Integration of High-Density Marker-Based QTL Mapping and RNA Sequencing to Assist Breeding for Aluminum Tolerance in Alfalfa (Medicago sativa L.).

Approximately 40% of the global arable land consists of acid soils. Aluminum toxicity can severely limit plant growth under high levels of soil acidity thus reducing yields and limiting the value of marginal lands for agricultural production. Alfalfa is the most important forage legume in the world due to its high yield, stand longevity and feed quality. However, alfalfa is sensitive to aluminum and germplasm variation for tolerance is relatively low. High-throughput sequencing technologies enable the identification of genome-scale sequence variants that can be used as molecular markers and the evaluation of gene expression differences between tolerant and sensitive genotypes. The goal of this research is to develop tools and resources for breeders aimed at increasing aluminum tolerance in alfalfa and consequently alfalfa productivity in acid soils. The genotyping-by-sequencing technology was utilized to generate SNP markers from a mapping population derived from a cross between the aluminum-tolerant alfalfa genotype Altet-4 and the aluminum-sensitive alfalfa genotype NECS-141. High-density genetic maps were used to confirm and refine the positions of quantitative trait loci (QTL) related to aluminum tolerance. The value of RNA sequencing data for transcription profiling in response to aluminum stress was evaluated. Gene expression data provided valuable insights on the mechanisms underlying the differential response of aluminum tolerant vs. aluminum sensitive alfalfa genotypes. The high-density marker-based QTL mapping and the RNA sequencing approaches can be used to develop markers for molecular breeding and selection strategies.