Chandra Amaresh, Jain Radha, Solomon Sushil, Shrivastava Shiksha, Roy Ajoy K
Division of Plant Physiology and Biochemistry, Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, Uttar Pradesh 226002, India.
BMC Res Notes. 2013 Feb 4;6:47. doi: 10.1186/1756-0500-6-47.
Sugarcane is an important cash crop, providing 70% of the global raw sugar as well as raw material for biofuel production. Genetic analysis is hindered in sugarcane because of its large and complex polyploid genome and lack of sufficiently informative gene-tagged markers. Modern genomics has produced large amount of ESTs, which can be exploited to develop molecular markers based on comparative analysis with EST datasets of related crops and whole rice genome sequence, and accentuate their cross-technical functionality in orphan crops like tropical grasses.
Utilising 246,180 Saccharum officinarum EST sequences vis-à-vis its comparative analysis with ESTs of sorghum and barley and the whole rice genome sequence, we have developed 3425 novel gene-tagged markers - namely, conserved-intron scanning primers (CISP) - using the web program GeMprospector. Rice orthologue annotation results indicated homology of 1096 sequences with expressed proteins, 491 with hypothetical proteins. The remaining 1838 were miscellaneous in nature. A total of 367 primer-pairs were tested in diverse panel of samples. The data indicate amplification of 41% polymorphic bands leading to 0.52 PIC and 3.50 MI with a set of sugarcane varieties and Saccharum species. In addition, a moderate technical functionality of a set of such markers with orphan tropical grasses (22%) and fodder cum cereal oat (33%) is observed.
Developed gene-tagged CISP markers exhibited considerable technical functionality with varieties of sugarcane and unexplored species of tropical grasses. These markers would thus be particularly useful in identifying the economical traits in sugarcane and developing conservation strategies for orphan tropical grasses.
甘蔗是一种重要的经济作物，提供了全球70%的原糖以及生物燃料生产的原材料。由于甘蔗具有庞大而复杂的多倍体基因组且缺乏足够信息丰富的基因标记，其遗传分析受到阻碍。现代基因组学产生了大量的EST（表达序列标签），可利用这些EST与相关作物的EST数据集以及水稻全基因组序列进行比较分析，从而开发分子标记，并突出它们在热带禾本科等非重点研究作物中的交叉技术功能。
通过使用246,180条甘蔗EST序列，并将其与高粱、大麦的EST以及水稻全基因组序列进行比较分析，我们利用在线程序GeMprospector开发了3425个新型基因标记——即保守内含子扫描引物（CISP）。水稻直系同源物注释结果表明，1096个序列与表达蛋白具有同源性，491个与假定蛋白具有同源性。其余1838个性质各异。总共在不同的样本组中测试了367对引物。数据表明，在一组甘蔗品种和甘蔗属物种中，41%的多态性条带得以扩增，产生了0.52的多态信息含量（PIC）和3.50的标记指数（MI）。此外，还观察到一组此类标记在非重点研究的热带禾本科植物（22%）和饲料兼谷物燕麦（33%）中具有一定的技术功能。
所开发的基因标记CISP在甘蔗品种和未开发的热带禾本科物种中表现出相当的技术功能。因此，这些标记在鉴定甘蔗的经济性状以及制定非重点研究的热带禾本科植物的保护策略方面将特别有用。
