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. © 2017 Society of Chemical Industry.

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.

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.

Genome-wide SNP discovery in mungbean by Illumina HiSeq.

Mungbean [Vigna radiata (L.) Wilczek], a self-pollinated diploid plant with 2n = 22 chromosomes, is an important legume crop with a high-quality amino acid profile. Sequence variation at the whole-genome level was examined by comparing two mungbean cultivars, Sunhwanokdu and Gyeonggijaerae 5, using Illumina HiSeq sequencing data. More than 40 billion bp from both mungbean cultivars were sequenced to a depth of 72×. After de novo assembly of Sunhwanokdu contigs by ABySS 1.3.2 (N50 = 9,958 bp), those longer than 10 kb were aligned with Gyeonggijaerae 5 reads using the Burrows-Wheeler Aligner. SAMTools was used for retrieving single nucleotide polymorphisms (SNPs) between Sunhwanokdu and Gyeonggijaerae 5, defining the lowest and highest depths as 5 and 100, respectively, and the sequence quality as 100. Of the 305,504 single-base changes identified, 40,503 SNPs were considered heterozygous in Gyeonggijaerae 5. Among the remaining 265,001 SNPs, 65.9 % (174,579 cases) were transitions and 34.1 % (90,422 cases) were transversions. For SNP validation, a total of 42 SNPs were chosen among Sunhwanokdu contigs longer than 10 kb and sharing at least 80 % sequence identity with common bean expressed sequence tags as determined with est2genome. Using seven mungbean cultivars from various origins in addition to Sunhwanokdu and Gyeonggijaerae 5, most of the SNPs identified by bioinformatics tools were confirmed by Sanger sequencing. These genome-wide SNP markers could enrich the current molecular resources and might be of value for the construction of a mungbean genetic map and the investigation of genetic diversity.

Molecular sequence variations of the lipoxygenase-2 gene in soybean.

Soybean lipoxygenase genes comprise a multi-gene family, with the seed lipoxygenase isozymes LOX1, LOX2, and LOX3 present in soybean seeds. Among these, the LOX2 isozyme is primarily responsible for the "beany" flavor of most soybean seeds. The variety, Jinpumkong 2, having null alleles (lx1, lx2, and lx3) lacks the three seed lipoxygenases; so, sequence variations between the lipoxygenase-2 genes of Pureunkong (Lx2) and Jinpumkong 2 (lx2) cultivars were examined. One indel, four single nucleotide polymorphisms (SNPs), a 175-bp fragment in the 5'-flanking sequence, and a missense mutation within the coding region were found in Jinpumkong 2. The distribution of the sequence variations was investigated among 90 recombinant inbred lines (RILs) derived from a cross of Pureunkong × Jinpumkong 2 and in 480 germplasm accessions with various origins and maturity groups. Evidence for a genetic bottleneck was observed: the 175-bp fragment was rare in Glycine max, but present in the majority of the G. soja accessions. Furthermore, the 175-bp fragment was not detected in the 5' upstream region of the Lx2 gene on chromosome (Chr) 13 in Williams 82; instead, a similar 175-bp fragment was positioned in the homeologous region on Chr 15. The findings indicated that the novel fragment identified was originally present in the Lx2 region prior to the recent genome duplication in soybean, but became rare in the G. max gene pool. The missense mutation of the conserved histidine residue of the lx2 allele was developed into a single nucleotide-amplified polymorphism (SNAP) marker. The missense mutation showed a perfect correlation with the LOX2-lacking phenotype, so the SNAP marker is expected to facilitate breeding of soybean cultivars which lack the LOX2 isozyme.

QTL identification of flowering time at three different latitudes reveals homeologous genomic regions that control flowering in soybean.

