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

Abstract

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