@article{fdi:010061228,
  title = {{B}ridging the genotyping gap : using genotyping by sequencing ({GBS}) to add high-density {SNP} markers and new value to traditional bi-parental mapping and breeding populations [+ erratum paru en janvier 2016]},
  author = {{S}pindel, {J}. and {W}right, {M}. and {C}hen, {C}. and {C}obb, {J}. and {G}age, {J}. and {H}arrington, {S}. and {L}orieux, {M}athias and {A}hmadi, {N}. and {M}c{C}ouch, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{G}enotyping by sequencing ({GBS}) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping {SNP}s in a variety of crop species and populations. {U}nlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of {GBS} makes it an attractive means of saturating mapping and breeding populations with a high density of {SNP} markers. {O}ne barrier to the widespread use of {GBS} has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous {SNP} calls which are not easily diagnosed or corrected. {I}n this study, we use a 384-plex {GBS} protocol to add 30,984 markers to an indica ({IR}64) x japonica ({A}zucena) mapping population consisting of 176 recombinant inbred lines of rice ({O}ryza sativa) and we release our imputation and error correction pipeline to address initial {GBS} data sparsity and error, and streamline the process of adding {SNP}s to {RIL} populations. {U}sing the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. {W}e mapped {QTL} for leaf width and aluminum tolerance, and were able to identify additional {QTL} for both phenotypes when using the full set of 30,984 {SNP}s that were not identified using a subset of only 1,464 {SNP}s, including a previously unreported {QTL} for aluminum tolerance located directly within a recombination hotspot on chromosome 1. {T}hese results suggest that adding a high density of {SNP} markers to a mapping or breeding population through {GBS} has a great value for numerous applications in rice breeding and genetics research.},
  keywords = {},
  booktitle = {},
  journal = {{T}heoretical and {A}pplied {G}enetics},
  volume = {126},
  numero = {11},
  pages = {2699--2716 [+ erratum, 2016, 129, 1, p. 201--202]},
  ISSN = {0040-5752},
  year = {2013},
  DOI = {10.1007/s00122-013-2166-x},
  URL = {https://www.documentation.ird.fr/hor/fdi:010061228},
}