Anchoring and ordering <scp>NGS</scp> contig assemblies by population sequencing (<scp>POPSEQ</scp>)

Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Muñoz‐Amatriaín, María; Close, Timothy J.; Wise, Roger P.; Schulman, Alan H.; Himmelbach, Axel; Mayer, Klaus; Scholz, Uwe; Poland, Jesse; Stein, Nils; Waugh, Robbie

doi:10.1111/tpj.12319

Cited by 257 publications

(344 citation statements)

References 30 publications

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“…However, chromosomal locations could be assigned to only about half of all physical contigs through the integration of marker sequences from various genetic maps with BAC contigs. In this study, we applied a new approach for integrating the physical map with genetic maps by extending the POPSEQ method originally developed (Mascher et al, 2013) for fragmented whole-genome assemblies to physical contig assemblies. This novel straightforward approach was able to anchor more contigs than the complex, multilayered strategy presented earlier.…”

Section: Discussionmentioning

confidence: 99%

“…3B). Similar to the anchoring of WGS contigs (Mascher et al, 2013), discordant contig placements mostly occurred in the genetic centromere. Although the POPSEQ anchoring contains 14% more contigs than the published physical and genetic framework (The International Barley Genome Sequencing Consortium, 2012), the cumulative length of all anchored contigs increases by only 1.3%.…”

Section: Anchoring the Physical Map By Popseqmentioning

confidence: 99%

“…As a proof of concept, shallow sequencing two small biparental mapping populations was shown to greatly improve the genetic anchoring of the International Barley Genome Sequencing Consortium whole-genome shotgun assembly of the barley cv Morex (Mascher et al, 2013). While we demonstrated that POPSEQ anchoring of a whole-genome shotgun assembly is independent of physical map construction, we also argued that the data obtained should expedite the ongoing physical mapping project.…”

mentioning

confidence: 92%

“…Most contigs without genetic or chromosomal positions were either short or lacked sequence or marker information. We recently introduced the POPSEQ approach to genetically anchor highly fragmented sequence assemblies by whole-genome sequencing of individuals of a segregating population (Mascher et al, 2013). The same methodology may be used to place BAC contigs or single BAC clones into a genetic framework.…”

Section: Anchoring the Physical Map By Popseqmentioning

confidence: 99%

“…We had previously anchored the whole-genome shotgun assembly of barley cv Morex (Mascher et al, 2013). Sequences of anchored WGS contigs were compared with fully sequenced BACs and BAC end sequences of barley (The International Barley Genome Sequencing Consortium, 2012) by megablast (Zhang et al, 2000) and thus assigned to physical contigs.…”

Section: Popseq Anchoring Of Physical Contigs and Bac Clonesmentioning

confidence: 99%

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A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

et al. 2013

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Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.

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Section: Discussionmentioning

confidence: 99%

Section: Anchoring the Physical Map By Popseqmentioning

confidence: 99%

mentioning

confidence: 92%

Section: Anchoring the Physical Map By Popseqmentioning

confidence: 99%

Section: Popseq Anchoring Of Physical Contigs and Bac Clonesmentioning

confidence: 99%

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A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

et al. 2013

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Development of barley introgression lines carrying the leaf rust resistance genes Rph1 to Rph15

et al. 2020

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In many production areas, barley (Hordeum vulgare L.) is attacked by the leaf rust pathogen (Puccinia hordei Otth), a basidiomycetous fungus that reduces both its yield and quality. Many leaf rust resistance genes, known as reaction to P. hordei (Rph) genes, have been described in barley. To differentiate genetic variants for virulence in pathogen populations, plant pathologists use differentials (i.e., sets of host lines carrying different resistance genes). The sources of Rph1–15 were derived from cultivars, landraces, and wild barley (H. vulgare ssp. spontaneum K. Koch) accessions with diverse geographic origins and agromorphological traits. Ideal differential sets comprise single‐gene lines backcrossed to a single adapted accession that is susceptible to all known races of a pathogen. In this study, sources of Rph1–15 and other Rph gene donors were backcrossed to the susceptible barley cultivar Bowman and then genotyped to characterize the chromosomal positions and sizes of introgressions. Overall, 95 Bowman introgression lines for leaf rust resistance were developed and characterized for their rust phenotypes and genotypes. A single line was selected to represent each of the 15 Rph genes for use as the new barley leaf rust differential set. The existence of possible new resistance genes in the studied germplasm was postulated. The new Bowman Rph1–15 differential lines will facilitate the efficient virulence phenotyping of P. hordei and serve as valuable genetic stocks for Rph gene stacking and cloning in barley.

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Identifying developmental QTL alleles with favorable effect on grain yield components under late‐terminal drought in spring barley MAGIC population

et al. 2023

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Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield‐related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above‐ground yield‐related traits under well‐watered (WW) and late‐terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd‐H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late‐terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.

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Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Cited by 257 publications

References 30 publications

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

Development of barley introgression lines carrying the leaf rust resistance genes Rph1 to Rph15

Identifying developmental QTL alleles with favorable effect on grain yield components under late‐terminal drought in spring barley MAGIC population

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