Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

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• 作者：Jun Zou ; Dandan Hu ; Peifa Liu ; Harsh Raman ; Zhongsong Liu ; Xianjun Liu…
• 关键词：Brassica juncea ; Dense genetic map ; Subgenome ; Genome organization ; Co ; linearity ; Divergence
• 刊名：BMC Genomics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：1
• 全文大小：1,889 KB
• 参考文献：1.Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, et al. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics. 2014;15:708.PubMed PubMedCentral CrossRef
  2.Delourme R, Falentin C, Fomeju BF, Boillot M, Lassalle G, Andre I, et al. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics. 2013;14:120.PubMed PubMedCentral CrossRef
  3.Castillo A, Ramirez MC, Martin AC, Kilian A, Martin A, Atienza SG. High-throughput genotyping of wheat-barley amphiploids utilising diversity array technology (DArT). BMC Plant Biol. 2013;13:87.PubMed PubMedCentral CrossRef
  4.Bus A, Hecht J, Huettel B, Reinhardt R, Stich B. High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics. 2012;13:281.PubMed PubMedCentral CrossRef
  5.Sharma A, Li X, Lim YP. Comparative genomics of Brassicaceae crops. Breed Sci. 2014;64(1):3–13.PubMed PubMedCentral CrossRef
  6.Parkin I. Chasing Ghosts: Comparative Mapping in the Brassicaceae. In: Bancroft I, Schmidt R, editors. Genetics and genomics of the Brassicaceae. New York: Springer; 2011. p. 153–70.CrossRef
  7.Lagercrantz U, Putterill J, Coupland G, Lydiate D. Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J. 1996;9(1):13–20.PubMed CrossRef
  8.Parkin IAP, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, et al. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics. 2005;171(2):765–81.PubMed PubMedCentral CrossRef
  9.Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, et al. 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.PubMed PubMedCentral CrossRef
  10.Guo S, Zou J, Li R, Long Y, Chen S, Meng J. A genetic linkage map of Brassica carinata constructed with a doubled haploid population. Theor Appl Genet. 2012;125(6):1113–24.PubMed CrossRef
  11.Cheung WY, Friesen L, Rakow GFW, Séguin-Swartz G, Landry BS. A RFLP-based linkage map of mustard [Brassica juncea (L.) Czern. and Coss.]. Theor Appl Genet. 1997;94:841–51.CrossRef
  12.Lionneton E, Ravera S, Sanchez L, Aubert G, Delourme R, Ochatt S. Development of an AFLP-based linkage map and localization of QTLs for seed fatty acid content in condiment mustard (Brassica juncea). Genome. 2002;45:1203–15.PubMed CrossRef
  13.Pradhan AK, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D. A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor Appl Genet. 2003;106:607–14.PubMed
  14.Liu L, Qu C, Wittkop B, Yi B, Xiao Y, He Y, et al. A High-Density SNP map for accurate mapping of seed fibre QTL in Brassica napus L. PLoS One. 2013;8(12):e83052. doi:10.1371/journal.pone.0083052.PubMed PubMedCentral CrossRef
  15.Zou J, Raman H, Guo S, Hu D, Wei Z, Luo Z, et al. Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata. Theor Appl Genet. 2014;127(7):1593–605.PubMed CrossRef
  16.Paritosh K, Gupta V, Yadava SK, Singh P, Pradhan AK, Pental D. 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. 2014;15:396.PubMed PubMedCentral CrossRef
  17.Cai GQ, Yang QY, Yi B, Fan CC, Zhang CY, Edwards D, et al. A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics. 2015;16:409.PubMed PubMedCentral CrossRef
  18.Sharma S, Padmaja KL, Gupta V, Paritosh K, Pradhan AK, Pental D. Two plastid DNA lineages-Rapa/Oleracea and Nigra-within the Tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: Evidence from divergence times of the plastid genomes and R-Block eenes of the A and B Genomes of Brassica juncea. Plos One. 2014;9(4):e93260.PubMed PubMedCentral CrossRef
  19.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):535–42.PubMed CrossRef
  20.Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell. 2006;18(6):1348–59.PubMed PubMedCentral CrossRef
  21.Lysak MA, Koch MA, Pecinka A, Schubert I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 2005;15(4):516–25.PubMed PubMedCentral CrossRef
  22.Li X, Ramchiary N, Dhandapani V, Choi SR, Hur Y, Nou I-S, et al. Quantitative trait loci mapping in Brassica rapa revealed the structural and functional conservation of genetic loci governing morphological and yield component traits in the A, B, and C subgenomes of Brassica species. DNA Res. 2013;20(1):1–16.PubMed PubMedCentral CrossRef
  23.Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345(6199):950–3.PubMed CrossRef
  24.Jiang CC, Ramchiary N, Ma YB, Jin MN, Feng J, Li RY, et al. Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa. Theor Appl Genet. 2011;123(4):927–41.PubMed CrossRef
  25.Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn JBot. 1935;7:389–452.
