A reference genome for common bean and genome-wide analysis of dual domestications

By J. Schmutz, P. McClean, S. Mamidi, G. A. Wu, Steven B. Cannon, J. Grimwood, J. Jenkins, S. Shu, Qijian Song, Carolina Chavarro and 31 more. Nature Genetics, 2014

1,188 citations recorded by the source corpus.

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/1d4d7d048a52bc10c87ed09718d7a80afaa81972

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In Plant Science

1. J. Beaver
2. M. Blair
3. Phillip N. Miklas
4. J. Kelly
5. Perry B. Cregan
6. Sezai Ercisli
7. M. Grusak
8. J. Osorno

Citations in the corpus

• (Non)Parallel Evolution (2018, background): “Across the 27,197 genes surveyed, 1,835 and 748 exhibited signatures of selection in these respective geographic replicates, but only 59 appear to be selected in both regions (0.2% of all genes, which does not exceed null expectations) (Schmutz et al. 2014).”
• Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics (2021, methodology): “[14] and is beneficial in the genome study of crops with higher genome size like soybean [10].”
• A Phaseolus vulgaris Diversity Panel for Andean Bean Improvement (2015, methodology): “55, september–october 2015 is created by a bottleneck that reduced diversity in wild Andean beans long before domestication (Bitocchi et al., 2013; Schmutz et al., 2014).”
• A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.) (2019, methodology): “Domestication bottlenecks have likely further reduced the capacity for responses to some stresses such as drought conditions and particular pathogens (Bitocchi et al. 2013; Schmutz et al. 2014).”
• COLLETOTRICHUM LINDEMUTHIANUM, THE CAUSAL AGENT OF BEAN ANTHRACNOSE (2017, background): “The availability of bean genome sequence (Schmutz et al., 2014) and SNP markers in BARCBean6K_3 BeadChip (Hyten et al., 2010; Song et al., 2015) has given fresh impetus to the bean scientific community to map R genes.”