Current Progress of Soybean Genomic Research in Indonesia

Thousands accessions of legume (soybean, peanut, mungbean, cowpea, etc.) in Indonesia have been conserved and mostly managed by the Indonesian Agency for Agricultural Research and Development (IAARD), Ministry of Agriculture. Given the importance of soybean for food production, 888 soybean accessions of total 3415 legume accessions housed at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD)-IAARD have served as valuable source for soybean breeders, geneticist and related field experts. To complement the multitude of results already obtained at conventional breeding and molecular level, development of genome-wide molecular markers for soybean improvement should become increasingly efficient. The soybean genome project was initiated in 2010 through a grant of the IAARD and collaborated with other commodity-based institutes under IAARD and Seoul National University, South Korea. The goals are (1) to develop molecular markers and/or SNP chip based on the genome of Indonesian soybean cultivars, (2) to develop linkage map for traits related to productivity and abiotic stress, (3) to develop integrated soybean genomic database. To provide genomic data resources, eight Indonesian soybean cultivars with diverse genetic background were re-sequenced. Among millions DNA variations, approximately 29% of them were novel SNPs unique to the Indonesian cultivars. Based on the SNP data, the Indonesian cultivars had genetic similarities to landraces from Japan dan China. The thousands SNPs found within exons related to known genes were identified and organized with detailed information in a genomic database, called IAARDGC (iaardgc.or.id) that was launched last October 2014. Validation of the SNPs with re-sequencing using Sanger method and SNAP primers is being conducted. Development of primers based on Indels/SSRs are also in progress. To develop QTL mapping using the markers/SNP chip, a number of soybean populations with targeted characters such as high productivity, tolerance to Al and salinity have been developed. Soybean Genome Browser is being developed and will be accommodated into the IAARD Genomic Database. Updating of the database will be continuously performed in line with completed data of related genomic analysis. The updated genomic information will be integrated with other genomic data, genotypic and phenotypic data, QTL map, primer repository of soybean and other crops under genome project supported by IAARD. In the future, these large number potential markers and new information of genomic analysis will be very important for future soybean germplasm improvement in Indonesia.