Characterization of soybean genome based on synteny analysis with Lotus japonicus
Characterization of soybean genome based on synteny analysis with Lotus japonicus
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DOI：
10.1270/jsbbs.58.157
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发表时间：
2008-06
期刊：
影响因子：
2.4
通讯作者：
Y. Tsubokura;Ryutaku Onda;Shusei Sato;Zhengjun Xia;M. Hayashi;Yukie Fukushima;S. Tabata;K. Harada
中科院分区：
文献类型：
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作者：
Y. Tsubokura;Ryutaku Onda;Shusei Sato;Zhengjun Xia;M. Hayashi;Yukie Fukushima;S. Tabata;K. Harada
为了将模式豆科植物百脉根的基因组信息应用于大豆研究，以百脉根基因组为参照，分析了大豆基因组的特征。他们被调查了。大豆与L.通过RFLP方法将相同的cDNA克隆定位在两个物种的图谱上，并通过鉴定L.定位在大豆图谱上的cDNA标记的分子标记图谱。在L的几个连锁群之间观察到相对大的同线区。大豆和大豆。大豆连锁群的主要部分由与L.染色体组。从大豆近缘同源物和直系同源物的分布可以看出，在不同的大豆连锁群上存在着许多同源区域。研究了大豆与L.同时，对3个大豆BAC克隆进行了GmNFR 1a、GmNFR 1b和Nts 1基因定位，结果表明，GmNFR 1a、GmNFR 1b和Nts 1基因分别定位在D1 b、B2和H1 re 3连锁群的大连锁区。我们发现这些BAC克隆与L. - 是的L.该方法可用于大豆DNA标记的开发、图位克隆和基因组测序的组装过程。大豆（L）梅里尔，百脉根（Regel）Larsen，大同线性，微同线性，同源异型区，基因组重复，简介豆科是豆科植物的第三大家族，被子植物包括约20000种豆科植物，蝶形花亚科包括农业上重要的物种如大豆、豌豆和菜豆，以及模式豆科植物，此外，豆科植物还能通过与根瘤菌的共生感染固氮，并具有种子蛋白质含量高的特点。豆科植物的基因组学研究有助于鉴定农业上有用的基因，进行高效育种和积累学术知识.与豆科植物M.蒺藜它显示了作为模型植物的适当特征（Handberg和Stougaard 1992），包括二倍体、自交能育、小基因组大小（432 Mb，Pedrosa等人，2002年，442 Mb，Ito等人，2000年，494 Mb，川崎和Murakami，2000年），生命周期短（约3个月），染色体数目少（n= 6），农杆菌转化率高。这些信息包括TAC/BAC克隆的序列和位置信息（http：//www.kazusa.or.jp/lotus/index.html）、EST文库（http：//www.kazusa.or.jp/en/plant/lotus/EST/index.html）以及叶绿体和共生根瘤菌Mesorhizobium loti的全序列数据（http：//www.kazusa.or.jp/rhizobase/Mesorhizobium/index.html）。除了TAC/BAC克隆的连锁图（http：//www.kazusa.or.jp/lotus）外，还构建了L.还利用AFLP、SSR和dCAPS标记构建了日本大豆（Hayashi et al. 2001）。大豆是世界上最重要的豆科作物。大豆的基因组大小估计为1.12Gb（Arumunganathan和Earle 1991），大约是L. - 是的据证实，大豆基因组是二倍体祖先（n = 11），经历非整倍体损失（n = 10）和亚二倍体多倍体化的产物（雷基1980）。许多研究者估计了两轮基因组复制或杂交和重排的发生（Shoemaker et al.1996，Shoemaker et al.2002，Blanc and Wolfe 2004，Schlutter et al.2004）。和M. truncatula提供了一个独特的
To apply genomic information of the model legume Lotus japonicus to soybean, the characteristics of thesoybean genome in reference to the genome of L. japonicus were investigated. Macrosynteny between soy-bean and L. japonicus was analyzed by mapping the same cDNA clones on the maps of both species by theRFLP method, and by identifying the positions of orthologs on the L. japonicus map for cDNA markers lo-cated on the soybean map. Relatively large synteny blocks were observed between a few linkage groups ofL. japonicus and soybean. The major parts of the soybean linkage groups consisted of mosaics of smallersegments syntenic with the L. japonicus genome. The presence of many homoeologous regions on differentsoybean linkage groups was suggested from the distribution of paralogs and orthologs. To investigate themicrosynteny between soybean and L. japonicus, three soybean BAC clones were selected for the GmNFR1a,GmNFR1b and Nts1 genes mapped on the macrosyntenic regions of the linkage groups D1b, B2 and H, re-spectively. We revealed a significantly high level of collinearity between these BAC clones and correspond-ing homologous genomic regions of L. japonicus. The information of L. japonicus could be used for thedevelopment of DNA markers, map-based cloning and assembling process of genome sequencing in soybean.Key Words: Glycine max (L) Merrill, Lotus japonicus (Regel) Larsen, macrosynteny, microsynteny,homoeologous region, genome duplication, paralog.IntroductionThe Fabaceae family is the third largest family of an-giosperm plants including around 20000 species of legumes.The subfamily Papilionoideae incl udes agriculturally impor-tant species such as soybean, pea and common bean, andmodel legumes, Lotus japonicus and Medicago truncatula.Additionally, legumes are able to fix nitrogen through sym-biotic infection with rhizobium bacteria and are character-istized by a high protein conten t in their seeds. The genomicsof legumes enables to identify agriculturally useful genesfor efficient breeding as well as accumulation of academicknowledge.L. japonicus is a model plant for the genomics of thefamily Fabaceae, as well as M. truncatula. It displays appro-priate features as a model plant (Handberg and Stougaard1992), including diploidy, self-fertility, small genome size(432 Mb, Pedrosa et al. 2002, 442 Mb, Ito et al. 2000, 494Mb, Kawasaki and Murakami 2000), short life cycle (ap-proximately 3 months), small number of chromosomes ( n= 6)and high transformability with Agrobacterium tumefaciense.The genome resources of L. japonicus, such as thesequence and positional information of TAC/BAC clones(http://www.kazusa.or.jp/lotus/index.html), EST libraries(http://www.kazusa.or.jp/en/plant/lotus/EST/index.html), andthe complete sequence data of chloroplast and symbioticrhizobium bacteria Mesorhizobium loti (http://www.kazusa.or.jp/rhizobase/Mesorhizobium/index.html) has beenexploited. In addition to the linkage map of TAC/BACclones (http://www.kazusa.or.jp/lotus), another linkage mapof L. japonicus was also constructed using AFLP, SSR anddCAPS markers (Hayashi et al. 2001).Soybean is the most important leguminous crop in theworld. The genome size of soybean is estimated at 1.12 Gb(Arumunganathan and Earle 1991), a value approximately2.5 times larger than that of L. japonicus. It was suggestedthat the soybean genome is the product of a diploid ancestor(n = 11), whichunderwent aneuploid loss (n = 10), and sub-sequent polyploidization (Lackey 1980). The occurrence oftwo rounds of genome duplications orhybridizations andrearrangements was estimated by many researchers(Shoemaker et al. 1996, Shoemaker et al. 2002, Blanc andWolfe 2004, Schlueter et al. 2004).The rapid accumulation of genome sequence informa-tion for L. japonicus and M. truncatula provides a unique