Article

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

United States Department of Agriculture-Agricultural Research Service, Plant Research Unit, St Paul, MN 55108, USA.
BMC Plant Biology (Impact Factor: 3.94). 03/2010; 10:41. DOI: 10.1186/1471-2229-10-41
Source: PubMed

ABSTRACT 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.

1 Follower
 · 
194 Views
  • Source
    [Show abstract] [Hide abstract]
    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 · 3.94 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Seed protein content is one of the most important traits controlled by quantitative trait loci (QTLs) in soybean. In this study, a Glycine soja accession (ZYD2738) was crossed with two elite cultivars Jidou 12 and Jidou 9 separately and subsequently the resulting F2:3 populations were used to identify QTLs associated with seed protein content. Protein contents in either population appeared to have a normal distribution with transgressive segregation. A total of five QTLs associated with high protein content were identified and mapped to chromosomes 2, 6, 13, 18 and 20, respectively. Of these QTLs, three (qPRO_2_1, qPRO_13_1 and qPRO_20_1) were identified in the same region in both the populations, whereas the other two (qPRO_6_1 and qPRO_18_1) were mapped in two different regions. qPRO_2_1 appears to be a novel protein QTL. qPRO_6_1, qPRO_18_1 and qPRO_20_1 had additive effects on seed protein content, while qPRO_13_1 had an over-dominant effect on seed protein content. These QTLs and their linked markers could serve as effective tools for marker-assisted selection to increase seed protein content.
    Plant Genetic Resources 07/2014; 12(S1):S104-S108. DOI:10.1017/S1479262114000379 · 1.06 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [Glycine max (L.) Merr.] recombinant inbred line (RIL) population and produced a genome-wide expression quantitative trait loci (eQTL) dataset. The validity of the dataset was confirmed by mapping the eQTL hotspot for flavonoid biosynthesis-related genes to a region containing repeats of chalcone synthase (CHS) genes known to correspond to the soybean inhibitor locus that regulates seed color. We then identified eQTL for genes with seed-specific expression and discovered striking eQTL hotspots at distinct genomic intervals on chromosomes (Chr) 20, 7, and 13. The main eQTL hotspot for transcriptional regulation of fatty acid biosynthesis genes also coincided with regulation of oleosin genes. Transcriptional upregulation of genesets from eQTL with opposite allelic effects were also found. Gene–eQTL networks were constructed and candidate regulatory genes were identified from these three key loci specific to seed expression and enriched in genes involved in seed oil accumulation. Our data provides new insight into the complex nature of gene networks in the immature soybean seed and the genetic architecture that contributes to seed development.
    The Plant Genome 03/2014; 7(1):1-14. DOI:10.3835/plantgenome2013.08.0027 · 3.88 Impact Factor

Full-text (3 Sources)

Download
59 Downloads
Available from
Jun 4, 2014