Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome

Abstract

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

“…The sequences from 57 consensus markers within the selected intervals from all seven target loci were used to survey the POPSEQ (Mascher et al, 2013a), the International Barley Genome Sequencing Consortium (2012), and the Muñoz‐Amatriaín et al (2015) datasets to integrate the genetic maps and the physical map of barley. In total, 44 (77.2%) newly developed markers showed a match to POPSEQ‐anchored WGS contigs.…”

“…The WGS contigs and the physical FPCs were linked to each other by BLAST using stringent criteria and only matches with at least 99% sequence identity and at least 90% sequence coverage of the smallest sequence (either WGS contig or a physical contig) were considered. The genetic markers from the seven loci were also compared with 15,622 recently sequenced barley clones (Muñoz‐Amatriaín et al, 2015). Marker sequences were assigned to a clone with help of the Harvest BLAST (http://www.harvest-blast.org/) when clones matched a marker with an e ‐value of ≤10 −5 and with a match length of at least 100 nucleotides.…”

“…Subsequently, the new information provided by POPSEQ was employed to order and genetically anchor the barley physical map, establishing a minimum tilling path (MTP) that comprises more than 65,000 BAC clones (Ariyadasa et al, 2014). Recently, 15,622 BACs representing the MTP of 72,052 physical‐mapped gene‐bearing BACs, were identified and sequenced (Muñoz‐Amatriaín et al, 2015).…”

A Cluster of Nucleotide‐Binding Site–Leucine‐Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL

“…However, other barley genes have not been cloned yet despite their known phenotypic effect and genetic localization, partly due to the lack of such resources until recently. The continuous improvement of barley physical resources (Ariyadasa et al, 2014; IBGSC, 2012; Mascher et al, 2013b; Muñoz‐Amatriaín et al, 2015) allows the adoption of more efficient methodologies for genetic studies involving high‐throughput genotyping, marker development, gene discovery, expression analysis, synteny and genome comparative studies. The exome capture probe set developed by Mascher et al (2013a) for barley is already being used for gene cloning purposes.…”

“…This cumbersome procedure was most challenging for species like barley due to the lack of genomic resources and its large and highly repetitive genome (Krattinger et al, 2009). However, the recent advent of high‐throughput sequencing, by means of NGS technologies, has accelerated the development of synteny resources (Mayer et al, 2011), sequenced enriched physical maps (Ariyadasa et al, 2014; International Barley Genome Sequencing Consortium [IBGSC], 2012; Mascher et al, 2013b; Muñoz‐Amatriaín et al, 2015), genotyping (Comadran et al, 2012; Poland et al, 2012), and sequence capture platforms (Mascher et al, 2013a). In consequence, gene cloning now benefits from the easier and faster genotyping of high‐resolution mapping populations, high‐throughput polymorphism detection in parental lines, and new fine mapping approaches, such as mapping‐by‐sequencing (Mascher et al, 2014).…”