Genomic differences between cultivated soybean, G. max and its wild relative G. soja (original) (raw)
Related papers
Plant Biotechnology Journal, 2020
Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
Current development and application of soybean genomics
Frontiers in Biology, 2011
Soybean (Glycine max), an important domesticated species originated in China, constitutes a major source of edible oils and high-quality plant proteins worldwide. In spite of its complex genome as a consequence of an ancient tetraploidilization, platforms for map-based genomics, sequence-based genomics, comparative genomics and functional genomics have been well developed in the last decade, thus rich repertoires of genomic tools and resources are available, which have been influencing the soybean genetic improvement. Here we mainly review the progresses of soybean (including its wild relative Glycine soja) genomics and its impetus for soybean breeding, and raise the major biological questions needing to be addressed. Genetic maps, physical maps, QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine. Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes, which are instrumental to comparative genomics and functional genomics. Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process. Microarrays resources, mutagenesis and efficient transformation systems become essential components of soybean functional genomics. Furthermore, phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development, in response to abiotic stresses, functioning in plant-pathogenic microbe interactions, and controlling the oil and protein content of seed. These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.
Genome-Wide Association Study for Agronomic Traits in Wild Soybean (Glycine soja)
Agronomy
The agronomic traits of soybean are important because they are directly or indirectly related to its yield. Cultivated soybean (Glycine max (L.) Merr) has lost genetic diversity during domestication and selective breeding. However, wild soybean (G. soja) represents a useful breeding material because it has a diverse gene pool. In this study, a total of 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were employed in the association analysis. Wild soybean accessions were divided into four clusters based on their genetic distance using ADMIXTURE, principal component analysis, and neighbor-joining clusters. The linkage disequilibrium decayed rapidly in wild soybean. A genome-wide association study was conducted for days to flowering (DtF), days to maturity (DtM), the number of pods (NoP), and the 100-seed weight (100SW), which are major agronomic traits for wild soybean accessions. A total of 22 significant SNPs were ...
Frontiers in Plant Science
Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain we...
Frontiers in Plant Science
Seed size and shape are important traits determining yield and quality in soybean. Seed size and shape are also desirable for specialty soy foods like tofu, natto, miso, and edamame. In order to find stable quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight, the current study used vegetable type and seed soybean-derived F2 and F2:3 mapping populations. A total of 42 QTLs were mapped, which were dispersed across 13 chromosomes. Of these, seven were determined to be stable QTLs and five of them were major QTLs, namely qSL-10-1, qSW-4-1, qSV-4-1, qSLW-10-1, and qSLH-10-1. Thirteen of the 42 QTLs detected in the current study were found at known loci, while the remaining 29 were discovered for the first time. Out of these 29 novel QTLs, 17 were major QTLs. Based on Protein Analysis Through Evolutionary Relationships (PANTHER), gene annotation information, and literature search, 66 genes within seven stable QTLs were predicted to be possible candidate g...
Landscape of genomic diversity and trait discovery in soybean OPEN
Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding. Legumes account for 27% of the world's primary crop production, and the legume seeds are an essential source for food and feed and also provide nitrogen fixation through symbioses with microorganisms 1. Soybean (Glycine max (L.) Merr.), a leguminous crop of major economic importance, is a main source of oil and protein 2,3. The domestication history of cultivated soybean traces back to around 5,000 years ago in China 4. Soybean was introduced to the United States (US) in the year 1765 5 , and at present soybean is the second-most planted field crop in the US. The US is currently the largest producer of soybean (34% of the global production), followed by Brazil and Argentina. The genetic diversity in soybean presumably declined to a low level due to man-made genetic bottlenecks, including selection for high yielding lines in modern plant breeding programs 6–8. Additionally, the cleistogamous characteristics of soybean may have a strong influence on genomic homogene-ity and reduced genomic variation, and this characteristic might become more sensitive during domestication practices 9. As a commercial cash crop in both the developing and developed world, the genomic information of soybean is essential for discovering traits for crop improvement. This information will help to further investigate the genetic bottleneck that causes a change in allele frequencies and causes low genetic diversity and high linkage disequilibrium (LD), eliminating rare alleles in the selected populations/lines. In 2010, the first cultivated soybean genome was sequenced 10. That was followed by Glycine soja, the undomesticated ancestor of Glycine max 11. This wild soybean genome represents a 97.65% coverage of the published G. max genome, and the comparative genomic analysis shows significant differences between the genomic compositions of the 2 soybean lines 12,13. Advances in the next generation sequencing (NGS) technologies have made crop genome sequencing easier and more cost effective, and as a result, several crop genomes were sequenced, for example, rice (Oryza sativa) 14 , maize (Zea maize) 15 , cucumber (Cucumis sativus) 16 , sorghum (Sorghum bicolor) 17 , and common bean (Phaseolus vulgaris) 18. Another key application of NGS technologies is in the re-sequencing of crop genomes at a desirable genomic equivalent depth to capture the domestication signature and any rare allelic variations 8,19–21. Only a few re-sequencing reports are available for soybean genomes 8,13,22,23,25. At the same time, more pan genomes, mainly
Genetics, Genomics, and Breeding of Soybean
CRC Press eBooks, 2016
xii Genetics, Genomics and Breeding of Soybean germplasm (Chapter 8) provide comprehensive reviews in the respective areas. In recent years an understanding of the composition and organization of the soybean genome has developed. This has been the result of numerous advances in functional and structural genomics. In addition to development of an integrated genetic-physical map and DNA sequencing, large scale comparative and functional genomics studies are in progress. Recently, the US Department of Energy Joint Genome Institute (DOE JGI) has released a 7x sequence coverage of the soybean genome, making it widely available to the research community to advance new breeding strategies. Two chapters describe the recent advances in soybean functional genomics (Chapter 9) and whole genome sequencing (Chapter 10). Soybean is also an attractive choice for comparative genomics and genome evolution studies as it is a major food crop, a legume (a large and diverse plant family that is both ecologically and economically important), and is an ancient polyploid. Soybean is known to have undergone two rounds of whole genome duplication since its divergence from the Rosid clade. The soybean genome is highly duplicated which complicates genome mapping and sequencing. Recent advances in soybean comparative genomics are highlighted in Chapter 11. Chapter 12, discusses common types of data that are currently available to be used in bioinformatic analysis including specific databases that exist and numerous tools that can be utilized and can aid the soybean community. Insights into soybean proteomics and metabolomics are accelerating at an impressive rate and are reviewed in chapters on proteomics (Chapter 13) and metabolomics (Chapter 14). The book ends with a chapter on future prospects of the soybean crop (Chapter 15). In the 15 chapters, reputed specialists provide concise and comprehensive reviews on the current status of soybean genome research. Each chapter has been written by one or more experts who have worked diligently in compiling information about their respective areas of expertise. We greatly appreciate their effort and time devoted to this book. We hope that this book is useful to soybean researchers as well as to people working with other crop species.