title: A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.
abstract: A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa.
authors.affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.
authors.forename: Xuehui
authors.initials: X
authors.lastname: Li
authors.affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.
authors.forename: Yanling
authors.initials: Y
authors.lastname: Wei
authors.affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.
authors.forename: Ananta
authors.initials: A
authors.lastname: Acharya
authors.affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.
authors.forename: Qingzhen
authors.initials: Q
authors.lastname: Jiang
authors.affiliation: The Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China 100193.
authors.forename: Junmei
authors.initials: J
authors.lastname: Kang
authors.affiliation: Plant Breeding Center and Department of Plant Sciences, The University of California, Davis, California 95616 ecbrummer@ucdavis.edu.
authors.forename: E Charles
authors.initials: EC
authors.lastname: Brummer
mesh_terms: D002874:Chromosome Mapping; D020090:Chromosome Segregation; D008040:Genetic Linkage; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D000455:Medicago sativa / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics*; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D057891:Tetraploidy
keywords: alfalfa; autotetraploid; genetic linkage map; genotyping-by-sequencing