Since the genetic control of flowering time is very important in photoperiod-sensitive soybean (Glycine max (L.) Merr.), genes affecting flowering under different environment conditions have been identified and described. The objectives were to identify quantitative trait loci (QTLs) for flowering time in different latitudinal and climatic regions, and to understand how chromosomal rearrangement and genome organization contribute to flowering time in soybean. Recombinant inbred lines from a cross between late-flowering 'Jinpumkong 2' and early-flowering 'SS2-2' were used to evaluate the phenotypic data for days to flowering (DF) collected from Kamphaeng Saen, Thailand (14°01'N), Suwon, Korea (37°15'N), and Longjing, China (42°46'N). A weakly positive phenotypic correlation (r = 0.36) was found between DF in Korea and Thailand; however, a strong correlation (r = 0.74) was shown between Korea and China. After 178 simple sequence repeat (SSR) markers were placed on a genetic map spanning 2,551.7 cM, four independent DF QTLs were identified on different chromosomes (Chrs). Among them, three QTLs on Chrs 9, 13 and 16 were either Thailand- or Korea-specific. The DF QTL on Chr 6 was identified in both Korea and China, suggesting it is less environment-sensitive. Comparative analysis of four DF QTL regions revealed a syntenic relationship between two QTLs on Chrs 6 and 13. All five duplicated gene pairs clustered in the homeologous genomic regions were found to be involved in the flowering. Identification and comparative analysis of multiple DF QTLs from different environments will facilitate the significant improvement in soybean breeding programs with respect to control of flowering time.

A case of takotsubo cardiomyopathy with ventricular fibrillation after gastroenterological endoscopy.

We describe a case of takotsubo cardiomyopathy with ventricular fibrillation after gastroenterological endoscopy in a 66-year-old woman. Ten minutes after the upper and lower gastrointestinal endoscopic examinations, the patient lost consciousness, went into respiratory arrest, and became cyanotic; an electrocardiogram (ECG) showed ventricular fibrillation. Electrical defibrillation was applied three times resulting in the patient's recovery. Subsequently, the ECG showed ST elevation in V2-V3; ultrasound cardiography showed a severely hyperkinetic base of the left ventricle, with the rest of the ventricle akinetic; and cardiac catheterization disclosed a normal coronary artery and normal contraction of the left ventricle.

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.

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.

Autoimmune thrombocytopenic purpura during pegylated interferon α treatment for chronic hepatitis C.

We describe a 72-year-old woman with chronic hepatitis C and autoimmune thrombocytopenic purpura (AITP) during pegylated interferon (PEG-IFN) alpha. Immunoglobulin G and antinuclear antibody were 2,113 mg/dL and 1,280 at the start, respectively. A liver biopsy negated autoimmune hepatitis. After a 48-week combination therapy with ribavirin, PEG-IFN alpha-2a was administered. At the 30th month, the platelet count was decreased to 1.1 x 10(4)/microL. Bone marrow biopsy disclosed normocellular marrow compatible with AITP. The platelet-associated IgG (PAIgG) titer rose to 500 ng/10(7) cells. Corticosteroid therapy was successful, and the platelet count and PAIgG titer reverted to 6.4 x 10(4)/microL and 57.3 ng/10(7) cells, respectively.

Application of comparative genomics in developing molecular markers tightly linked to the virus resistance gene Rsv4 in soybean.

The Rsv4 gene confers resistance to all the known strain groups of soybean mosaic virus in soybean (Glycine max (L.) Merr.). To construct a fine genetic map near Rsv4 in soybean, we employed a comparative genomics approach that used genome sequence information of the model legume Lotus japonicus. Sequences of the soybean expressed sequence tags (ESTs) AI856415 and BF070293 mapping to one side of the Rsv4 gene showed high similarity with gene sequences of the transformation-competent artificial chromosome (TAC) clone LjT32P24 of Lotus. LjT32P24 is tightly linked to another sequenced TAC clone, LjT26I01, in Lotus. A new marker, AW307114A, developed from soybean EST AW307114, which is homologous to a Lotus gene within LjT26I01, was mapped to the other side of the Rsv4 gene. The identification of the microsyntenic relationship facilitated the development of additional 2 EST markers between BF070293-S and AW307114A bracketing the Rsv4 gene. Several other markers developed in this study were mapped to putative homoeologous or duplicated chromosomal regions in soybean. Alignment between the soybean maps indicated that Rsv4 is located near a local chromosomal rearrangement. This targeted comparative mapping serves to provide a foundation for marker-assisted selection and cloning of the Rsv4 gene.