Vishek Choudhary1,2, Deepika Shekhawat1, Anita Choudhary1,2, Vandana Jaiswal3,4. 1. CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. 2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India. 3. CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. vandana@ihbt.res.in. 4. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India. vandana@ihbt.res.in.
Abstract
BACKGROUND: 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. METHODS AND RESULTS: 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. CONCLUSIONS: 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.
BACKGROUND: 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. METHODS AND RESULTS: 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. CONCLUSIONS: 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.
Authors: Chad E Niederhuth; Adam J Bewick; Lexiang Ji; Magdy S Alabady; Kyung Do Kim; Qing Li; Nicholas A Rohr; Aditi Rambani; John M Burke; Joshua A Udall; Chiedozie Egesi; Jeremy Schmutz; Jane Grimwood; Scott A Jackson; Nathan M Springer; Robert J Schmitz Journal: Genome Biol Date: 2016-09-27 Impact factor: 13.583