Alfalfa Breeder’s Toolbox (ABT): An Integrated Database for Alfalfa Genomics, Genetics and Breeding

The Alfalfa Breeder’s Toolbox (ABT) is a user-friendly web-based portal that provides access to and visualization of multiple datasets to assist breeding activities in alfalfa. The site was developed using the Chado-Drupal-Tripal data modules to integrate basic, translational and phenotypic data in alfalfa. The ABT site currently includes the Medicago truncatula (v4.0) and diploid alfalfa (CADL v0.95) genomes as the backbone that anchors the alfalfa transcript sequences, gene models, molecular markers, genetic linkage maps, quantitative trait loci (QTLs), and allele frequencies visualized through JBrowse and phenotypic data collected from field trials. The current alfalfa gene models include 96% of the conservative gene orthologs in the plant kingdom based on the MAKER and SPADA pipelines and BUSCO evaluation. The alfalfa gene expression atlas enables users to evaluate differential gene expression and co-expression of target genes between alfalfa genotypes grown under various abiotic stress conditions. In silico PCR, BLAST and other advanced search tools can be used to develop primers targeting specific genes of interest and identify genes and molecular markers in specific genomic regions. The phenotypic data can be used to generate selection indices that combine multiple traits to identify the best germplasm based on agronomic performance in the field. Alfalfa breeders can utilize the integrated tools to improve traits of agronomic importance such as biomass yield, abiotic and biotic stress tolerance, forage quality and other key traits through the implementation of molecular breeding strategies facilitated by the availability of the ABT.