Soon-Chun Jeong

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja, the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja. This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max. In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja/G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes

Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.

Genetic Analysis of Genes Controlling Natural Variation of Seed Coat and Flower Colors in Soybean

Soybean exhibits natural variation in flower and seed coat colors via the deposition of various anthocyanin pigments in the respective tissues. Although pigmentation in seeds or flowers has been well dissected at molecular level in several plant species, the genes controlling natural variation in anthocyanin traits in the soybean are not completely understood. To evaluate the genetic correlation between genetic loci and genes, 8 enzyme-encoding gene families and a transcription factor were localized in a soybean genome-wide genetic map. Among the seed coat color-controlling loci, the genetic location of the gene encoding for W1 was substantiated in the context of the current soybean molecular genetic map and O was postulated to correspond to anthocyanidin reductase. Among the genetic loci that regulate flower pigmentation, the genetic locations of the genes encoding for W1, W4, and Wp were identified, W3 was mapped on soybean linkage group B2 (chromosome 14), and W2 was postulated to correspond to an MYB transcription factor. Correlation studies between the developed markers and 3 color-controlling loci provided important empirical data that should prove useful in the design of marker-assisted breeding schemes as well as future association studies involving soybean.

Development, validation and genetic analysis of a large soybean SNP genotyping array

Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180,961 SNPs for creation of the Axiom(®) SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170,223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.

Expression of the Arabidopsis AtMYB44 gene confers drought/salt-stress tolerance in transgenic soybean

AtMYB44, a member of the subgroup 22 R2R3 MYB transcription factors, positively regulates abscisic acid signaling to induce stomatal closure, thus conferring drought/salt-stress tolerance in Arabidopsis thaliana. In this study, AtMYB44 was transformed into soybean [Glycine max (L.) Merrill] using the cotyledonary-node method. The resulting homozygous lines were shorter than the non-transgenic controls (Bert) throughout the growth period when grown in a greenhouse. The transgenic soybeans exhibited significantly enhanced drought/salt-stress tolerance, as observed in Arabidopsis. In field cultivation studies, the transgenic soybean plants showed reduced growth, but much higher yields upon seed harvest, demonstrating improved environmental stress tolerance. The amino acid and fatty acid compositions were not significantly altered in seeds harvested from the transgenic lines. These results suggest that the interaction of AtMYB44 with specific sequences in target gene promoters and/or specific proteins activates a tolerance mechanism that is conserved in Arabidopsis and soybean.

Transgenic poplar trees expressing yeast cadmium factor 1 exhibit the characteristics necessary for the phytoremediation of mine tailing soil.

Genetic engineering of plants for phytoremediation is thought to be possible based on results using model plants expressing genes involved in heavy metal resistance, which improve the plants tolerance of heavy metals and accumulation capacity. The next step of progress in this technology requires the genetic engineering of plants that produce large amounts of biomass and the testing of these transgenic plants in contaminated soils. Thus, we transformed a sterile line of poplar Populus alba X P. tremula var. glandulosa with a heavy metal resistance gene, ScYCF1 (yeast cadmium factor 1), which encodes a transporter that sequesters toxic metal(loid)s into the vacuoles of budding yeast, and tested these transgenic plants in soil taken from a closed mine site contaminated with multiple toxic metal(loid)s under greenhouse and field conditions. The YCF1-expressing transgenic poplar plants exhibited enhanced growth, reduced toxicity symptoms, and increased Cd content in the aerial tissue compared to the non-transgenic plants. Furthermore, the plants accumulated increased amounts of Cd, Zn, and Pb in the root, because they could establish an extensive root system in mine tailing soil. These results suggest that the generation of YCF1-expressing transgenic poplar represents the first step towards producing plants for phytoremediation. The YCF1-expressing poplar may be useful for phytostabilization and phytoattenuation, especially in highly contaminated regions, where wild-type plants cannot survive.

The Rsv3 Locus Conferring Resistance to Soybean Mosaic Virus is Associated with a Cluster of Coiled-Coil Nucleotide-Binding Leucine-Rich Repeat Genes

