Barabaschi Delfina, Magni Federica, Volante Andrea, Gadaleta Agata, Šimková Hana, Scalabrin Simone, Prazzoli Maria Lucia, Bagnaresi Paolo, Lacrima Katia, Michelotti Vania, Desiderio Francesca, Orrù Luigi, Mazzamurro Valentina, Fricano Agostino, Mastrangelo AnnaMaria, Tononi Paola, Vitulo Nicola, Jurman Irena, Frenkel Zeev, Cattonaro Federica, Morgante Michele, Blanco Antonio, Doležel Jaroslav, Delledonne Massimo, Stanca Antonio M, Cattivelli Luigi, Valè Giampiero
Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017.
Institute of Applied Genomics, Udine, I-33100.
Plant Genome. 2015 Nov;8(3):eplantgenome2015.03.0011. doi: 10.3835/plantgenome2015.03.0011.
The huge size, redundancy, and highly repetitive nature of the bread wheat [Triticum aestivum (L.)] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC). A total of 95,812 bacterial artificial chromosome (BAC) clones of short-arm chromosome 5A (5AS) and long-arm chromosome 5A (5AL) arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) tools. Combined anchoring approaches based on polymerase chain reaction (PCR) marker screening, microarray, and sequence homology searches applied to several genomic tools (i.e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs), genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. In the genome of grasses, Brachypodium [Brachypodium distachyon (L.) Beauv.], rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects.
面包小麦（Triticum aestivum (L.)）基因组的巨大规模、冗余性和高度重复性使其成为最难测序的物种之一。为克服这些限制，在国际小麦基因组测序联盟（IWGSC）的框架内，建立了一种基于分离单个染色体或染色体臂并随后构建物理图谱的策略。对短臂染色体5A（5AS）和长臂染色体5A（5AL）臂特异性细菌人工染色体（BAC）文库的总共95,812个BAC克隆进行了指纹识别，并通过基于指纹连续克隆（FPC）和线性拓扑连续克隆（LTC）工具的互补分析方法组装成重叠群。基于聚合酶链反应（PCR）标记筛选、微阵列和序列同源性搜索的组合锚定方法应用于多种基因组工具（即遗传图谱、缺失 bins 图谱、邻接图谱、BAC 末端序列（BESs）、基因组拉链和染色体调查序列），从而构建了高质量的物理图谱，5AS的锚定物理覆盖率为75%，5AL的为53%，且大部分重叠群（分别为64%和48%）沿染色体有序排列。在禾本科植物的基因组中，由于进化过程中的易位和倒位，小麦染色体5A上基因的短柄草（Brachypodium distachyon (L.) Beauv.）、水稻（Oryza sativa L.）和高粱（Sorghum bicolor (L.) Moench）同源基因被分离到不同染色体上的同线区域。所呈现的物理图谱是精细遗传定位和基于图谱克隆农艺相关性状的重要资源，也是5A测序项目的参考依据。
