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Journal ArticleDOI: 10.1016/J.CELL.2021.01.013

A route to de novo domestication of wild allotetraploid rice

04 Mar 2021-Cell (Cell Press)-Vol. 184, Iss: 5
Abstract: Summary Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness However, a workable route remains elusive Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece With these resources, we show that six agronomically important traits could be rapidly improved by editing O alta homologs of the genes controlling these traits in diploid rice Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security

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Topics: Domestication (53%), Genome evolution (50%)
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41 results found


Journal ArticleDOI: 10.1016/J.CELL.2021.01.005
Caixia Gao1Institutions (1)
18 Mar 2021-Cell
Abstract: Feeding the ever-growing population is a major challenge, especially in light of rapidly changing climate conditions. Genome editing is set to revolutionize plant breeding and could help secure the global food supply. Here, I review the development and application of genome editing tools in plants while highlighting newly developed techniques. I describe new plant breeding strategies based on genome editing and discuss their impact on crop production, with an emphasis on recent advancements in genome editing-based plant improvements that could not be achieved by conventional breeding. I also discuss challenges facing genome editing that must be overcome before realizing the full potential of this technology toward future crops and food production.

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Topics: Genome editing (55%), Population (51%)

43 Citations


Journal ArticleDOI: 10.1007/S00299-021-02708-2
Sukumar Biswas1, Dabing Zhang1, Jianxin Shi1Institutions (1)
11 May 2021-Plant Cell Reports
Abstract: Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.

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Topics: CRISPR (55%), Population (51%)

7 Citations


Journal ArticleDOI: 10.1093/JXB/ERAB276
Ali Razzaq1, Shabir H. Wani2, Fozia Saleem1, Min Yu3  +3 moreInstitutions (4)
Abstract: To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year–1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.

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Topics: Climate resilience (54%), Food security (53%), Domestication (52%)

6 Citations


Open accessJournal ArticleDOI: 10.1016/J.XPLC.2021.100211
Shaoya Li1, Chen Zhang1, Jingying Li1, Lei Yan1  +2 moreInstitutions (1)
12 Jul 2021-
Abstract: Wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) is one of the most important staple food crops in the world. Despite the fact that wheat production has significantly increased over the past decades, future wheat production will face unprecedented challenges from global climate change, increasing world population, and water shortages in arid and semi-arid lands. Furthermore, excessive applications of diverse fertilizers and pesticides are exacerbating environmental pollution and ecological deterioration. To ensure global food and ecosystem security, it is essential to enhance the resilience of wheat production while minimizing environmental pollution through the use of cutting-edge technologies. However, the hexaploid genome and gene redundancy complicate advances in genetic research and precision gene modifications for wheat improvement, thus impeding the breeding of elite wheat cultivars. In this review, we first introduce state-of-the-art genome-editing technologies in crop plants, especially wheat, for both functional genomics and genetic improvement. We then outline applications of other technologies, such as GWAS, high-throughput genotyping and phenotyping, speed breeding, and synthetic biology, in wheat. Finally, we discuss existing challenges in wheat genome editing and future prospects for precision gene modifications using advanced genome-editing technologies. We conclude that the combination of genome editing and other molecular breeding strategies will greatly facilitate genetic improvement of wheat for sustainable global production.

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4 Citations


Open accessJournal ArticleDOI: 10.3389/FGENE.2021.637141
Rakesh Kumar1, Vinay Sharma2, S. Suresh1, Devade Pandurang Ramrao1  +9 moreInstitutions (4)
Abstract: In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants

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Topics: Domestication (50%)

4 Citations


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139 results found


Open accessJournal ArticleDOI: 10.1093/NAR/22.22.4673
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

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Topics: Gap penalty (62%), Multiple sequence alignment (61%), Structural alignment (58%) ... read more

61,038 Citations


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP352
Heng Li1, Bob Handsaker2, Alec Wysoker2, T. J. Fennell2  +5 moreInstitutions (4)
01 Aug 2009-Bioinformatics
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

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Topics: Variant Call Format (62%), Stockholm format (61%), FASTQ format (56%) ... read more

35,747 Citations


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP324
Heng Li1, Richard Durbin1Institutions (1)
01 Jul 2009-Bioinformatics
Abstract: Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: [email protected]

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Topics: Hybrid genome assembly (54%), Sequence assembly (53%), 2 base encoding (52%) ... read more

35,234 Citations


Open accessJournal Article
01 Jan 1989-Cladistics
Topics: Inference (55%)

16,846 Citations


Open accessJournal ArticleDOI: 10.1101/GR.107524.110
Aaron McKenna1, Matthew Hanna, Eric Banks, Andrey Sivachenko  +7 moreInstitutions (1)
01 Sep 2010-Genome Research
Abstract: Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

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Topics: Variant Call Format (52%), Software framework (50%)

16,404 Citations


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