2020
DOI: 10.1016/j.cell.2020.05.023
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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

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Cited by 643 publications
(625 citation statements)
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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%
“…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 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%
“…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%