Abstract Detail

Comparative Genomics/Transcriptomics

Unamba, Chibuikem I.N. [1], Singh, Gagandeep [2], Singh, Pradeep [2], Seth, Romit [2], Agbagwa, Ikechukwu O [3], Sharma, Ram K [2].

Transcriptome sequencing for development and assessment of genic SSR marker in Ipomoea species.

Ipomoea is a large and diverse genus in the family Convolvulaceae, with over 600 species distributed in the tropics and subtropics. The species have nutritional, medicinal, and agricultural economic importance. Simple sequence repeat (SSR) markers are one of the most informative and widely used DNA-based markers, hence we have attempted employing the cost effective method of Next Generation Sequencing (NGS) to develop and assess their reliability for genetic studies in Ipomoea species. In this study, transcriptomes of two Ipomoea cairica genotypes from India were sequenced using Illumina paired-end sequencing technology. De novo assembly of generated sequencing reads yielded more than 50,000 unigenes with an average length of 768 bp. More than 6000 sequences identified contain one or more SSRs. 96 primer pairs were randomly selected to validate the assembly quality and developed SSR markers.The result revealed that 84 primer pairs were successfully amplified in initial screening tests. Further, 18 polymorphic markers were used for validation of the amplifications and assessment of polymorphism in genomic DNA pools from individuals across regions of Nigeria and India. Similarly, significant number of SSR markers recorded transferability to 10 species of the genus Ipomoea. This study added ample genic SSR marker resource for genomic studies in the genus Ipomoea.

1 - Imo State University, Plant Science and Biotechnology, Faculty of Science, Owerri, IMO, 460222, Nigeria
2 - CSIR-Institute of Himalayan Bioresource Technology, Biotechnology, Palampur, Himachal Pradesh, India
3 - University of Port Harcourt, Plant Science and Biotechnology, Faculty of Science, Port Harcourt, Rivers, Nigeria

Keywords:
Transcriptome
SSR marker 
Ipomoea
Next Generation Sequencing
Sequencing.

Presentation Type: Oral Paper
Session: CG2, Comparative Genetics/Genomics II
Location: Tucson I/Starr Pass
Date: Tuesday, July 30th, 2019
Time: 1:45 PM
Number: CG2001
Abstract ID:160
Candidate for Awards:Margaret Menzel Award