Key messageSeven 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.AbstractTo 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 BC1 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 BC1 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 materialThe online version of this article (doi:10.1007/s00122-015-2455-7) contains supplementary material, which is available to authorized users.

In Brassica species microspore derived doubled haploid lines are an important tool in breeding and research. A limiting step in the production of doubled haploid lines is the diploidization of the microspores. Strong differences have been observed in diploidization rates between different genotypes but little is know about the genetic control of these differences. To identify genomic regions that carry genetic factors controlling the diploidization rate of isolated microspores of rapeseed, marker segregations were compared between segregating populations of diploid and haploid microspore derived embryos and a BC 1 from a cross between 'Express 617' and 'RS239'. After map construction ten intervarietal substitution lines from the same cross were selected with donor segments covering five genomic regions that showed a pattern of skewed marker segregations across the three populations indicative of the segregation of genes controlling the diploidization rates. The diploidization rates of microspores of the ten lines ranged from 23.9 to 58.7 % while the recurrent parent 'Express 617' showed a rate of 52.5 %. For three lines the diploidization rates were significantly lower (P = 0.05) than the rate of 'Express 617'. By comparing donor segments between the significant and the non-significant lines, seven genomic regions that cover just between 4.17 and 6.16 % of the rapeseed genome were identified that may contain genetic factors controlling diploidization rates in rapeseed. In addition, one marker was found that has a high probability to be linked to such a factor. The significant lines represent an ideal material for further in depth studies of this trait.

Microspore culture has become an important tool in many species, including Brassicas, for the production of entirely homozygous lines, so called double haploid (DH) lines. The primary products of microspore culture are embryo-like structures, called microspore-derived embryos (MDEs). A major problem in the development of DH lines is the often low efficiency of Direct Embryo to Plant Conversion (DEPC). During the development of DH populations, favourable alleles of genes affecting the DEPC rate will be under selection. This selection should lead to skewed segregations at markers linked to these genes. By comparing skewed marker segregations in four populations, a population of doubled haploid plantlets, a haploid and a doubled haploid MDE population, and a BC 1 population, 20 genomic regions were identified, which showed patterns of skewed segregations across the populations, indicative of the segregation of genetic factors controlling DEPC rates. Four regions and eight intervarietal substitution lines (ISLs) with donor segments overlapping these regions were selected for further studies. Three ISLs, ER654, ER661 and ER653 with DEPC rates of 49.1, 54.5 and 57.2 %, showed significantly reduced DEPC rates compared to the rate of the recurrent parent of 76.5 %. By comparing donor segments between the significant and the non-significant lines, eight genomic regions were identified that may contain genetic factors controlling the DEPC rate in rapeseed. These regions range in size from 0 (represented by just one marker) to 16.5 cM and cover together just 1.33 % of the genetic map used to characterize the donor segments in the ISLs.