Impact of Phenotypic Selection on the Frequencies of SSR-Defined Genomic Regions Associated with Drought Tolerance in Alfalfa.

Drought is a major abiotic stress that limits the productivity of crops worldwide. Alfalfa (Medicago sativa L.) is the most economically important forage crop in the U.S., and is the number one cash crop of New Mexico (NM). Large proportions of alfalfa acreage in the western U.S. experience water deficit on a regular basis. Breeding efforts involving a combination of conventional and molecular approaches might be more effective than either individual approach to improve alfalfa productivity in arid environments. This study was conducted to determine the effect of phenotypic selection for drought tolerance on the frequencies of six genomic regions that were previously shown to be associated with alfalfa biomass production during drought. A semi-elite base population previously developed by marker assisted selection (MAS), designated as MLS2, was evaluated under deficit irrigation management conditions for three years near Las Cruces, NM.  Subsequently, 96 MLS2 plants were selected from replicated field plots based on their overall vigor. These plants were intermated to develop an advanced population, MLS2-PS (PS, phenotypic selection), from which 224 individuals were genotyped for SSR marker alleles associated with six genomic regions affecting shoot or root biomass production under drought conditions. Expected frequencies of MLS2-PS plants possessing target genomic regions were estimated based on their observed frequencies in the MLS2 base population parents. Phenotypic selection for drought resilient plants altered all marker allele frequencies in the desirable direction in MLS2-PS, i.e. favorable alleles increased and unfavorable alleles decreased relative to their expected frequencies.  These changes were significant (P<0.05) for marker alleles defining four of the six genomic regions. Analyses of four additional populations developed by similar approaches are currently underway and will be presented. Results from this study indicate the complementarity of phenotypic and marker assisted selection for enhancing drought tolerance of alfalfa.