RNA-seq based SNPs for mapping in Brassica juncea (AABB): synteny analysis between the two constituent genomes A (from B. rapa) and B (from B. nigra) shows highly divergent gene block arrangement and unique block fragmentation patterns

BMC Genomics

Deepak Pental¹  Akshay K Pradhan¹  Priyansha Singh¹  Satish K Yadava²  Vibha Gupta²  Kumar Paritosh² 

[1] Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India;Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India

关键词: Evolution;    Comparative genomics;    Linkage map;    SNP;    RNA-seq;    Brassica species;   

Others  :  1217201
DOI  :  10.1186/1471-2164-15-396

 received in 2013-12-13, accepted in 2014-05-20,  发布年份 2014

【 摘 要 】

Background

Brassica juncea (AABB) is an allotetraploid species containing genomes of B. rapa (AA) and B. nigra (BB). It is a major oilseed crop in South Asia, and grown on approximately 6–7 million hectares of land in India during the winter season under dryland conditions. B. juncea has two well defined gene pools – Indian and east European. Hybrids between the two gene pools are heterotic for yield. A large number of qualitative and quantitative traits need to be introgressed from one gene pool into the other. This study explores the availability of SNPs in RNA-seq generated contigs, and their use for general mapping, fine mapping of selected regions, and comparative arrangement of gene blocks on B. juncea A and B genomes.

Results

RNA isolated from two lines of B. juncea – Varuna (Indian type) and Heera (east European type) – was sequenced using Illumina paired end sequencing technology, and assembled using the Velvet de novo programme. A and B genome specific contigs were identified in two steps. First, by aligning contigs against the B. rapa protein database (available at BRAD), and second by comparing percentage identity at the nucleotide level with B. rapa CDS and B. nigra transcriptome. 135,693 SNPs were recorded in the assembled partial gene models of Varuna and Heera, 85,473 in the A genome and 50,236 in the B. Using KASpar technology, 999 markers were added to an earlier intron polymorphism marker based map of a B. juncea Varuna x Heera DH population. Many new gene blocks were identified in the B genome. A number of SNP markers covered single copy homoeologues of the A and B genomes, and these were used to identify homoeologous blocks between the two genomes. Comparison of the block architecture of A and B genomes revealed extensive differences in gene block associations and block fragmentation patterns.

Conclusions

Sufficient SNP markers are available for general and specific -region fine mapping of crosses between lines of two diverse B. juncea gene pools. Comparative gene block arrangement and block fragmentation patterns between A and B genomes support the hypothesis that the two genomes evolved from independent hexaploidy events.

