title: Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits.
abstract: Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.
authors.affiliation: Council for Agricultural Research and Economics-Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Biazzi
authors.affiliation: Council for Agricultural Research and Economics-Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy.
authors.forename: Nelson
authors.initials: N
authors.lastname: Nazzicari
authors.affiliation: Council for Agricultural Research and Economics-Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Pecetti
authors.affiliation: Plant Breeding Center, Department of Plant Sciences, University of California, Davis, CA, United States of America.
authors.forename: E Charles
authors.initials: EC
authors.lastname: Brummer
authors.affiliation: Department of Veterinary Medicine, University of Bologna, Bologna, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Palmonari
authors.affiliation: Council for Agricultural Research and Economics-Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy.
authors.forename: Aldo
authors.initials: A
authors.lastname: Tava
authors.affiliation: Council for Agricultural Research and Economics-Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy.
authors.forename: Paolo
authors.identifier: http://orcid.org/0000-0001-8027-1035
authors.initials: P
authors.lastname: Annicchiarico
mesh_terms: D002874:Chromosome Mapping; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D000455:Medicago sativa / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers