2018
DOI: 10.1126/science.aar7191
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Shifting the limits in wheat research and breeding using a fully annotated reference genome

Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat developme… Show more

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Cited by 2,092 publications
(1,428 citation statements)
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References 184 publications
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“…The GWAS was performed by fitting the compressed mixed linear model (Zhang et al, 2010) using the rrBLUP package version 4.5 (Endelman, 2011) in the R environment, version 3.4.0 (R Core Team, 2013). Marker S1B_83207071 (the marker naming implies the 83,207,071th nucleotide position alongside chromosome 1B, according to assembly v1.0 reported by Appels et al, 2018) was significantly associated with FY, WA, and SO; markers IWB27057 and S7D_394187210 were significantly associated with SO and SU; and marker S2A_610999949 was associated with FY and SU. Descriptive statistics and heritability of the milling and baking quality traits.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…The GWAS was performed by fitting the compressed mixed linear model (Zhang et al, 2010) using the rrBLUP package version 4.5 (Endelman, 2011) in the R environment, version 3.4.0 (R Core Team, 2013). Marker S1B_83207071 (the marker naming implies the 83,207,071th nucleotide position alongside chromosome 1B, according to assembly v1.0 reported by Appels et al, 2018) was significantly associated with FY, WA, and SO; markers IWB27057 and S7D_394187210 were significantly associated with SO and SU; and marker S2A_610999949 was associated with FY and SU. Descriptive statistics and heritability of the milling and baking quality traits.…”
Section: Resultsmentioning
confidence: 99%
“…The wheat lines were grown at Wooster, OH, and Warsaw, VA, in 2 yr (2012 and 2013). Based on the annotated wheat genome IWGSC RefSec v1.0 (Appels et al, 2018), we screened for any gene within 250-kb physical distance of the SNP representing the identified MTAs. The same germplasm was used by Huang et al (2016) to study genomic selection for trait stability.…”
Section: Methodsmentioning
confidence: 99%
“…Bread wheat possesses an allohexaploid genome composed of three closely related subgenomes, causing substantial redundancy. The bread wheat genome was sequenced fairly recently, using a chromosome‐based approach, and high‐quality sequence information and annotations are available only now (Eversole, , Appels et al, ). The resulting data have begun to reveal how interchromosomal and intrachromosomal gene duplication has been driving wheat adaptation (Choulet et al, ).…”
Section: Discussionmentioning
confidence: 99%
“…The TASSEL 5 (Trait Analysis by aSSociation Evolution and Linkage) GBS v2 pipeline (Glaubitz et al 2014) was used to call marker polymorphisms, and the minor allele frequency for single nucleotide polymorphism (SNP) discovery was set to 0.01. The markers were anchored to the International Wheat Genome Sequencing Consortium’s (IWGSC) first version of the reference sequence (RefSeq v1.0) assembly of the bread wheat variety Chinese Spring (The International Wheat Genome Sequencing Consortium 2018). The alignment of 6,075,743 unique tags with Bowtie2 (Langmead and Salzberg 2012) resulted in the overall alignment of 63.98% of the tags, with 28.92% unique alignments and 35.06% multiple alignments.…”
Section: Methodsmentioning
confidence: 99%