A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq).

MAIN CONCLUSION: This genetic map for Agropyron Gaertn. contained 1023 markers on seven linkage groups, with a total of 907.8 cM and an average distance of 1.5 cM between adjacent loci. Many wheat- Agropyron cristatum derivative lines exhibit superior agronomic traits, and part of them are valuable for future wheat breeding. To date, no high-density genetic map for Agropyron Gaertn. has been published. Specific-locus amplified fragment sequencing (SLAF-seq), a recently developed strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms (SNPs), was employed in this study to develop sufficient markers for a segregating Agropyron F1 population derived from an interspecific cross between two cross-pollinated diploid collections A. cristatum (L.) Beauv. 'Z1842' and A. mongolicum Keng 'Z2098'. In total, we obtained raw data consisting of 128,932,358 pair-end reads of ~80 bp long after sequencing. Then 69,325 high-quality SLAFs were detected, of which 26,248 SLAFs were polymorphic and 1752 of the polymorphic markers were used for the genetic map construction. The final map contained 1023 markers on the seven linkage groups (LGs), which spanned a total of 907.8 cM with an average number of 146 markers and 89 loci per LG and an average distance of 1.5 cM between adjacent loci. To our knowledge, this map is the densest genetic linkage map for Agropyron so far. Through BLAT alignment of Agropyron SLAF marker sequences with the draft genome assemblies of wheat and barley, the Agropyron LGs were assigned as LG1-7 according to their corresponding homoeologous chromosomal groups of wheat. Results of this study will not only provide a platform for gene/QTL fine mapping, but also serve as a reference to assist the assembling of the P genome sequence in future.