P1138Genome-wide comparison of low- and high-phytate soybean isogenic lines
Phytic acid (myo-inositol-1, 2, 3, 4, 5, 6-hexakis-phosphate or phytate) is a major source of phosphorous in seeds and an essential component of numerous developmental and signaling processes in plants. Non-ruminant animals cannot digest phytate from seed-based animal-feed causing eutrophication. Breeding of low phytic acid (lpa) crops is an eco-friendly alternative to avoid the phosphorus unavailability issue. Soybean (Glycine max) lpa line, ‘V99-5089’, carries a point mutation in myo-inositol phosphate synthase (MIPS1) gene that affects phytate biosynthesis, causing low levels of phytate and stachyose, reduced emergence and high-sucrose phenotype. For genome-wide comparison of the lpa soybean with normal phytic acid line, we made a cross of ‘Essex’ (normal-phytate, stachyose and emergence) with V99-5089. We screened advanced generation progenies using SNP assay to identify individuals heterozygous for the MIPS1 gene. Two near-isogenic lines (NILs) designated as SoyE and SoyV, originating from selfing of a single heterozygous individual showed contrasting phytate, stachyose, and emergence phenotypes due to different MIPS1 alleles. We mapped whole genome sequencing data generated from these NILs with ~22.5X mean read-depth to the soybean ‘Williams82’ reference genome. We detected copy-number variations (CNVs) with a high resolution (100 base-pair window) using event-wise significance testing approach from RDXplorer (Yoon S et al., 2009). Preliminary results indicate substantial CNV differences between the two NILs. We will identify genes that show significantly different copy numbers and perform functional enrichment analysis to identify the processes represented by them. These results will help to better understand the genetic basis of the lpa trait in soybean.
Neelam Redekar
Virginia Tech
Email: neelamrr@vt.edu