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Construction and comparison of three reference-quality genome assemblies for soybean.
Babu Valliyodan1,2, Steven B Cannon3, Philipp E Bayer4
1Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA.
The Plant Journal : for Cell and Molecular Biology
|August 22, 2019
Summary
Reference-quality genome assemblies for two soybean (Glycine max) cultivars and their wild relative (Glycine soja) reveal high structural conservation and genetic diversity. These resources aid in identifying traits for soybean improvement.
Area of Science:
- Genomics
- Plant Science
- Crop Science
Background:
- Soybean (Glycine max) is a crucial crop, yet comprehensive genomic resources for diverse accessions are limited.
- Understanding genetic variation between cultivated soybean and its wild progenitor (Glycine soja) is key for crop improvement.
Purpose of the Study:
- To generate high-quality genome assemblies and annotations for two key US soybean cultivars (Williams 82 and Lee) and one Glycine soja accession.
- To compare these genomes to understand structural conservation, nucleotide diversity, and patterns of introgression.
- To identify genetic variants underlying domestication and improvement traits in soybean.
Main Methods:
- High-quality genome sequencing and assembly for Glycine max (Williams 82, Lee) and Glycine soja.
- Comparative genomics to analyze structural variations, single-nucleotide polymorphisms (SNPs), and haplotype structures.
- Analysis of a pan-gene collection and investigation of five key domestication loci.
Main Results:
- Generated reference-quality genome assemblies for Williams 82, Lee, and Glycine soja.
- Identified significant nucleotide differences (1.7-4.7 SNPs/kb) and numerous inversions between accessions.
- Found distinct alleles with functional differences at five domestication loci between wild and cultivated soybean.
Conclusions:
- The new genome assemblies provide a valuable resource for soybean research and breeding.
- Comparative analysis reveals insights into soybean domestication, introgression, and genetic diversity.
- These findings will accelerate the identification of causal variants for enhancing soybean traits.
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