The SynDH1 population used in this study was derived from the interspecific hybridization of T. turgidum with Ae. tauschii, followed by spontaneous chromosome doubling . We demonstrated in this study that such a population can be effectively used to generate genetic maps. This map has been successfully used to locate high-molecular-weight glutenin subunits on loci Glu-A1 and Glu-B1, and to identify five QTLs of three agronomic traits. However, this study identified as many as 24 linkage groups, which is significantly larger than the number of the 14 haploid chromosomes of the A and B genomes. To reduce the number of the linkage groups, additional markers are needed for a better covered, high-density map.
Low map coverage, duplicated marker loci, or segregation distortion can cause inconsistent marker order in genetic maps . Chromosome rearrangements (such as small translocations, deletions, and inversions) can also result in marker inconsistency . Compared to previously reported CIMMYT integrated map (CIMMYT) , durum wheat integrated map (C-L) , and triticale genetic map (S-M) , discrepant marker orders were observed in some regions, mostly on chromosomes 1A and 2A. According to the marker order in the genetic maps of these two chromosomes (see Additional file 1), these discrepancies appear to have been caused by chromosome inversions. In a recently reported genetic map for triticale, deletion of a fragment of chromosome 1A and translocation of 2A caused discrepancies in marker positions and order across populations .
Segregation distortion is a common phenomenon that can be influenced by factors affecting fertility of either gametes or zygotes . Environmental effects also affect segregation distortion and are assumed to influence gametophyte selection . Compared with F2 and DH, RILs (recombinant inbred lines) are more prone to segregation distortion because of repeated selective forces . Segregation distortion markers have been reported in common wheat [8, 12–15] and its two ancestral species of T. turgidum[16–20] and Ae. tauschii.
If a biological segregation distortion locus exists, the concerned locus and those flanking region would all deviate from the expected Mendelian segregation ratio . Therefore, biological segregation distortion affects a cluster of loci that form a segregation distorted region (SDR). Using the criterion of Paillard et al. , a SDR should contain at least three closely adjacent loci. Based on this criterion, SDRs were only found on chromosomes 1A, 3B, and 6B in this study (Figure 1, 2). Other distortion loci scattered along the chromosomes 3A, 4A, 7A, 1B, 2B, 4B, 5B, and 7B were likely a result of non-biological factors. The limited number of the SynDH lines used could be one of these factors.
Because all the F1 haploid hybrid plants from LDN/AS313//AS60 produced F2 doubled haploid plants , segregation distortion in the present study was most likely generated in the production process of the haploid hybrids by wide hybridization between T. turgidum and Ae. tauschii. Because no in vitro culture was applied during this interspecific hybridization procedure , its involvement in the segregation distortion can be ruled out. The production of conventional haploids via in vitro culture may lead to segregation distortion, because the ability of in vitro regeneration is genotype-dependent. When crossing T. turgidum with Ae. tauschii, different alleles of crossability QTL between LDN and AS313 may affect segregation differently. It is known that crossability genes control the ability of crossing between different species, and affect the seed-setting of interspecific crosses [23, 24]. Crossability can be promoted by recessive alleles and inhibited by dominant alleles. The inhibiting effect of chromosome 6B  and the promoting effect of 3B  on crossability in LDN may cause marker segregation favoring AS313 on 6B and LDN on 3B (Figure 2). Because Xgwm626 and Xbarc79 on chromosome 6B gave the most severe segregation distortions, and their flanking markers were all less skewed, the crossability QTL may be situated between these two markers. Likewise, a QTL affecting segregation may also exist near wPt-6945 on 3B. The distorted segregation favoring AS313 near wPt-3836 on 1A suggests that this genotype may have a recessive crossability QTL in this region . These results suggest that the distorted segregation in the SynDH population depends on variations in crossability alleles between the two T. turgidum parents. In this regard, genotypic effects on crossability need to be considered when using SynDH populations for genetic mapping.