1RS.1BL molecular resolution provides novel contributions to wheat improvement

Ru, Zhengang; Juhász, Angéla; Li, Danping; Deng, Pingchuan; Zhao, Jing; Gao, Lifeng; Wang, Kai; Keeble‐Gagnère, Gabriel; Yang, Zujun; Li, Chang-Jiu; Wang, Daowen; Bose, Utpal; Colgrave, Michelle L.; Kong, Chuizheng; Zhao, Guangyao; Zhang, Xueyong; Liu, Xu; Cui, Guoqing; Wang, Yuquan; Niu, Zhipeng; Wu, Liang; Cui, Dangqun; Jia, Jizeng; Appels, R.; Kong, Xiuying

doi:10.1101/2020.09.14.295733

Cited by 14 publications

(10 citation statements)

References 56 publications

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“…The second map from the left is the IWGSC RefSeq 1.0 with the HC ver1.1 gene annotation, the 90k SNP annotation, the LC ver1.1 gene annotations and the SSR annotations included. The left most map is the genome sequence for the 1RS.1BL sequence from wheat cv Aikan58 ( Ru et al, 2020 ) with three sources of gene annotations included. The red dots identify the gene models predicted to be located in the QTL identified in the Svevo x Zavitan QTL.…”

Section: Wheat Reference-genome and In Silico Bioi...mentioning

confidence: 99%

Capturing Wheat Phenotypes at the Genome Level

et al. 2022

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Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

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Section: Wheat Reference-genome and In Silico Bioi...mentioning

confidence: 99%

Capturing Wheat Phenotypes at the Genome Level

et al. 2022

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“…The recent sequencing of the 1RS arm (Ru et al., 2020) revealed the presence of a large inversion between the distal region of chromosome arms 1RS (telomere to 13.875 Mb) and 1BS (telomere to 15.579 Mb; Figure 2a), which suggests that lines with breakpoints within this region, such as T‐9, T‐21 and 1B+40, may be more complex than originally thought. The 1RS RW line was generated by a crossover of the primary recombinant lines T‐9 (distal 1BS segment in a 1RS arm) and 1B+40 (distal 1RS segment in a 1BS arm) (Lukaszewski, 2000), and the previous results indicate that 1RS RW has retained the 1RS‐1BS breakpoints of T‐9 and 1B+40 (Figure 2a).…”

Section: Resultsmentioning

confidence: 94%

“…The sequencing reads were preprocessed to trim adapters with Trimmomatic v0.39 (Bolger, Lohse, & Usadel, 2014). Since the capture included both wheat and rye reads, we mapped the reads to a combined reference including wheat Chinese Spring (CS) RefSeq v1.0 chromosome 1B and the rye chromosome arm 1RS AK58 from the 1RS.1BL translocation in cultivar Aikang58 (Ru et al., 2020). To minimize off‐target mapping, we mapped the reads at high‐stringency with ‘bwa aln’ v0.7.16a‐r1181 (Li & Durbin, 2009), allowing only perfectly mapped reads (zero single nucleotide polymorphisms [SNPs]).…”

Section: Methodsmentioning

confidence: 99%

“…We report wheat gene coordinates using CS RefSeq v1.1 (International Wheat Genome Sequencing Consortium et al., 2018) and rye gene coordinates using the 1RS AK58 genome as references (Ru et al., 2020), which is almost identical to our 1RS sequence. The other available genome reference for rye inbred line Lo7 (Rabanus‐Wallace et al., 2019) is less similar to the 1RS sequences from Hahn 1RS.1BL translocation.…”

Section: Methodsmentioning

confidence: 99%

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Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length

et al. 2021

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Good understanding of the genes controlling root development is required to engineer root systems better adapted to different soil types. In wheat (Triticum aestivum L.), the 1RS.1BL wheat–rye (Secale cereale L.) translocation has been associated with improved drought tolerance and a large root system. However, an isogenic line carrying an interstitial segment from wheat chromosome arm 1BS in the distal region of the 1RS arm (1RSRW) showed reduced grain yield and shorter roots both in the field and in hydroponic cultures relative to isogenic lines with the complete 1RS arm. In this study, we used exome capture to characterize 1RSRW and its parental lines T‐9 and 1B+40. We show that 1RSRW has a 7.0 Mb duplicated 1RS region and a 4.8 Mb 1BS insertion colinear with the 1RS duplication, resulting in triplicated genes. Lines homozygous for 1RSRW have short seminal roots, while lines heterozygous for this chromosome have roots of intermediate length. By contrast, near‐isogenic lines carrying only the 1BS distal region or the 1RS‐1BS duplication have long seminal roots similar to 1RS, suggesting a limited effect of the 1BS genes. These results suggest that the dosage of duplicated 1RS genes is critical for seminal root length. An induced deletion encompassing 38 orthologous wheat and rye duplicated genes restored root length and confirmed the importance of gene dosage in the short‐root phenotype. We explored the expression profiles and functional annotation of these genes and discuss their potential as candidate genes for the regulation of seminal root length in wheat.

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“…Eventually, in the year, 2017–2018, the wheat genome of Chinese spring wheat was sequenced and released as the first reference wheat genome. With the rapid advancements in sequencing and assembly tools, many wheat cultivars were resequenced including the Chinese wheat-rye 1RS.1BL translocation cultivar “Aikang 58” ( Ru et al, 2020 ), French bread wheat cultivar “Renan” ( Aury et al, 2022 ), transformation-amenable common wheat cultivar “Fielder” ( Sato et al, 2021 ), etc.…”

Section: Whole Genome Sequencing Of Wheatmentioning

confidence: 99%

Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat

et al. 2022

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Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.

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1RS.1BL molecular resolution provides novel contributions to wheat improvement

Cited by 14 publications

References 56 publications

Capturing Wheat Phenotypes at the Genome Level

Capturing Wheat Phenotypes at the Genome Level

Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length

Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat

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