【 授权许可】

   
2014 Paritosh et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]UN: Genome analysis of Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Japan J Bot 1935, 7:389-452.
• [2]Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML: Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 2011, 12(7):499-510.
• [3]Kaur S, Francki MG, Forster JW: Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species. Plant Biotechnol J 2012, 10(2):125-138.
• [4]Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S: SNP markers and their impact on plant breeding. Int J Plant Genomics 2012, 2012:728398.
• [5]Edward D, Batley J, Parkin IA, Kole C: Genetics, Genomics and Breeding of Oilseed Brassicas. Boca Raton, FL, USA: CRC Press; 2012.
• [6]Ramchiary N, Lim YP: Genetics of Brassica rapa L. In Genetics and Genomics of the Brassicaceae. Volume Volume 9. Edited by Schmidt R, Bancroft I. New York: Springer; 2011::215-260.
• [7]Quiros CF, Fernham MW: The Genetics of Brassica oleracea. In Genetics and Genomics of the Brassicaceae. Volume Volume 9. Edited by Schmidt R, Bancroft I. New York: Springer; 2011::261-290.
• [8]Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, The Brassica rapa Genome Sequencing Project Consortium, et al.: The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011, 43(10):1035-1039.
• [9]Brassica oleracea database [http://ocri-genomics.org/bolbase webcite]
• [10]Pradhan AK, Pental D: Genetics of Brassica juncea L. In Genetics and Genomics of the Brassicaceae. Volume Volume 9. Edited by Schmidt R, Bancroft I. New York: Springer; 2011::323-346.
• [11]Chauhan JS, Singh KH, Singh VV, Satyanshu K: Hundred years of rapeseed-mustard breeding in India: accomplishments and future strategies. Indian J Agr Sci 2011, 81(12):1093-1109.
• [12]Pradhan AK, Sodhi YS, Mukhopadhyay A, Pental D: Heterosis breeding in Indian mustard (Brassica juncea L. Czern & Cross): analysis of component characters contributing to heterosis for yield. Euphytica 1993, 69:219-229.
• [13]Srivastava A, Gupta V, Pental D, Pradhan AK: AFLP-based genetic diversity assessment amongst agronomically important natural and some newly synthesized lines of Brassica juncea. Theor Appl Genet 2001, 102:193-199.
• [14]Burton WA, Ripley VL, Potts DA, Salisbury PA: Assessment of genetic diversity in selected breeding lines and cultivars of canola quality Brassica juncea and their implications for canola breeding. Euphytica 2004, 136:181-192.
• [15]Ramchiary N, Padmaja KL, Sharma S, Gupta V, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK: Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas. Theor Appl Genet 2007, 115(6):807-817.
• [16]Ramchiary N, Bisht NC, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK: QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: importance of recurrent selection backcross scheme for the identification of ‘true’ QTL. Theor Appl Genet 2007, 116(1):77-85.
• [17]Bisht NC, Gupta V, Ramchiary N, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK: Fine mapping of loci involved with glucosinolate biosynthesis in oilseed mustard (Brassica juncea) using genomic information from allied species. Theor Appl Genet 2009, 118(3):413-421.
• [18]Panjabi-Massand P, Yadava SK, Sharma P, Kaur A, Kumar A, Arumugam N, Sodhi YS, Mukhopadhyay A, Gupta V, Pradhan AK, Pental D: Molecular mapping reveals two independent loci conferring resistance to Albugo candida in the east European germplasm of oilseed mustard Brassica juncea. Theor Appl Genet 2010, 121(1):137-145.
• [19]Padmaja LK, Agarwal P, Gupta V, Mukhopadhyay A, Sodhi YS, Pental D, Pradhan AK: Natural mutations in two homoeologous TT8 genes control yellow seed coat trait in allotetraploid Brassica juncea (AABB). Theor Appl Genet 2014, 127(2):339-347.
• [20]Jagannath A, Sodhi YS, Gupta V, Mukhopadhyay A, Arumugam N, Singh I, Rohatgi S, Burma PK, Pradhan AK, Pental D: Eliminating expression of erucic acid-encoding loci allows the identification of “hidden” QTL contributing to oil quality fractions and oil content in Brassica juncea (Indian mustard). Theor Appl Genet 2011, 122(6):1091-1103.
• [21]Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK: Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene. Theor Appl Genet 2004, 108(4):743-749.
• [22]Paritosh K, Yadava SK, Gupta V, Panjabi-Massand P, Sodhi YS, Pradhan AK, Pental D: RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping. BMC Genomics 2013, 14(1):463. BioMed Central Full Text
• [23]Lysak MA, Koch MA: Phylogeny, genome and karyotype evolution of crucifers (Brassicaceae). In Genetics and Genomics of the Brassicaceae. Volume Volume 9. Edited by Schmidt R, Bancroft I. New York: Springer; 2011::1-32.
• [24]Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC: Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 2012, 190(4):1563-1574.
• [25]Cheng F, Mandakova T, Wu J, Xie Q, Lysak MA, Wang X: Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 2013, 25(5):1541-1554.
• [26]Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X: BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 2011, 11:136. BioMed Central Full Text
