2012, 13:571.
• [14]Wang W, Huang S, Liu Y, Fang Z, Yang L, Hua W, Yuan S, Liu S, Sun J, Zhuang M, Zhang Y, Zeng A: Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata). BMC Genomics 2012, 13:523.
• [15]Smith LB, King GJ: The distribution of BoCAL-a alleles in Brassica oleracea is consistent with a genetic model for curd development and domestication of the cauliflower. Mol Breed 2000, 6:603-613.
• [16]Lowe AJ, Moule C, Trick M, Edwards KJ: Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 2004, 108:1103-1112.
• [17]Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger M-J, Vincourt P, Blanchard P: Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet 2005, 111:1514-1523.
• [18]Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, Hou J, Zhao J, Shi L, Park BS, Choi SR, Lim YP, Meng J: Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genome wide alignment with arabidopsis. Genetics 2007, 177(4):2433-2444.
• [19]Radoev M, Becker HC, Ecke W: Genetic analysis of heterosis for yield and yield components in rapeseed (Brassica napus L.) by quantitative trait locus mapping. Genetics 2008, 179:1547-1558.
• [20]Cheng X, Xu J, Xia S, Gu J, Yang Y, Fu J, Qian X, Zhang S, Wu J, Liu K: Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor Appl Genet 2009, 118(6):1121-1131.
• [21]Kim H, Choi SR, Bae J, Hong CP, Lee SY, Hossain MJ, Nguyen DV, Jin M, Park BS, Bang JW, Bancroft I, Lim YP: Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 2009, 10:432.
• [22]Mun J-H, Kwon S-J, Yang T-J, Seol Y-J, Jin M, Kim J-A, Lim M-H, Kim JS, Baek S, Choi B-S, Yu H-J, Kim D-S, Kim N, Lim K-B, Lee S-I, Hahn J-H, Lim YP, Bancroft I, Park B-S: Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 2009, 10:R111.
• [23]Uzunova MI, Ecke W: Abundance, polymorphism and genetic mapping of microsatellites in oilseed rape (Brassica napus L). Plant Breed 1999, 118:323-326.
• [24]Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg GC, Edwards D, Batley J: Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Mol Ecol Notes 2006, 6:1191-1194.
• [25]Suwabe K, Iketani H, Nunome T, Kage T, Hirai M: Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 2002, 104:1092-1098.
• [26]Louarn S, Torp AM, Holme IB, Andersen SB, Jensen BD: Database derived microsatellite markers (SSRs) for cultivar differentiation in Brassica oleracea. Genet Resour Crop Evol 2007, 54:1717-1725.
• [27]Sandler L, Hiraizum Y, Sandler I: Meiotic drive in natural populations of Drosophila melanogaster. I. The cytogenetic basis of segregation distortion. Genetics 1959, 44:233-250.
• [28]Uzunova M, Ecke W, Weissleder K, Uzunova M, Ecke W, Weissleder K, Röbbelen G: Mapping the genome of rapeseed (Brassica napus L.). I. Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content. Theor Appl Genet 1995, 90:194-204.
• [29]Varghese JP, Rudolph B, Uzunova MI, Ecke W: Use of 5’-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L. Theor Appl Genet 2000, 101:115-119.
• [30]Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS, Lim YP: The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 2007, 115:777-792.
• [31]Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC, Edwards D: Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences. Mol Ecol Notes 2007, 7:886-889.
• [32]Iniguez-Luy FL, Voort AV, Osborn TC: Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. Genotype. Theor Appl Genet 2008, 117(6):977-985.
• [33]Kresovich S, Szewc-McFadden AK, Bliek SM, McFerson JR: Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 1995, 91:206-211.
• [34]Szewc-McFadden AK, Kresovich S, Bliek SM, Mitchell SE, McFerson JR: Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species. Theor Appl Genet 1996, 93:534-538.
• [35]Bell CJ, Ecker JR: Assignment of 30 microsatellite loci to the linkage map of arabidopsis. Genomics 1994, 19:137-144.
• [36]Lagercrantz U, Ellegren H, Andersson L: The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 1993, 21(5):1111-1115.
• [37]Sebastian RL, Howell EC, King GJ, Marshall DF, Kearsey MJ: An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations. Theor Appl Genet 2000, 100:75-81.
• [38]Saito M, Kubo N, Matsumoto S, Suwabe K, Tsukada M, Hirai M: Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa. Theor Appl Genet 2006, 114:81-91.
• [39]Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647.
• [40]Kumar S, Blaxter ML: Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010, 11:571.
• [41]Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang F, Chen X, Li Y: De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 2010, 11:726.
• [42]Fu N, Wang Q, Shen H-L: De novo assembly, gene annotation and marker development using illumina paired-end transcriptome sequences in celery (Apium graveolens L). PLoS ONE 2013, 8(2):e57686.
• [43]Wong CE, Bhalla PL, Ottenhof H, Singh MB: Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance. BMC Plant Biol 2008, 8:73.
• [44]Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanpraset J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S: Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res 2011, 18:471-482.
