Pan-Genome of Wild and Cultivated Soybeans

Liu, Yucheng; Du, Huilong; Li, Pengcheng; Shen, Yanting; Peng, Hua; Liu, Shulin; Guo, Ziyi; Zhang, Haikuan; Li, Zhi; Shi, Miao; Huang, Xuehui; Li, Yan; Zhang, Min; Wang, Zheng; Bao-cheng, Zhu; Han, Bin; Liang, Chengzhi; Tian, Zhixi

doi:10.1016/j.cell.2020.05.023

Cited by 563 publications

(571 citation statements)

References 129 publications

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“…With the advance of soybean genomics, more and more high-quality soybean genome assemblies are available (Shen et al, 2018;Valliyodan et al, 2019;Xie et al, 2019). A high-quality pan-genome of wild and cultivated soybeans are also reported recently (Liu et al, 2020). These genomes allow direct comparison of sequence of clock components from different soybean accessions which resulted in more accurate discovery of variants.…”

Section: Discussionmentioning

confidence: 99%

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Lam

2020

Front. Genet.

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Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.

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Section: Discussionmentioning

confidence: 99%

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Lam

2020

Front. Genet.

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“…The whole genome sequence of soybean Williams 82 was available in 2010 [ 138 ], which facilitated the fine mapping of genes located on quantitative trait loci (QTLs) enriched chromosomes that were associated with flooding tolerance. Since different genetic backgrounds might demonstrate varying genetic mechanisms, a pan-genome of wild and cultivated soybeans was constructed to capture the entire genomic diversity, which helped to link genetic variations for genes responsible for agronomic traits [ 139 ]. Recently, the SUB1, a QTL for the submergence tolerance for rice, was demonstrated to play a role in the combination of submergence and long-term water stagnation [ 140 ].…”

Section: Differences Between Response and Tolerant Mechanisms Agaimentioning

confidence: 99%

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Wang

Komatsu

2020

IJMS

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Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

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“…To be able to accurately call variants and represent in one dataset the variation coming from diverged lineages one needs a graph structure (Figure 2b). This is an active area of research, which has been already used in cattle and soybean [72,73]. This is also the topic of a new effort, PanOryza, led by Prof. Andy Jones, University of Liverpool, with collaborators from the European Bioinformatics Institute (EMBL-EBI), Oregon State University, University of Arizona, and IRRI.…”

Section: Digital Rice Genebank For Game-changing Researchmentioning

confidence: 99%

Advanced Strategic Research to Promote the Use of Rice Genetic Resources

et al. 2020

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International genebanks have a collection of over 760 K conserved accessions of various plants, most of these accessions are within the multi-lateral system governed by the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). However, in spite of the success in collection and conservation, only a small portion of the genetic diversity has been used in crop breeding programs. As climate change-induced new or enhanced constraints seriously hamper crop productions, researchers and breeders should be able to swiftly choose an appropriate set of genetic resources from the genebank and use them for improving crop varieties. Here, we present some advanced technologies that can effectively promote the use of diverse rice accessions held at national/international genebanks. High throughput phenotyping using multispectral imaging systems and unmanned aerial vehicles (UAV) can quickly screen large numbers of accessions for various useful traits. Such data, when combined with that from the digital rice genebank consisting of genome sequencing data, will significantly increase the efficiency in breeding efforts. Recent genome sequencing data of the rice wild species will also add to the resources available for pre-breeding efforts such as the introgression of useful genes into modern rice varieties. We expect that these advanced technologies and strategies developed through the global rice research programs will be applicable for many closely related species as well.

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Pan-Genome of Wild and Cultivated Soybeans

Abstract: Highlights d de novo genome assemblies for 26 representative soybeans d Construction of a graph-based genome d Identification of large structural variations and gene fusion events d Link structural variations to gene expressions and agronomic traits

Cited by 563 publications

References 129 publications

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Advanced Strategic Research to Promote the Use of Rice Genetic Resources

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