title: Development and characterization of simple sequence repeat (SSR) markers based on RNA-sequencing of Medicago sativa and in silico mapping onto the M. truncatula genome.
abstract: Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa.
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zan
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China; Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Guohui
authors.initials: G
authors.lastname: Yu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Binbin
authors.initials: B
authors.lastname: Shi
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xuemin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Haiping
authors.initials: H
authors.lastname: Qiang
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Hongwen
authors.initials: H
authors.lastname: Gao
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D017343:Genes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D000455:Medicago sativa / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics*; D018895:Microsatellite Repeats; D011003:Ploidies; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers