Choudhary Vishek, Shekhawat Deepika, Choudhary Anita, Jaiswal Vandana
CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
Mol Biol Rep. 2022 Dec;49(12):11695-11703. doi: 10.1007/s11033-022-07967-0. Epub 2022 Oct 1.
Saffron (Crocus sativus) is high valued spice crop, but due to its sterile nature, the crop is propagated exclusively through corms. Thus, the genetic base of this crop is very narrow, however, frequency of phenotypic variability is observed; and suggested the potential role of epigenetics in saffron crop growth and development.
To facilitate epigenetic studies in saffron, we developed 1525 methylation-specific PCR (MSP) markers using MethPrimer. For this purpose, we used 6767 EST sequences of saffron available on the NCBI database. We also mine CpG islands (2555) and found that 32.7% of EST sequences had CpG islands. Out of 1525 MSP markers developed during the present study, 725 covered the CpG islands and 800 were without CpG islands. PCR amplification was found successful for 82% of MSP markers. A preliminary analysis suggested that 53.7% of genomic sites were methylated and more prominent (60% methylations) in non-CpG island regions, although, more comprehensive studies are required to validate it further.
The epigenetic resource developed during the present study will strengthen the epigenetic studies like epiQTL mapping, epiGWAS to explore the molecular mechanisms and genomic/epigenomic regions associated with phenotype; and further may be utilized for saffron improvement programs through epibreeding.
藏红花（番红花）是一种高价值的香料作物，但由于其不育特性，该作物仅通过球茎进行繁殖。因此，这种作物的遗传基础非常狭窄，然而，观察到表型变异的频率；并表明表观遗传学在藏红花作物生长发育中的潜在作用。
为了促进藏红花的表观遗传学研究，我们使用MethPrimer开发了1525个甲基化特异性PCR（MSP）标记。为此，我们使用了NCBI数据库中可获得的6767条藏红花EST序列。我们还挖掘了CpG岛（2555个），发现32.7%的EST序列含有CpG岛。在本研究中开发的1525个MSP标记中，725个覆盖了CpG岛，800个没有CpG岛。发现82%的MSP标记PCR扩增成功。初步分析表明，53.7%的基因组位点发生了甲基化，在非CpG岛区域更为显著（60%甲基化），不过，需要更全面的研究来进一步验证。
本研究中开发的表观遗传资源将加强表观遗传学研究，如epiQTL定位、epiGWAS，以探索与表型相关的分子机制和基因组/表观基因组区域；并且进一步可通过表观育种用于藏红花改良计划。
