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.
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.
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DOI：
10.1186/1471-2164-15-396
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发表时间：
2014-05-23
期刊：
影响因子：
4.4
通讯作者：
Pental D
中科院分区：
文献类型：
--
作者：
Paritosh K;Gupta V;Yadava SK;Singh P;Pradhan AK;Pental D
芥菜（Brassica juncea，AABB）是一种含有B染色体组的异源四倍体植物。rapa（AA）和B.黑（BB）。它是南亚的一种主要油料作物，在印度冬季干旱条件下种植在大约600万至700万公顷的土地上。B。Juncea有两个明确的基因库--印度和东欧。这两个基因库之间的杂种在产量上具有杂种优势。大量的质量和数量性状需要从一个基因库渗入到另一个基因库中。本研究探讨了RNA-seq生成的重叠群中SNP的可用性，以及它们在一般作图、选定区域的精细作图和B上基因块的比较排列中的用途。芥菜A和B基因组。从B的两个系中分离RNA。juncea - Varuna（印度型）和Heera（东欧型）-使用Illumina配对末端测序技术测序，并使用Velvet de novo程序组装。分两步鉴定A和B基因组特异性重叠群。首先，通过将重叠群与B比对。rapa蛋白数据库（可在布拉德获得），第二种是通过比较与B在核苷酸水平上的同一性百分比。rapa CDS和B.黑质转录组。在Varuna和Heera组装的部分基因模型中记录了135，693个SNP，其中85，473个在A基因组中，50，236个在B中。使用KASpar技术，将999个标记添加到早期基于内含子多态性标记的B图谱中。juncea Varuna x Heera DH种群。在B基因组中发现了许多新的基因块。许多SNP标记覆盖了A和B基因组的单拷贝同源物，这些标记用于鉴定两个基因组之间的同源同源块。A和B基因组的块结构的比较揭示了基因块关联和块片段化模式的广泛差异。足够的SNP标记可用于两个不同B的品系之间的杂交的一般和特定区域精细定位。芥菜基因库。A和B基因组之间的基因块排列和块断裂模式的比较支持这两个基因组从独立的六倍体事件进化的假设。本文的在线版本（doi：10.1186/1471-2164-15-396）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi: 10.1186/1471-2164-15-396) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
Delourme R;Falentin C;Fomeju BF;Boillot M;Lassalle G;André 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
通讯作者：
Pauquet J
DOI：
10.1093/dnares/dsr027
发表时间：
2011-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Li F;Hasegawa Y;Saito M;Shirasawa S;Fukushima A;Ito T;Fujii H;Kishitani S;Kitashiba H;Nishio T
通讯作者：
Nishio T
影响因子：
1.9
作者：
Burton, WA;Ripley, VL;Salisbury, PA
通讯作者：
Salisbury, PA
影响因子：
3.4
作者：
Arias, Tatiana;Pires, J. Chris
通讯作者：
Pires, J. Chris
影响因子：
5.4
作者：
Jagannath, Arun;Sodhi, Yashpal Singh;Pental, Deepak
通讯作者：
Pental, Deepak