Advances in Soybean Genomics

Abstract

Soybean is an agronomically important crop that is endowed with rich seed protein and oil. It enriches the soil by fixing nitrogen through symbiosis with bacteria. In addition to human consumption, soybean is a major protein source in animal feeds and is also becoming a major crop for biodiesel production. A major landmark in soybean genomics research was its draft genome sequence assembly (cultivar Williams 82) following whole-genome shot gun (WGS) approach. It revealed 950 Mb (megabases) of assembled and anchored sequence as against the predicted 1,115 Mb genome consequently representing 85 % of the whole genome. Development of comprehensive physical map employing chiefly Bacterial artificial chromosomes (BAC) and Binary large-insert BAC clones (BIBAC) have assisted in the whole genome sequencing venture and in targeted genetic marker development, accelerating positional cloning approaches along with the generation of rapid and robust EST maps. Comprehensive Expressed Sequence Tags (ESTs) repository and genome sequence of the crop have helped in sound integration of physical map with the genetic map. In order to perform genetic and genomic analysis various molecular markers like RFLP, RAPD, AFLP, SSR, SNP etc. have been employed on RIL or F2 populations. In addition the genome is typified with single nucleotide polymorphisms (SNPs) and its utilization in molecular breeding applications like QTL mapping, positional cloning and association mapping studies is gaining impetus. QTLs associated with foremost traits of agronomic interests including QTLs for Aphid resistance, Soybean Cyst Nematode (SCN) resistance among others have been identified and validated. Further molecular marker assisted QTL introgression and gene pyramiding for traits like enhanced seed protein concentration and Soybean Mosaic Virus (SMV) resistance, insect resistance etc. have been accomplished. Legume comparative genomics using orthologous genomic regions have addressed queries relating to Nucleotide binding-Leucine rich repeat (NB-LRRs) genes, polyploidy, and genome evolution. In the soybean functional genomics arena, in addition to the conventional assays involving qRT-PCR, Northern blotting, global gene expression analysis like Serial analysis of gene expression (SAGE), microarrays kind strategies are being widely employed. With the identification of micro RNAs (miRNAs) as ultimate gene effector molecules identification and characterization of novel miRNAs in soybean is gaining a momentum. Thus the rapid development of soybean genomics and transcriptomics has provided tremendous opportunity for the genetic improvement of soybean.