• [45]Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. Trends Biotechnol 2005, 23:48-55.
• [46]Morgante M, Hanafey M, Powell W: Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 2002, 30:194-200.
• [47]Gao L, Tang J, Li H, Jia J: Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 2003, 12:245-261.
• [48]Kumpatla SP, Mukhopadhyay S: Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 2005, 48:985-998.
• [49]Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R: Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 2000, 156:847-854.
• [50]Cloutier S, Niu Z, Datla R, Duguid S: Development and analysis of EST-SSRs for flax (Linum usitatissimum L). Theor Appl Genet 2009, 119:53-63.
• [51]Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X: Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biol 2011, 11:139.
• [52]Metzgar D, Bytof J, Wills C: Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 2000, 10:72-80.
• [53]Yi G, Lee JM, Lee S, Choi D, Kim B-D: Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theor Appl Genet 2006, 114:113-130.
• [54]Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S: An EST-SSR linkage Map of Raphanus sativus and comparative genomics of the brassicaceae. DNA Res 2011, 18:221-232.
• [55]He C, Poysa V, Yu K: Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor Appl Genet 2003, 106:363-373.
• [56]Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W: Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 2002, 104:399-407.
• [57]Gupta PK, Rustgi S: Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genom 2004, 4:139-162.
• [58]Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S: Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L). Theor Appl Genet 2000, 100:713-722.
• [59]Neff M, Neff J, Chory J, Pepper A: dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 1998, 14(3):387-392.
• [60]Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC: Genome redundancy and plasticity within ancient and recent brassica crop species. Biol J Linn Soc 2004, 82:665-674.
• [61]Yang T-J, Kim JS, Kwon SJ, Lim KB, Kim JA, Choi BS, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong J-H, Kim C-B, Bhak J, Bancroft I, Park B-S: Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 2006, 18:1339-1347.
• [62]Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB: A new integrated genetic linkage map of the soybean. Theor Appl Genet 2004, 109:122-128.
• [63]Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE: An integrated genetic linkage map of the soybean. Crop Sci 1999, 39:1464-1490.
• [64]Lyttle TW: Segregation distorters. Annu Rev Genet 1991, 25:511-557.
• [65]Harushima Y, Nakagahra M, Yano M, Sasaki T, Kurata N: Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 2002, 160:313-322.
• [66]Mangelsdorf PC, Jones DF: The expression of mendelian factors in the gametophyte of maize. Genetics 1926, 11:423-455.
• [67]Xu Y, Zhu L, Xiao J, Huang N, McCouch SR: Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L). Mol Gen Genet 1997, 253(5):535-545.
• [68]Faris JD, Laddomada B, Gill BS: Molecular mapping of segregation distortion loci in Aegilops tauschii. Genetics 1998, 149:319-327.
• [69]Torjek O, Witucka-Wall H, Meyer RC, von Korff M, Kusterer B, Rautengarten C, Altmann T: Segregation distortion in Arabidopsis C24/Co1-0 and Co1-0/C24 recombinant inbred line populations is due to reduced fertility caused by epistatic interaction of two loci. Theor Appl Genet 2006, 113:1551-1561.
• [70]Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA, Miedaner T, Würschum T: Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genomics 2011, 12:380.
• [71]Liu X, Guo L, You J, Liu X, He Y, Yuan J, Liu G, Feng Z: Progress of segregation distortion in genetic mapping of plants. Res J Agro 2010, 4(4):78-83.
• [72]Zhang LY, Wang SQ, Li HH, Deng QM, Zheng AP, Li SC, Li P, Li ZL, Wang JK: Effects of missing marker and segregation distortion on QTL mapping in F2 populations. Theor Appl Genet 2010, 121:1071-1082.
• [73]McDaniel SF, Willis JH, Shaw AJ: A linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus. Genetics 2007, 176:2489-2500.
• [74]Plomion C, O’Malley DM, Durel CE: Genomic analysis in maritime pine (Pinus pinaster): comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. Theor Appl Genet 1995, 90:1028-1034.
• [75]Perfectti F, Pascual L: Segregation distortion of isozyme loci in cherimoya (Annona cherimola mill). Theor Appl Genet 1996, 93(3):440-446.
• [76]Izzah NK, Lee J, Perumal S, Park JY, Ahn K, Fu D, Kim G-B, Nam Y-W, Yang T-J: Microsatellite-based analysis of genetic diversity in 91 commercial Brassica oleracea L. cultivars belonging to six varietal groups. Genet Resour Crop Evol 2013, 60:1967-1986.
• [77]Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF: A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Prot 2006, 1:2320-2325.
• [78]Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A: High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36:3420-3435.
• [79]Neff M, Turk E, Kalishman M: Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 2002, 18(12):613-615.
• [80]Van Ooijen J, Voorrips R: JoinMap 3.0, Software for the Calculation of Genetic Linkage Maps, Plant Research International. The Netherlands: Wageningen; 2001.
• [81]Kosambi D: The estimation of map distance from recombination values. Ann Hum Genet 1943, 12:172-175.
• [82]Voorrips RE: MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 2002, 93:77-78.