Open AccessSequence‐based SNP genotyping in durum wheat
Author(s) -
Poecke Remco M.P.,
Maccaferri Marco,
Tang Jifeng,
Truong Hoa T.,
Janssen Antoine,
Orsouw Nathalie J.,
Salvi Silvio,
Sanguineti Maria C.,
Tuberosa Roberto,
Vossen Edwin A.G.
Publication year - 2013
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12072
Subject(s) - biology , contig , genotyping , snp , single nucleotide polymorphism , genetics , snp genotyping , molecular inversion probe , genetic marker , molecular marker , genome , computational biology , population , snp array , genotype , gene , demography , sociology
Summary Marker development for marker‐assisted selection in plant breeding is increasingly based on next‐generation sequencing ( NGS ). However, marker development in crops with highly repetitive, complex genomes is still challenging. Here we applied sequence‐based genotyping ( SBG ), which couples AFLP ® ‐based complexity reduction to NGS , for de novo single nucleotide polymorphisms ( SNP ) marker discovery in and genotyping of a biparental durum wheat population. We identified 9983 putative SNP s in 6372 contigs between the two parents and used these SNP s for genotyping 91 recombinant inbred lines ( RIL s). Excluding redundant information from multiple SNP s per contig, 2606 (41%) markers were used for integration in a pre‐existing framework map, resulting in the integration of 2365 markers over 2607 cM . Of the 2606 markers available for mapping, 91% were integrated in the pre‐existing map, containing 708 SSR s, DA r T markers, and SNP s from CR o PS technology, with a map‐size increase of 492 cM (23%). These results demonstrate the high quality of the discovered SNP markers. With this methodology, it was possible to saturate the map at a final marker density of 0.8 cM /marker. Looking at the binned marker distribution (Figure 2), 63 of the 268 10‐ cM bins contained only SBG markers, showing that these markers are filling in gaps in the framework map. As to the markers that could not be used for mapping, the main reason was the low sequencing coverage used for genotyping. We conclude that SBG is a valuable tool for efficient, high‐throughput and high‐quality marker discovery and genotyping for complex genomes such as that of durum wheat.