Varshney Rajeev K, Mir Reyazul Rouf, Bhatia Sabhyata, Thudi Mahendar, Hu Yuqin, Azam Sarwar, Zhang Yong, Jaganathan Deepa, You Frank M, Gao Jinliang, Riera-Lizarazu Oscar, Luo Ming-Cheng
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India,
Funct Integr Genomics. 2014 Mar;14(1):59-73. doi: 10.1007/s10142-014-0363-6. Epub 2014 Mar 8.
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
利用靶向71,094个克隆（约12倍覆盖率）的细菌人工染色体（BAC）文库，为鹰嘴豆参考基因型（ICC 4958）构建了物理图谱。对这些克隆进行的高信息含量指纹分析（HICF）为67,483个克隆提供了高质量的指纹数据，并确定了由46,112个克隆和3,256个单克隆组成的1,174个重叠群。简而言之，574 Mb的基因组大小被组装成1,174个重叠群，每个重叠群平均为0.49 Mb，3,256个单克隆代表407 Mb的基因组。借助245个BAC末端序列（BES）衍生的简单序列重复（SSR）标记，将物理图谱与两个遗传图谱进行了关联。这使得一些BAC能够定位在一些重要的耐旱、抗枯萎病和抗褐斑病数量性状位点（QTL）附近。此外，指纹重叠群（FPC）组装也与鹰嘴豆的基因组草图序列进行了整合。结果，约965个BAC（包括163个最小种植路径（MTP）克隆）可以定位到鹰嘴豆的8条假分子上，形成491个假设重叠群，代表基因组草图的54,013,992 bp（约54 Mb）。对非生物和生物胁迫耐受性QTL区域的标记进行综合分析，分别在耐旱“QTL热点”区域、抗褐斑病QTL区域和抗枯萎病QTL区域鉴定出654个、306个和23个基因。整合的物理、遗传和基因组图谱应为克隆和分离用于性状分子剖析的QTL/基因以及用于鹰嘴豆改良的分子育种标记提供基础。
