Using Selection Mapping to Assess the Genetic Control of Fall Dormancy in Cultivated Alfalfa

Manipulating the fall dormancy reaction in alfalfa to allow extensive vegetative fall growth independent of the ability to survive winter conditions remains a long-standing breeding goal of the alfalfa community. The possibility of improving autumn biomass production in regions with limited winter may be realized quickly if genomic regions controlling fall dormancy could be targeted by marker-assisted selection. Historically, dissecting the genetic control of the trait has been rendered difficult by the biology of the taxon, allogamous autotetraploid, coupled with the limitations of the plant materials, differing in their origin and genetic background, used for evaluation of the trait. Selection mapping in experimental populations presents a viable approach to evaluate the genetic control of fall dormancy in alfalfa. That selection increases the frequency of favorable alleles in a population is a cornerstone of evolutionary theory. Here we leverage this principle and use GBS based pooled sequencing to assess temporal shifts in allele frequency in experimental populations subjected to a divergent selection regime for autumn regrowth (a proxy for fall dormancy) in Davis, CA. We demonstrate that in absence of a reference genome, window-based analyses may be successfully implemented using only those markers that map to the highly syntenic genome of Medicago truncatula. Our genomic scan for divergence within a genetic background (CUF 101) finds both previously undetected regions and regions recently reported to be associated with fall dormancy. Preliminary findings in a second genetic background (Lahontan) show evidence for shared regions controlling fall dormancy in different germplasm.