Yeong-Ho Lee

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.

Genome sequence of mungbean and insights into evolution within Vigna species

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

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.

Draft genome sequence of adzuki bean, Vigna angularis

Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.

QTL identification of yield-related traits and their association with flowering and maturity in soybean

Two soybean recombinant inbred line populations, Jinpumkong 2 × SS2-2 (J × S) and Iksannamulkong × SS2-2 (I x S) showed population-specific quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) and these were closely correlated within population. In the present study, we identified QTLs for six yield-related traits with simple sequence repeat markers, and biological correlations between flowering traits and yield-related traits. The yield-related traits included plant height (PH), node numbers of main stem (NNMS), pod numbers per plant (PNPP), seed numbers per pod (SNPP), 100-seed weight (SW), and seed yield per plant (SYPP). Eighteen QTLs for six yield-related traits were detected on nine chromosomes (Chrs), containing four QTLs for PH, two for NNMS, two for PNPP, three for SNPP, five for SW, and two for SYPP. Two highly significant QTLs for PH and NNMS were identified on Chr 6 (LG C2) in both populations where the major flowering gene, E1, and two DF and DM QTLs were located. One other PNPP QTL was also located on this region, explaining 12.9% of phenotypic variation. Other QTLs for yield-related traits showed population-specificity. Two significant SYPP QTLs potentially related with QTLs for SNPP and PNPP were found on the same loci of Chrs 8 (Satt390) and 10 (Sat_108). Also, highly significant positive phenotypic correlations (P < 0.01) were found between DF with PH, NNMS, PNPP, and SYPP in both populations, while flowering was negatively correlated with SNPP and SW in the J × S (P < 0.05) and I × S (P < 0.01) populations. Similar results were also shown between DM and yield-related traits, except for one SW. These QTLs identified may be useful for marker-assisted selection by soybean breeders.

Molecular Evidence for Soybean Domestication

Crop domestication is a good example of plant–human co-evolution. Seed gathering and human cultivation of crops were observed since the Neolithic period, as shown by archeological evidence. Numerous studies have been conducted to identify genes related to domestication. With the development of molecular techniques (molecular markers and next-generation sequencing) and bioinformatics, a greater understanding of crop domestication and improvement has been established, including the origins of crops, the numbers of independent domestication events, the molecular diversity of domestication-related traits (DRTs), and the selection pressures. A comparison of the genome sequences between wild species and cultivated crops may provide key information regarding the genetic elements involved in speciation and domestication. Therefore, sequencing projects of currently important crops and their wild relatives are in progress. Accordingly, whole genome sequencing of soybean could provide new knowledge about domestication of this important crop. In this review, we introduce the archaeological evidence of soybean domestication and summarize the DRTs in soybean populations of crosses between cultivated (Glycine max) and wild soybean (G. soja). Soybean domestication is discussed at the sequence level. The current hypothesis of soybean domestication considers that G. max was domesticated from G. soja. However, our previous work suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. This review explores soybean domestication history by focusing on nucleotide diversity using resequencing. Analysis of genes around DRTs at the population level may clarify the domestication history of soybean.

Identification of Gy4 nulls and development of multiplex PCR-based co-dominant marker for Gy4 and α’ subunit of β-conglycinin in soybean

Alpha prime (α’) subunit of β-conglycinin and Gy4 subunit of glycinin are two important subunits of soybean storage protein which have negative effects on food processing, total amino acid content, and hypersensitivity reactions. It has been possible to reduce or remove some of these problems from soybean by screening or developing mutant lines. The objective of this study was to establish a simple, cheap DNA marker for Gy4 and α’ subunit for use in non-seed destructive, marker-assisted selection (MAS) that can identify these two mutants at the same time in a unique PCR reaction. To achieve this objective, we identified eight of Gy4 mutants from diverse soybean accessions from the USDA Soybean Germplasm Collection and described a multiplex PCR based co-dominant DNA marker for Gy4 subunit of glycinin. Then we crossed one of these Gy4 mutants with Keburi (α’ mutant) for development of double mutant variety and established a multiplex PCR based, co-dominant DNA marker for screening Gy4 and α’ mutants. Thus, using this newly developed marker to identify Gy4 and α’ mutants in breeding programs we could save our time, labor, and resources.

