Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Dan; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz‐Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse; Bellgard, M.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul J.; Clark, Matthew D.; Cáccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

doi:10.1038/sdata.2017.44

Cited by 139 publications

(128 citation statements)

References 76 publications

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“…In graph (d), colour‐coded dots (enlarged for better visualization) correspond to positions in which 4 cM sliding windows values exceed those thresholds. Crosses at the bottom of this graph indicate the positions of well‐known flowering time and domestication genes, according to the updated popseq map (Beier et al, ), and listed in…”

Section: Resultsmentioning

confidence: 99%

“…Markers matching unmapped contigs (chrUn) or with multiple mappings, spanning different chromosomes or more than 200 kb apart, were discarded. After quality checks, 7,479 markers (5,261 Infinium, 2,218 DArTseq) were assigned unique physical positions, and their respective genetic positions (in cM) taken from the closest marker in the POPSEQ2017 map (Beier et al, ). The genetic positions of markers SCRI_RS_224392, SCRI_RS_187102, SCRI_RS_167463, BOPA2_12_30895, and BOPA2_12_30894 were interpolated based on their physical distances.…”

Section: Methodsmentioning

confidence: 99%

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Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

et al. 2019

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Landraces are local populations of crop plants adapted to a particular environment. Extant landraces are surviving genetic archives, keeping signatures of the selection processes experienced by them until settling in their current niches. This study intends to establish relationships between genetic diversity of barley ( Hordeum vulgare L.) landraces collected in Spain and the climate of their collection sites. A high‐resolution climatic data set (5 × 5 km spatial, 1‐day temporal grid) was computed from over 2,000 temperature and 7,000 precipitation stations across peninsular Spain. This data set, spanning the period 1981–2010, was used to derive agroclimatic variables meaningful for cereal production at the collection sites of 135 barley landraces. Variables summarize temperature, precipitation, evapotranspiration, potential vernalization and frost probability at different times of the year and time scales (season and month). SNP genotyping of the landraces was carried out combining Illumina Infinium assays and genotyping‐by‐sequencing, yielding 9,920 biallelic markers (7,479 with position on the barley reference genome). The association of these SNPs with agroclimatic variables was analysed at two levels of genetic diversity, with and without taking into account population structure. The whole data sets and analysis pipelines are documented and available at https://eead-csic-compbio.github.io/barley-agroclimatic-association . We found differential adaptation of the germplasm groups identified to be dominated by reactions to cold temperature and late‐season frost occurrence, as well as to water availability. Several significant associations pointing at specific adaptations to agroclimatic features related to temperature and water availability were observed, and candidate genes underlying some of the main regions are proposed.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

et al. 2019

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“…Previous studies also showed that some LHCB members of Arabidopsis were positively involved in ABA dependent processes, such as stomatal movement, response to drought [10] and seed germination [11]. This study found that there were one to five ABREs in the promoter regions of 16 HvLHCs which indicated that expression of them may be responsive to ABA. They may also play some roles in ABA regulated pathways.…”

Section: Expression Of Hvlhcs During Barley Development and Response mentioning

confidence: 62%

“…The release of the genome of barley [16] will help us a lot in the cloning and characterization of this gene family in barley. The present study focused on extensive genome-wide …”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Light Harvesting Chlorophyll a/b Binding Protein Genes in Barley (Hordeum vulgare L.)

Qin¹,

Dong²,

Xu³

et al. 2017

Adv Crop Sci Tech

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Light harvesting chlorophyll a/b binding proteins (LHC) play an important role in photosynthesis and development of plant. However, limited data is available for this important gene family in barley, especially for their biological functions. In this study, sequences of rice and Arabidopsis LHCs were used as queries to identify the respective orthologues from available barley genomic database. Total 17 non-reduntant HvLHCs were identified. Genomic sequences of these genes were ranged from 780 bp to 2779 bp in length, and ORF sequence of 738 bp to 933 bp. The phylogenetic relationship of members from barley, rice and Arabidopsis revealed that most of them were common to the three species, while some of them were specific to Arabidopsis or the poaceae family. Cis-element analysis showed that along with the universal transcription initiation and enhancement relevant elements, there were also light as well as biotic and abiotic stresses responsive elements in promoter regions of these HvLHCs. Additionally, these genes exhibited quite similar expression pattern during the development of barley plant according to the public normalized RNA-seq and barley array datasets, but responded distinctively to different treatments including dark, heat, salinity and drought, which were confirmed by quantitative real-time PCR analysis. This is the first report of identification of HvLHCs at the genome level, and results presented here would be useful not only for determining the precise role of HvLHCs during barley development and abiotic stress responses, but also for using them in molecular breeding of barley varieties with high yield or high tolerance to stresses.

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“…them to deduce sequence orders and to orient the assembly on the basis of the physical proximity of each sequence to others 4 . This approach was validated in work on the human genome 5 , and last year was used to construct a new genome 6 for the frog Xenopus laevis.…”

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confidence: 99%

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2017

Nature

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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Cited by 139 publications

References 76 publications

Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

Genome-Wide Identification and Characterization of Light Harvesting Chlorophyll a/b Binding Protein Genes in Barley (Hordeum vulgare L.)

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