Publisher Correction: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

He, Fei; Pasam, Raj K.; Shi, Fan; Kant, Surya; Keeble‐Gagnère, Gabriel; Kay, Pippa; Forrest, Kerrie; Fritz, Allan K.; Hucl, P.; Wiebe, Krystalee; Knox, Ron; Cuthbert, Richard D.; Pozniak, Curtis; Akhunova, Alina; Morrell, Peter L.; Davies, John P.; Webb, Steve R.; Spangenberg, Germán; Hayes, Ben J.; Daetwyler, Hans D.; Tibbits, Josquin; Hayden, Matthew; Akhunov, Eduard

doi:10.1038/s41588-019-0463-2

Cited by 8 publications

(11 citation statements)

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“…Several large introgression blocks in pericentromeric regions have been reported 3 , 5 , 26 , 48 , and the chromosome-scale mosaic pan-ancestry haploblock map also revealed large stable AHG blocks in the central zone of the chromosome (centAHG) (Supplementary Fig. 10 ).…”

Section: Resultsmentioning

confidence: 92%

“…Wild emmer wheat is regarded as the progenitor of domesticated tetraploid wheat 7 , and accumulated evidence indicates that pervasive introgression in hexaploid wheat occurs from wild emmers 3 – 5 , implying a complicated phylogeny. We computed the AHG-based contribution of each WE accession to the domesticated polyploid wheat gene pool and identified a total of 12 WE accessions in the Fertile Crescent, belonging to six lineages (Supplementary Data 1 ), that were basal to DT (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Routes (curves) were inferred from the phylogenetic relationship of the three main 3B centAHGs in landraces (pie chart) and directions (arrows) were determined by manual consolidation of the literatures. An additional 281 landraces from previously published studies with geographical information available were added 5 , 18 , 48 . The geographical locations of WE accessions carrying 3B-Cent-H1 and DT accessions carrying 3B-Cent-H2 and 3B-Cent-H3 are labeled.…”

Section: Resultsmentioning

confidence: 99%

“…As one of the staple crops worldwide, the reticulate evolutionary nature of wheat has long been recognized, and pervasive introgressions have been reported among (sub-)species 2 . Recent studies showed that bread wheat received composite introgression from tetraploid relatives 3 – 5 , facilitating its adaptation to diverse environments and resistance to biotic stress 5 , by bringing allelic resources available 6 . The genetic mechanism of the reticulate evolution is crucial to understand the domestication process of polyploid wheat and the origin of their broad adaptation.…”

Section: Introductionmentioning

confidence: 99%

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Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference

Wang

Xie

et al. 2022

Nat Commun

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Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference

Wang

Xie

et al. 2022

Nat Commun

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“…There are three basic approaches for generating sequence data for genome wide variant detection against a genome reference including whole genome sequencing (WGS), genotype-by-sequencing (GBS), and whole exome capture (WEC) sequencing, each with different strengths and applications. WGS covers the whole genome including the large non-coding genomic sequence regions [ 1 , 2 ] while WEC focuses on the coding exome [ 3 , 4 ]. GBS applies specific restriction enzymes for genome reduction followed by barcoding samples, and works for both large and small genomes [ 5 – 10 ].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of variant calling tools for large plant genome re-sequencing

et al. 2020

Self Cite

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Background Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies for eco-geographical adaption, genotyping crop germplasm collections, and others. Accurately detecting SNPs from large polyploid crop genomes such as wheat is crucial and challenging. A few variant calling methods have been previously developed but they show a low concordance between their variant calls. A gold standard of variant sets generated from one human individual sample was established for variant calling tool evaluations, however hitherto no gold standard of crop variant set is available for wheat use. The intent of this study was to evaluate seven SNP variant calling tools (FreeBayes, GATK, Platypus, Samtools/mpileup, SNVer, VarScan, VarDict) with the two most popular mapping tools (BWA-mem and Bowtie2) on wheat whole exome capture (WEC) re-sequencing data from allohexaploid wheat. Results We found the BWA-mem mapping tool had both a higher mapping rate and a higher accuracy rate than Bowtie2. With the same mapping quality (MQ) cutoff, BWA-mem detected more variant bases in mapping reads than Bowtie2. The reads preprocessed with quality trimming or duplicate removal did not significantly affect the final mapping performance in terms of mapped reads. Based on the concordance and receiver operating characteristic (ROC), the Samtools/mpileup variant calling tool with BWA-mem mapping of raw sequence reads outperformed other tests followed by FreeBayes and GATK in terms of specificity and sensitivity. VarDict and VarScan were the poorest performing variant calling tools with the wheat WEC sequence data. Conclusion The BWA-mem and Samtools/mpileup pipeline, with no need to preprocess the raw read data before mapping onto the reference genome, was ascertained the optimum for SNP calling for the complex wheat genome re-sequencing. These results also provide useful guidelines for reliable variant identification from deep sequencing of other large polyploid crop genomes.

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