title: Gene-based SNP discovery and genetic mapping in pea.
abstract: Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.
authors.affiliation: Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
authors.forename: Anoop
authors.initials: A
authors.lastname: Sindhu
authors.forename: Larissa
authors.initials: L
authors.lastname: Ramsay
authors.forename: Lacey-Anne
authors.initials: LA
authors.lastname: Sanderson
authors.forename: Robert
authors.initials: R
authors.lastname: Stonehouse
authors.forename: Rong
authors.initials: R
authors.lastname: Li
authors.forename: Janet
authors.initials: J
authors.lastname: Condie
authors.forename: Arun S K
authors.initials: AS
authors.lastname: Shunmugam
authors.forename: Yong
authors.initials: Y
authors.lastname: Liu
authors.forename: Ambuj B
authors.initials: AB
authors.lastname: Jha
authors.forename: Marwan
authors.initials: M
authors.lastname: Diapari
authors.forename: Judith
authors.initials: J
authors.lastname: Burstin
authors.forename: Gregoire
authors.initials: G
authors.lastname: Aubert
authors.forename: Bunyamin
authors.initials: B
authors.lastname: Tar'an
authors.forename: Kirstin E
authors.initials: KE
authors.lastname: Bett
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Warkentin
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
mesh_terms: D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D027806:Lens Plant / Q000235:genetics; D046913:Medicago truncatula / Q000235:genetics; D018532:Pisum sativum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D026801:Synteny; D059467:Transcriptome
chemical_list: D018744:DNA, Plant