  26.Zou J, Zhu J, Huang S, Tian E, Xiao Y, Fu D, et al. Broadening the avenue of intersubgenomic heterosis in oilseed Brassica. Theor Appl Genet. 2010;120(2):283–90.PubMed CrossRef
  27.Zou J, Fu D, Gong H, Qian W, Xia W, Pires JC, et al. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. Plant J. 2011;68(2):212–24.PubMed CrossRef
  28.Pires JC, Gaeta RT. Structural and Functional Evolution of Resynthesized Polyploids. In: Bancroft I, Schmidt R, editors. Genetics and genomics of the Brassicaceae. New York: Springer; 2011. p. 323–45.
  29.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):1541–54.PubMed PubMedCentral CrossRef
  30.Mei J, Li Q, Qian L, Fu Y, Li J, Frauen M, et al. Genetic investigation of the origination of allopolyploid with virtually synthesized lines: Application to the C subgenome of Brassica napus. Heredity. 2011;106(6):955–61.PubMed PubMedCentral CrossRef
  31.Navabi ZK, Parkin IA, Pires JC, Xiong Z, Thiagarajah MR, Good AG, et al. Introgression of B-genome chromosomes in a doubled haploid population of Brassica napus x B. carinata. Genome. 2010;53(8):619–29.PubMed CrossRef
  32.Chen S, Nelson MN, Chevre A-M, Jenczewski E, Li Z, Mason AS, et al. Trigenomic Bridges for Brassica Improvement. Crit Rev Plant Sci. 2011;30(6):524–47.CrossRef
  33.Chèvre AM, Barret P, Eber F, Dupuy P, Brun H, Tanguy X, et al. Selection of stable Brassica napus-B. juncea recombinant lines resistant to blackleg (Leptosphaeria maculans). 1. Identification of molecular markers, chromosomal and genomic origin of the introgression. Theor Appl Genet. 1997;95(7):1104–11.CrossRef
  34.Chen S, Wan Z, Nelson MN, Chauhan JS, Redden R, Burton WA, et al. Evidence from genome-wide simple sequence repeat markers for a polyphyletic origin and secondary centers of genetic diversity of Brassica juncea in China and India. J Hered. 2013;104:416–27.PubMed CrossRef
  35.Sharma R, Aggarwal RAK, Kumar R, Mohapatra T, Sharma RP. Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea). Genome. 2002;45:467–72.PubMed CrossRef
  36.Christianson JA, Rimmer SR, Good AG, Lydiate DJ. Mapping genes for resistance to Leptosphaeria maculans in Brassica juncea. Genome. 2006;49:30–41.PubMed CrossRef
  37.Liu XJ, Yuan MZ, Guan CY, Chen SY, Liu SY, Liu ZS. Inheritance, mapping, and origin of yellow-seeded trait in Brassica juncea. Acta Agron Sin. 2009;35:839–47.CrossRef
  38.Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, et al. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011;43(10):1035–U1157.PubMed CrossRef
  39.Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, et al. Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. Plos One. 2014;9(7):13.CrossRef
  40.Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–59.PubMed PubMedCentral
  41.Jansen J, de Jong AG, van Ooijen JW. Constructing dense genetic linkage maps. Theor Appl Genet. 2001;102(6–7):1113–22.CrossRef
  42.Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, et al. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol. 2011;29(8):762–U128.PubMed CrossRef
