From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

Abstract

BackgroundThe improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology.ResultsMore than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool.ConclusionsThe established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.

Reticulate Evolution of the Rye Genome

“…A high-density gene-based marker map of rye was developed by genotyping 495 recombinant inbred lines (RILs) from four mapping populations with a previously published Rye5K Infinium Bead Chip (Haseneyer et al, 2011) comprising 5234 SNP markers (Table 1). In addition, 271 Expressed Sequence Tag (EST)-SSR (for simple sequence repeat) markers were genotyped in two of the populations.…”

“…Recently, a large data set of gene-based single nucleotide polymorphisms (SNPs) could be data-mined from RNA sequencing data of rye, providing the basis for developing a high-throughput SNP genotyping assay comprising 5234 markers (Haseneyer et al, 2011). In this study, this SNP assay was employed to build a high-density transcript map of rye.…”

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences

“…To analyze the differences in SNP frequencies, which should reflect the presence or absence of selective pressure, we compared genic sequences from the As and Bs to rye RNAseq-based contigs (12) by BLASTN and identified SNPs in regions present in all three of the datasets. As expected, the genic sequences of rye A chromosomes revealed a lower SNP frequency (1/72 bp) than their B-located homologs (1/ 47 bp) compared with the rye RNAseq assemblies (Table S3).…”

Hybrid breeding boosted molecular genetics in rye

“…Маркерные технологии на основе микрочипов, как, например, �ArT (diversity arrays technology -ДНК-чип технология для изучения разнообразия) или SNP (single-singlenucleotide polymorphism -однонуклеотидный полимор--однонуклеотидный полимор-физм), в частности SNP-чип ржи «Rye5K-SNP GenotypGenotyping Array» (Haseneyer et al, 2011), хорошо подходят не » (Haseneyer et al, 2011), хорошо подходят не только для картирования генов, но и для популяционных исследований. Bolibok-Bragoszewska с коллегами (2009) получили �ArT-маркеры на основе свыше 1 022 клонов, полиморфные в генотипированных изогенных линиях и сортах, и на основе 1 965 клонов, которые различались в родительских линиях L318 и L9.…”

“…С помощью et al, 2009Hackauf et al, 2009). С помощью RNAseq-анализа удалось выявить большой набор свя-занных с генами SNP-маркеров, которые стали основой для развития высокопроизводительного генотипирования ржи с использованием 5 234 маркеров (Haseneyer et al, 2011;Milczarski et al, 2011). Позднее SNP анализ был использован для построения карты транскриптов ржи с высокой плотностью.…”