Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries.
Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries.
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DOI：
10.3389/fpls.2020.598039
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发表时间：
2020
影响因子：
5.6
通讯作者：
Heslop-Harrison JP
中科院分区：
文献类型：
--
作者：
Agrawal N;Gupta M;Banga SS;Heslop-Harrison JP
作物甘蓝包括三个二倍体[油菜(AA；2n=2x=16)，黑甘蓝(Bb；2n=2x=18)和甘蓝(CC；2n=2x=20)]和三个衍生的异源四倍体物种。甘蓝属植物的染色体很小，形态相似，很难区分。我们的目标是开发一种基于基因组序列的细胞遗传学工具包，用于可重复地鉴定油菜染色体及其结构变异。利用生物信息学流水线从油菜全基因组中提取无重复序列。随后使用鉴定的序列来开发包含27、100、11,084、9,291和16,312个寡核苷酸的四个c.47-mer寡核苷酸文库。我们从18个已鉴定的位点(500-1,000 kb)中剔除重复序列后选择了这些寡核苷酸，其中1,997-5,420个寡核苷酸位于白菜的每个位点。对于一组探针，描述了一种扩增或永生化文库的新方法。寡核苷酸探针为所有属于A、B、C和R(萝卜)基因组的染色体产生了特异和可重复的原位杂交图谱。这些探针能够识别基因组之间的结构变化，包括易位、融合和缺失。此外，这些探针还能够鉴定出白菜和萝卜品种之间的结构易位。总体而言，比较染色体图谱有助于理解染色体结构变化在十字花科基因组进化和物种形成中的作用。这些探针还可以用来识别非整倍体中的染色体，如用于基因定位的附加系，以及在杂交和育种计划中跟踪染色体的转移。
Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500–1,000 kb) with 1,997–5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.
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影响因子：
1.6
作者：
Idziak D;Betekhtin A;Wolny E;Lesniewska K;Wright J;Febrer M;Bevan MW;Jenkins G;Hasterok R
通讯作者：
Hasterok R
影响因子：
5.4
作者：
Gupta, Mehak;Atri, Chhaya;Banga, Surinder Singh
通讯作者：
Banga, Surinder Singh
影响因子：
1.6
作者：
Danilova, Tatiana V.;Friebe, Bernd;Gill, Bikram S.
通讯作者：
Gill, Bikram S.
影响因子：
1.6
作者：
Huang, Yongji;Chen, Hong;Wang, Kai
通讯作者：
Wang, Kai
染色体涂色及其在栽培稻和野生稻中的应用
影响因子：
5.3
作者：
Hou L;Xu M;Zhang T;Xu Z;Wang W;Zhang J;Yu M;Ji W;Zhu C;Gong Z;Gu M;Jiang J;Yu H
通讯作者：
Yu H