Identification and genetic characterization by high-throughput SNP analysis of intervarietal substitution lines of rapeseed (Brassica napus L.) with enhanced embryogenic potential

KEY MESSAGE: Seven intervarietal substitution lines were identified with embryogenic potentials up to 40.4 times that of the recurrent parent, providing an ideal material for further in depth studies of this trait. ABSTRACT: To identify genomic regions that carry genetic factors controlling embryogenic potential of isolated microspores of rapeseed, marker segregations were analysed in a segregating population of haploid microspore-derived embryos and a BC(1) population from a cross between ‘Express 617’ and ‘RS239’. After map construction 15 intervarietal substitution lines from the same cross with ‘Express 617’ as recurrent parent were selected with donor segments covering five genomic regions that had shown skewed segregations in the population of microspore-derived embryos but not in the BC(1) population. By comparing the embryogenic potential of microspores of the 15 substitution lines and ‘Express 617’, seven lines were identified with significantly enhanced embryogenic potential ranging from 4.1 to 40.4 times that of ‘Express 617’. To improve the genetic characterization of the selected lines, they were subjected to a high-throughput SNP analysis using the Illumina Infinium 60K chip for rapeseed. Based on 7,960 mapped SNP markers, one to eight donor segments per line, which cover 0.64–6.79 % of the 2,126.1 cM of the SNP map, were found. The SNP analysis also gave evidence that homoeologous exchanges had occurred during the development of the substitution line population, increasing the genetic diversity within this population. By comparing donor segments between lines with significantly enhanced embryogenic potential and non-significant lines, 12 genomic regions were identified that may contain genetic factors controlling embryogenic potential in rapeseed. These regions range in size from 0 (represented by just one marker) to 26.8 cM and cover together just 5.42 % of the SNP map. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-015-2455-7) contains supplementary material, which is available to authorized users.