The Soybean mosaic virus (SMV) resistance locus, Rsv3, previously mapped between markers A519F/R and M3Satt in the soybean molecular linkage group B2 (chromosome 14), has been characterized by examination of the soybean genome sequence. The 154 kbp interval encompassing Rsv3 contains a family of closely related coiled‐coil nucleotide‐binding leucine‐rich repeat (CC‐NB‐LRR) genes. Tightly linked to this region are additional CC‐NB‐LRR genes and several leucine‐rich repeat receptor‐like kinase (LRR‐RLK) genes, thereby indicating that members of both multigene families constitute a heterogeneous cluster at the Rsv3 chromosomal region. To further confirm the sequence and genetic map concordance, we developed 16 markers from the genomic sequence including predicted CC‐NB‐LRR genes and their flanking sequences. Mapping of the resultant markers in three populations showed parallel alignment between the genetic and sequence maps in the Rsv3‐containing region. Phylogenetic analysis of five CC‐NB‐LRR genes including a pseudogene showed they were highly similar to each other and formed a subclade within a CC‐NB‐LRR gene clade with representatives from several plant families including legume species. These results demonstrate that the Rsv3 locus is associated with this cluster of CC‐NB‐LRR genes, thereby suggesting that the Rsv3 gene most likely encodes a member of this gene family. In addition, information from this study should facilitate marker‐assisted selection and pyramiding of resistance genes.

Ln Is a Key Regulator of Leaflet Shape and Number of Seeds per Pod in Soybean

Whether the leaflet shape gene Ln has a pleiotropic effect on the number of seeds per pod (NSPP) trait or not has long been debated in soybean research. This study shows that both the leaflet shape and NSPP traits are regulated by a single gene, which is a homolog of Arabidopsis JAGGED that regulates leaf and flower development, and establishes a novel role for JAGGED in fruit development. Narrow leaflet soybean (Glycine max) varieties tend to have more seeds per pod than broad leaflet varieties. Narrow leaflet in soybean is conferred by a single recessive gene, ln. Here, we show that the transition from broad (Ln) to narrow leaflet (ln) is associated with an amino acid substitution in the EAR motif encoded by a gene (designated Gm-JAGGED1) homologous to Arabidopsis JAGGED (JAG) that regulates lateral organ development and the variant exerts a pleiotropic effect on fruit patterning. The genomic region that regulates both the traits was mapped to a 12.6-kb region containing only one gene, Gm-JAG1. Introducing the Gm-JAG1 allele into a loss-of-function Arabidopsis jagged mutant partially restored the wild-type JAG phenotypes, including leaf shape, flower opening, and fruit shape, but the Gm-jag1 (ln) and EAR-deleted Gm-JAG1 alleles in the jagged mutant did not result in an apparent phenotypic change. These observations indicate that despite some degree of functional change of Gm-JAG1 due to the divergence from Arabidopsis JAG, Gm-JAG1 complemented the functions of JAG in Arabidopsis thaliana. However, the Gm-JAG1 homoeolog, Gm-JAG2, appears to be sub- or neofunctionalized, as revealed by the differential expression of the two genes in multiple plant tissues, a complementation test, and an allelic analysis at both loci.

Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds

Despite their medicinal, pharmaceutical, and nutritional importance of isoflavones, the genetic basis controlling the amounts of isoflavones in soybean seeds is still not well understood. The main obstacle is the great variability in the content of isoflavone in seeds harvested from different environments. In this study, quantitative trait loci (QTL) for the content of different isoflavones including daidzein, genistein, and glycitein were investigated in a population of recombinant inbred lines derived from the cross of “Hwangkeum” (Glycine max) by “IT182932” (Glycine soja). Seeds analyzed were harvested in three different experimental environments. QTL analyses for isoflavone content were conducted by composite interval mapping across a genomewide genetic map. Two major QTL were mapped to soybean chromosomes 5 and 8, which were designated QDZGT1 and QDZGT2, respectively. Both loci have not been previously reported in other isoflavone sources. The results from this study will be useful in cloning genes that can control the contents of isoflavones in soybean and for the development of soybean lines containing a high or low isoflavone content.

Monitoring the occurrence of genetically modified soybean and maize around cultivated fields and at a grain receiving port in Korea

Increased imports of genetically modified (CM) soybean and maize might cause genetic contamination of those crops that are conventionally bred, as well as wild soybeans within Korea. Leaves of maize and both cultivated and wild soybeans were sampled in and near rural fields to detect the presence of transgenes. Roadsides around a major grain port in Incheon were also surveyed to monitor the occurrence of incoming CM soybean and maize. The amplificability of DNA extracted from the collected samples was determined by PCR using soybean- or maize-specific primers: lectin and zein genes, respectively. The presence or absence of transgenes was detected by primer sets for the 35S and nos genes. Transgenes were not found in the cultivated or wild soybean or in the maize collected from cultivated fields. However, we obtained one GM maize plant among seven along the roadsides around Incheon Port. Although the effect of a single GM maize plant would be negligible and would not pose any threat to natural environments, an increase in the import of GM plants might lead to future, unapproved cultivation of GM crops. Therefore, appropriate monitoring is necessary to detect the occurrence of GM plants in areas around grain receiving ports and within agroecosystems.