Construction of a high-density genetic map using SNPs makers and QTL analysis for tillering related traits in Psathyrostachys juncea perennial grass

Abstract

Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass which plays important role in forage and rangeland restoration due to its tiller producing abilities, nevertheless, no genetic map has been constructed owing to lacking of efficient and reliable molecular markers which are also constrains in identifying, locating, and cloning its economically important tiller density related traits during breeding. Therefore, this study was designed by creating a F₁ mapping population with 147 individuals and their two parents based on different tiller densities. This mapping population was subsequently used for specific-locus amplified fragment sequencing (SLAF-seq) to produce SLAF markers and single nucleotide polymorphisms (SNPs) discovery. Initially, a total of 1,438.38 million pair-end reads were generated based on the average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F₁ individual, respectively. After filtering low-depth SLAF tags, a total of 558,344 high-quality SLAFs were detected. A total of 1,519,903 SNP markers were obtained and 62,424 polymorphic SNPs were discovered. Finally, 4,644 polymorphic SNPs selected from 62,424 SNPs were used for genetic map construction in seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance between adjacent markers for 0.31 cM. Comparisons between seven linkage groups of RWR SLAF tag to whole-genome sequences in Barley (Hordeum vulgare L.) revealed homology value ranged from 17.5–34.6% and the collinearity between RWR linkage groups and Barley homology groups ranged from 0.6787 to 0.9234 with the value of 0.8158 on average. Totally sixteen significant QTLs for tiller related traits were detected using a BC1 population further verified the map’s reliability.