Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biol 10:41

United States Department of Agriculture-Agricultural Research Service, Plant Research Unit, St Paul, MN 55108, USA.
BMC Plant Biology (Impact Factor: 3.81). 03/2010; 10(1):41. DOI: 10.1186/1471-2229-10-41
Source: PubMed


The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content.
A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix Soy GeneChip and high-throughput Illumina whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region.
This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

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    • "A large number of quantitative trait loci (QTL) and genome-wide association study loci determining population variation in protein concentration have been described (Zhao-Ming et al. 2011, Pathan et al. 2013, Yesudas et al. 2013, Hwang et al. 2014, Qi et al. 2014, Wang et al. 2014, Sonah et al. 2015). However , the corresponding genes remain to be identified (Bolon et al. 2010, Joshi et al. 2013, Lestari et al. 2013). "
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    DESCRIPTION: In soybean seed, increased asparaginase activity was associated with a reduction in free asparagine levels as a percentage of total free amino acids, by 11–18%, and an increase in free aspartic acid levels, by 25–60%.
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    • "doi:10.3835/plantgenome2015.04.0024 This genetic map interval has a corresponding physical distance of 8.4 Mb, from 24.54 Mb to 32.92 Mb on chromosome 20 (Bolon et al., 2010). Hwang et al. (2014) further narrowed down the candidate region to a 3 Mb region located between 27.6 Mb to 30.0 Mb on the same chromosome. "
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    ABSTRACT: Population structure analyses and genome-wide-association studies (GWAS) conducted on crop germplasm collections provide valuable information on the frequency and distribution of alleles governing economically important traits. The value of these analyses is substantially enhanced when the accession numbers can be increased from ~1K to~ 10K or more. In this research we conducted the first comprehensive analysis of population structure on the collection of 14K soybean accessions (Glycine max and G. soja) using a 50K SNP chip. Accessions originating from Japan were relatively homogenous and distinct from the Korean accessions. As a whole, both Japanese and Korean accessions diverged from the Chinese accessions. The ancestry of founders of the American accessions derived mostly from two Chinese subpopulations, which reflects the composition of the American accessions as a whole. A 12K-accession GWAS conducted on seed protein and oil is the largest reported to date in plants and identified SNPs with strong signals on chromosomes 20 and 15. A chromosome 20 region previously reported to be important for protein and oil content was further narrowed and now contains only three plausible candidate genes. The haplotype effects show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects or multiple closely linked loci in repulsion phase linkage. The vast majority of accessions carry the haplotype allele conferring lower protein and higher oil. Our results provide a fuller understanding of the distribution of genetic variation contained within the USDA soybean collection and how it relates to phenotypic variation for economically important traits.
    The Plant Genome 07/2015; doi: 10.3835/plantgenome2015.04.0024(3). DOI:10.3835/plantgenome2015.04.0024 · 3.93 Impact Factor
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    • "SSR markers in the vicinity of QTL underlying traits of agronomic importance tend to show a stronger level of genetic differentiation between wild and cultivated types than those unlinked to a known QTL [57]. When the location of the present SNP set was aligned with domestication-related QTL, it was established that six SNP locus outliers were linked to a domestication QTL, controlling the traits such as twining habit, maturity time, flower color, seed weight, protein content and resistance to soybean cyst nematode [58-62] (Additional file 3). In addition, eight of the SNP locus outliers are located around 1 Mbp distant from a QTL mapped in a population bred from a cross between a wild accession and a cultivated line [59-62]. "
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    ABSTRACT: Background Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication.ResultsThe wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color.Conclusions Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool.
    BMC Plant Biology 09/2014; 14(1):251. DOI:10.1186/s12870-014-0251-1 · 3.81 Impact Factor
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