Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement

Zhou, Yun; Bai, Shenglong; Li, Hao; Sun, Guiling; Zhang, Dale; Ma, Feifei; Zhao, Xinpeng; Nie, Fang; Li, Jingyao; Chen, Liyang; Lv, Linlin; Zhu, Lele; Fan, Ruixiao; Ge, Yifan; Shaheen, Aaqib; Guo, Guanghui; Zhang, Zhen; Ma, Jianchao; Liang, Huihui; Qiu, Xiaolong; Hu, Jiamin; Sun, Taixiang; Hou, Jingyi; Xu, Hongxing; Xue, Shulin; Jiang, Wenkai; Huang, Jinling; Li, Suoping; Zou, Changsong; Song, Chun‐Peng

doi:10.1038/s41477-021-00934-w

Cited by 92 publications

(59 citation statements)

References 105 publications

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“…tauschii (Additional file 2 : Fig. S6a-e, Additional file 1 : Table S7) [ 35 ]. To reduce the effects of genome assembly errors on the analysis of chromatin interactions, we re-mapped OCEAN-C data of the T. durum and Ae.…”

Section: Resultsmentioning

confidence: 99%

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

et al. 2022

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Background Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome. Results Here we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions show expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives. Conclusions Our results reveal open chromatin interactions in different wheat species, which provide new insights into the role of open chromatin interactions in gene expression during the evolution of polyploid wheat.

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Section: Resultsmentioning

confidence: 99%

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

et al. 2022

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“…The genomes of wild progenitors and wheat relatives, especially for the pan-genome, are still required to identify new NLRs, such as diploid DD lineage strangulata, meyeri, and anathera. Song's group has assembled four new reference genomes for the diploid DD lineage and established a rapid introgression platform for wheat breeding and improvement [42]. This will help to restore the diversity of the modern wheat D genome, which seriously restricts current selective breeding.…”

Section: Discussionmentioning

confidence: 99%

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Cheng

2021

CIMB

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Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.

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“…tauschii accession that has been introgressed, we also looked at the genes within the orthologous region in four other available chromosome-level Ae. tauschii assemblies (28). Between accessions, this region varies between 1.49Mbp and 1.82Mbp in length from and contains between 26 and 33 genes ( Table S6 ).…”

Section: Resultsmentioning

confidence: 99%

“…Paired-end whole-genome sequencing data for the Ae. tauschii reference accession AL8/78 (26) and 5 additional accessions that represent 5 different clades (28), 4 Secale cereale accessions (68), Secale. vavilovii (68), Thinopyrum ponticum (69), and T. aestivum cultivars Weebil (69), Norin61 (69) and Pavon76 (46) were mapped to RefSeq v1.0 (27), filtered and SNP called as described for the genotyping above and in (25).…”

Section: Methodsmentioning

confidence: 99%

Exotic alleles contribute to heat tolerance in wheat under field conditions

Molero

Coombes

Joynson

et al. 2022

Preprint

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Global warming is one of the most significant threats to food security. With temperatures predicted to rise and extreme weather events becoming more common we must safeguard food production by developing crop varieties that are more tolerant to heat stress without compromising yield under favourable conditions. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genome-wide association analysis revealed three marker trait associations, which together increase yield under heat stress by over 50% compared to lines without the advantageous alleles and was associated with approximately 2°C lower canopy temperature. We identified an Aegilops tauschii introgression underlying the most significant of these associations. By comparing overlapping recombination of this introgressed segment between lines, we identified a 1.49Mbp region of the introgression responsible for this association that increases yield under heat stress by 32.4%. The genes within this region were extracted from diverse Ae. tauschii genomes, revealing a novel Ae. tauschii MAPK gene, a SOC1 orthologue and a pair of type-B two-component response regulators. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climate uncertainty with no yield penalty under favourable conditions.

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Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement

Cited by 92 publications

References 105 publications

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Exotic alleles contribute to heat tolerance in wheat under field conditions

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