  43.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):1217–28.PubMed PubMedCentral
  44.Beilstein MA, Al-Shehbaz IA, Kellogg EA. Brassicaceae phylogeny and trichome evolution. Am J Bot. 2006;93(4):607–19.PubMed CrossRef
  45.Warwick SI, Sauder CA, Mayer MS, Al-Shenbaz IA. Phylogenetic relationships in the tribes Schizopetaleae and Thelypodieae (Brassicaceae) based on nuclear ribosomal ITS region and plastid ndhF DNA sequences. Botany-Botanique. 2009;87(10):961–85.CrossRef
  46.Navabi ZK, Huebert T, Sharpe AG, O’Neill CM, Bancroft I, Parkin IAP. 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.PubMed PubMedCentral CrossRef
  47.Gupta MGS, Kumar H, Kumar N, Banga SS. Population structure and breeding value of a new type of Brassica juncea created by combining A and B genomes from related allotetraploids. Theor Appl Genet. 2015;128(2):221–34.PubMed CrossRef
  48.Tian ET, Jiang YF, Chen LL, Zou J, Liu F, Meng JL. Synthesis of a Brassica trigenomic allohexaploid (B. carinata x B. rapa) de novo and its stability in subsequent generations. Theor Appl Genet. 2010;121(8):1431–40.PubMed CrossRef
  49.Yu F, Lydiate DJ, Gugel RK, Sharpe AG, Rimmer SR. Introgression of Brassica rapa subsp. sylvestris blackleg resistance into B. napus. Mol Breeding. 2012;30(3):1495–506.CrossRef
  50.Girke A, Schierholt A, Becker HC. Extending the rapeseed genepool with resynthesized Brassica napus L. I: Genetic diversity. Genet Resour Crop Ev. 2012;59(7):1441–7.CrossRef
  51.Girke A, Schierholt A, Becker HC. Extending the rapeseed gene pool with resynthesized Brassica napus II: Heterosis. Theor Appl Genet. 2012;124(6):1017–26.PubMed PubMedCentral CrossRef
  52.Bennett RA, Seguin-Swartz G, Rahman H. Broadening genetic diversity in canola using the C-genome species Brassica oleracea L. Crop Sci. 2012;52(5):2030–9.CrossRef
  53.Van Ooijen JW: JoinMap 4.0, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, Netherlands. 2006.
  54.Nei MTF, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol. 1983;19(2):153–70.PubMed CrossRef
  55.Liu KJ, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005;21(9):2128–9.PubMed CrossRef
  56.Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24(8):1596–9.PubMed CrossRef
  57.Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14(8):2611–20.PubMed CrossRef
  
• 作者单位：Jun Zou (1)
  Dandan Hu (1)
  Peifa Liu (1)
  Harsh Raman (2)
  Zhongsong Liu (3)
  Xianjun Liu (3)
  Isobel A. P. Parkin (4)
  Boulos Chalhoub (5)
  Jinling Meng (1)
  
  1. National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
  2. Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
  3. Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China
  4. Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
  5. Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d’Evry Val d’Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex, France
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, ArAr; B. nigra, BniBni; B. oleracea, CoCo) and the derived allotetraploid species (i.e.: B. juncea, AjAjBjBj; B. napus, AnAnCnCn; B. carinata, BcBcCcCc). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).