Resequencing in a mapping population

Over the past decade, investment in soybean cv. Forrest systems biology have resulted in the development of many resources: (i) a saturated 50K SNP genetic map; (ii) three RIL populations (96>n>975); (iii) ~200 NILs; (iv) 115,220 BACs and BIBACs; (v) a physical map; (vi) 4 different minimum tiling path (MTP) sets; (vii) 25,123 BAC end sequences (BES) that encompass 18.5 Mbp spaced out from the MTPs; (viii) a map of 2,408 regions each found at a single position in the genome and 2,104 regions found in 2 or 4 similar copies at different genomic locations (each of  >150 kbp); (ix) a map of homoeologous regions among both sets of regions; (x) a set of transcript abundance measurements that address biotic stress resistance; (xi) methods for transformation; (xii) methods for RNAi;  (xiii) a TILLING resource for directed mutant isolation and (xiv) analyses of conserved synteny with other sequenced genomes; (xv) maps of the proteome; (xvi) understanding of the metabolome. Genes isolated from Forrest-derived BACs include Rhg4 and rhg1, Rps5, Rps1; Rfs2, Rfs3, Rfs1, GmNark, and GmNod. Genes underlying many quantitative and qualitative loci are targeted for isolation. Twenty five thousand BES and 20 whole BAC sequences have provided a framework for pyrosequence. The most diverse 67 RILs and 6 most informative NILs genomic DNAs were barcoded and pooled for sequencing on one lane of an Illumina GAII.  Approximately 25.5 million 100 bp reads were generated. Reads were aligned to the JGI soybean genome assembly v7.0.  Alignments produced a mean of 12,628 contigs of length 104 bp with 19x coverage.  Over 50% of reads from could not be mapped. Single nucleotide variation between the Essex and Forrest parental lines were identified from the GBS reads among the RIL samples.  A total of 7,755 SNP positions were identified. To date 309 SNP positions were identified in the RILs and 153 in the NILs.  These SNPs have read coverage from the majority of individuals (>50% individuals) and segregate close to 1:1 in the population.  Also, the base variant of the SNPs have been confirmed to match with at least one of the two parents based on GBS reads. SNP markers were intergrated to the existing genetic map using MSTmap. QTL for 173 traits were reanalyzed. New QTL and improved markers for existing QTL will be discovered. The SoyGD portal at http:/soybeangenome.siu.edu integrates the chromosome map with the genome sequences that identifies complete genes, a partial genome annotation and many thousands of SNP candidates in introns and promoters of protein-coding genes.