• [27]Brassica database [http://brassicadb.org/brad webcite]
• [28]Schranz ME, Lysak MA, Mitchell-Olds T: The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 2006, 11(11):535-542.
• [29]Parkin IA, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ: Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 2005, 171(2):765-781.
• [30]Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I: Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006, 18(6):1348-1359.
• [31]Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Pires JC, Paterson AH, Town C, Bancroft I: Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell 2009, 21(7):1912-1928.
• [32]Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D: Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics 2008, 9:113. BioMed Central Full Text
• [33]Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829.
• [34]Navabi ZK, Huebert T, Sharpe AG, O’Neill CM, Bancroft I, Parkin IA: Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea. BMC Genomics 2013, 14:250. BioMed Central Full Text
• [35]Delcher AL, Salzberg SL, Phillippy AM: Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics 2003, 10:10-13.
• [36]KBiosciences Ltd [http://www.kbioscience.co.uk webcite]
• [37]Lagercrantz U: Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 1998, 150(3):1217-1228.
• [38]Ziolkowski PA, Kaczmarek M, Babula-Skowronska D, Sadowski J: Brassica genome evolution: dynamics and plasticity. In Genetics, Genomics and Breeding of Oilseed Brassicas. Edited by Edwards D, Batley J, Parkin IA, Kole C. Boca Raton, FL, USA: CRC Press; 2012:14-46.
• [39]Liu Z, Adamczyk K, Manzanares-Dauleux M, Eber F, Lucas MO, Delourme R, Chevre AM, Jenczewski E: Mapping PrBn and other quantitative trait loci responsible for the control of homeologous chromosome pairing in oilseed rape (Brassica napus L.) haploids. Genetics 2006, 174(3):1583-1596.
• [40]Cifuentes M, Eber F, Lucas MO, Lode M, Chevre AM, Jenczewski E: Repeated polyploidy drove different levels of crossover suppression between homoeologous chromosomes in Brassica napus allohaploids. Plant Cell 2010, 22(7):2265-2276.
• [41]Lysak MA, Koch MA, Pecinka A, Schubert I: Chromosome triplication found across the tribe Brassiceae. Genome Res 2005, 15(4):516-525.
• [42]Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T: Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 2011, 18(5):401-411.
• [43]Nelson MN, Lydiate DJ: New evidence from Sinapis alba L. for ancestral triplication in a crucifer genome. Genome 2006, 49(3):230-238.
• [44]Javidfar F, Cheng B: Construction of a genetic linkage map and QTL analysis of erucic acid content and glucosinolate components in yellow mustard (Sinapis alba L.). BMC Plant Biol 2013, 13:142. BioMed Central Full Text
• [45]Yang YW, Lai KN, Tai PY, Li WH: Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol 1999, 48(5):597-604.
• [46]Cho K, O’Neill CM, Kwon SJ, Yang TJ, Smooker AM, Fraser F, Bancroft I: Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci. Plant J 2010, 61(4):591-599.
• [47]Warwick SI, Black LD: Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae) – chloroplast genome and cytodeme congruence. Theor Appl Genet 1991, 82(1):81-92.
• [48]Pradhan AK, Prakash S, Mukhopadhyay A, Pental D: Phylogeny of Brassica and allied genera based on variation in chloroplast and mitochondrial DNA patterns: molecular and taxonomic classifications are incongruous. Theor Appl Genet 1992, 85(2–3):331-340.
• [49]Warwick SI, Sauder CA: Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences. Can J Bot 2005, 83:467-483.
• [50]Hall JC, Tisdale TE, Donohue K, Wheeler A, Al-Yahya MA, Kramer EM: Convergent evolution of a complex fruit structure in the tribe Brassiceae (Brassicaceae). Am J Bot 2011, 98(12):1989-2003.
• [51]Arias T, Pires C: A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications. Taxon 2012, 61(5):980-988.
• [52]Delourme R, Falentin C, Fomeju BF, Boillot M, Lassalle G, Andre I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon JP, Ribière N, Trotoux G, Blanchard P, Rivière N, Martinant JP, Pauquet J: High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics 2013, 14:120. BioMed Central Full Text
• [53]Sharma S, Padmaja KL, Gupta V, Paritosh K, Pradhan AK, Pental D: Two plastid DNA lineages within an otherwise monophyletic tribe Brassiceae (family Brassicaceae) can be best explained by reciprocal crosses at the time of hexaploidy: evidence from nucleotide substitution rates in the plastid genomes and R block genes of the A and B genomes of Brassica juncea (AABB). PLoS One 2014, 9(4):e93260. doi:10.1371/journal.pone.0093260
• [54]Fastx-toolkit [http://hannonlab.cshl.edu/fastx_toolkit webcite]
• [55]van Ooijen JW: Join Map® 4 - Software for the Calculation of Genetic Linkage Maps in Experimental Populations. Wageningen, The Netherlands: Kyazma BV; 2006.
• [56]Kosambi DD: The estimation of the map distance from recombination values. Ann Eugen 1944, 12:172-175.
• [57]Voorrips RE: Map Chart: software for the graphical presentation of linkage maps and QTLs. J Hered 2002, 93(1):77-78.