title: RADtyping: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations.
abstract: Genetic linkage maps are indispensable tools in genetic, genomic and breeding studies. As one of genotyping-by-sequencing methods, RAD-Seq (restriction-site associated DNA sequencing) has gained particular popularity for construction of high-density linkage maps. Current RAD analytical tools are being predominantly used for typing codominant markers. However, no genotyping algorithm has been developed for dominant markers (resulting from recognition site disruption). Given their abundance in eukaryotic genomes, utilization of dominant markers would greatly diminish the extensive sequencing effort required for large-scale marker development. In this study, we established, for the first time, a novel statistical framework for de novo dominant genotyping in mapping populations. An integrated package called RADtyping was developed by incorporating both de novo codominant and dominant genotyping algorithms. We demonstrated the superb performance of RADtyping in achieving remarkably high genotyping accuracy based on simulated and real mapping datasets. The RADtyping package is freely available at http://www2.ouc.edu.cn/mollusk/ detailen.asp?id=727.
authors.affiliation: Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong Province, China.
authors.forename: Xiaoteng
authors.initials: X
authors.lastname: Fu
authors.forename: Jinzhuang
authors.initials: J
authors.lastname: Dou
authors.forename: Junxia
authors.initials: J
authors.lastname: Mao
authors.forename: Hailin
authors.initials: H
authors.lastname: Su
authors.forename: Wenqian
authors.initials: W
authors.lastname: Jiao
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
authors.forename: Xiaoting
authors.initials: X
authors.lastname: Huang
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D005799:Genes, Dominant; D005819:Genetic Markers; D005838:Genotype; D015183:Restriction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D005819:Genetic Markers