Genetic analysis of new short petiole gene in soybean

The short petiole trait is valuable for the development of plant ideotype with high yield. Soybean breeding line, SS98206SP, showed extremely short petioles in greenhouse and field. In this study, the short petiole of two mutant lines, SS98206SP and D76-1609, were investigated to determine the genetic segregations. These two mutants were crossed with each other and with two normal petiole genotypes. Genetic analysis indicated that the short petioles in D76-1609 and SS98206SP were controlled by a single recessive gene, respectively. The short petiole gene in SS98206SP was non-allelic with lps, conferring short petiole in D76-1609. Two recessive genes showed complementary relationship having short petioles with recessive homozygote (LPS1-lps?lps?, lps1lps1LPS?-, lps1lps1lps?lps?). Our data indicated that the short petioles in SS98206SP were controlled by a single recessive gene designated as lps3.

Evaluation of soybean cultivars for resistance to Phomopsis seed decay in Korea

Phomopsis seed decay (PSD), primarily caused by Phomopsis longicolla, is one of the most important seed-borne diseases and causes serious seed yield loss in soybean. This study was performed to evaluate reactions to P. longicolla in Korean soybean major elite cultivars, which were mainly used for parents of genetic mapping populations. The natural incidence of P. longicolla and other seed-borne fungi was determined in the fields at three different locations in South Korea during 2009–2010. The significant differences in sensitivity to seed-borne diseases were shown among cultivars. Taekwangkong exhibited the greatest resistance to P. longicolla with average incidence of 0.33% and other seed-borne fungi with average incidence of 6.17%. Moreover, Taekwangkong was free of P. longicolla infection both in Milyang and in Daegu. To confirm the effective resistance source, the Korean virulent strain of P. longicolla, SSLP-3, was inoculated artificially on soybean of R4–R7 growth stage in the greenhouse. Taekwangkong exhibited a higher level of resistance to P. longicolla with significantly lower incidence (8.67%) than any other Korean elite cultivars (78.0–99.33%) and the previously reported resistant PI genotypes (35.0–55.67%). Further verification of resistance in Taekwangkong to P. longicolla by testing germination vigor of healthy seeds in vitro showed a higher germination rate than those of the susceptible cultivars. It could be suggested that Taekwangkong is a newly identified resistance source and the better source of resistance to P. longicolla to develop breeding populations for exploiting resistance gene(s) in further studies.

Transcriptomic Variation in Proanthocyanidin Biosynthesis Pathway Genes in Soybean (Glycine spp.)

BACKGROUND Proanthocyanidins are oligomeric or polymeric end products of flavonoid metabolic pathways starting with the central phenylpropanoid pathway. Although soybean (Glycine spp.) seeds represent a major source of nutrients for the human diet, as well as components for the cosmetics industry as a result of their high levels of flavonoid metabolites, including isoflavonoids, anthocyanins and proanthocyanidins, the genetic regulatory mechanisms underlying proanthocyanidin biosynthesis in soybean remain unclear. RESULTS We evaluated interspecific and intraspecific variability in flavonoid components in soybean using 43 cultivars, landraces and wild soybean accessions. We performed transcriptomic profiling of genes encoding enzymes involved in flavonoid biosynthesis using three soybean genotypes, Hwangkeum (elite cultivar), IT109098 (landrace) and IT182932 (wild accession), in seeds. We identified a Glycine max landrace, IT109098, with a proanthocyanidin content as high as that of wild soybean. Different homologous genes for anthocyanidin reductase, which is involved in proanthocyanidin biosynthesis, were detected as differentially expressed genes between IT109098 and IT182932 compared to Hwangkeum. CONCLUSION We detected major differences in the transcriptional levels of genes involved in the biosynthesis of proanthocyanidin and anthocyanin among genotypes beginning at the early stage of seed development. The results of the present study provide insights into the underlying genetic variation in proanthocyanidin biosynthesis among soybean genotypes.