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

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.