Pembentukan Pustaka Genom, Resekuensing, dan Identifikasi SNP Berdasarkan Sekuen Genom Total Genotipe Kedelai Indonesia

I Made Tasma, Dani Satyawan, Habib Rijzaani

Abstract


Resequencing of the soybean genome facilitates SNP marker discoveries useful for supporting the national soybean breeding
programs. The objectives of the present study were to construct soybean genomic libraries, to resequence the whole genome of
five Indonesian soybean genotypes, and to identify SNPs based on the resequence data. The studies consisted of genomic
library construction and quality analysis, resequencing the whole-genome of five soybean genotypes, and genome-wide SNP
identification based on alignment of the resequence data with reference sequence, Williams 82. The five Indonesian soybean
genotypes were Tambora, Grobogan, B3293, Malabar, and Davros. The results showed that soybean genomic library was
successfully constructed having the size of 400 bp with library concentrations range from 21.2–64.5 ng/μl. Resequencing of the
libraries resulted in 50.1 x 109 bp total genomic sequence. The quality of genomic library and sequence data resulted from this
study was high as indicated by Q score of 88.6% with low sequencing error of only 0.97%. Bioinformatic analysis resulted in a
total of 2,597,286 SNPs, 257,598 insertions, and 202,157 deletions. Of the total SNPs identified, only 95,207 SNPs (2.15%) were
located within exons. Among those, 49,926 SNPs caused missense mutation and 1,535 SNPs caused nonsense mutation. SNPs
resulted from this study upon verification will be very useful for genome-wide SNP chip development of the soybean genome to
accelerate breeding program of the soybean.


Keywords


Soybean; genomic library; NGS; SNP; genome variation.

Full Text:

PDF


DOI: http://dx.doi.org/10.21082/jbio.v11n1.2015.p7-16

Refbacks

  • There are currently no refbacks.




Copyright (c) 2016 Jurnal AgroBiogen

 Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.


           


P-ISSN : 1907-1094
E-ISSN : 2549-1547


Jurnal AgroBiogen

Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Jl. Tentara Pelajar 3A, Bogor 16111
Jawa Barat, Indonesia
Telp.: (0251) 8339793, 8337975
Faks.: (0251) 8338820
E-mail: jurnal.agrobiogen@gmail.com
Situs: http://biogen.litbang.pertanian.go.id



View My Stats