Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

/pdf/genome-sequence-of-the-palaeopolyploid-soybean-2s3cr5djfl.pdf

Genome sequence of the palaeopolyploid soybean

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

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Many plants contain carbohydrate-binding proteins that are commonly designated as lectins, agglutinins, or hemagglutinins. Due to the obvious differences in molecular structure, biochemical properties, and carbohydrate-binding specificity, plant lectins are usually considered a complex and heterogeneous group of proteins. Recent advances in the structural analysis of lectins and molecular cloning of lectin genes enable subdividision of plant lectins in a limited number of subgroups of structurally and evolutionary related proteins. Four major lectin families, namely, the legume lectins, the chitin-binding lectins composed of hevein domains, the type 2 ribosome-inactivating proteins, and the monocot mannose-binding lectins comprise the majority of all currently known plant lectins. In addition to these four large families the jacalin-related lectins, the amaranthin family, and the Cucurbitaceae phloem lectins are now recognized as separate subgroups. Each of the above-mentioned lectin families is discussed...

Plant Lectins: A Composite of Several Distinct Families of Structurally and Evolutionary Related Proteins with Diverse Biological Roles

Resequencing of 302 soybean accessions and GWAS provide a comprehensive resource for soybean geneticists and breeders.

/pdf/resequencing-302-wild-and-cultivated-accessions-identifies-59gfsrsjp3.pdf

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Photosensitivity plays an essential role in the response of plants to their changing environments throughout their life cycle. In soybean [Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. The FT3 locus is one of the quantitative trait loci (QTL) for flowering time that corresponds to the maturity locus E3. To identify the gene responsible for this QTL, a map-based cloning strategy was undertaken. One phytochrome A gene (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete loss of function, respectively. High red/far-red (R/FR) long-day conditions enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than the original Bay (E3/E3; PI553043) under similar conditions. These results suggest that the variation in phytochrome A may contribute to the complex systems of soybean flowering response and geographic adaptation.

https://www.genetics.org/content/genetics/182/4/1251.full.pdf

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

Various species of bruchid beetles including Callosobruchus chinensis, C. maculatus and C. analis cause post-harvest damage of azuki bean seeds, an important East Asian grain legume. The α-amylase in the midguts of these insects is inhibited by the α-amylase inhibitor (αAI) present in common bean seeds. Transformation of azuki bean with the αAI gene driven by the promoter of phytohemagglutinin results in high levels of αAI in the seeds and the complete block of bruchid development on the seeds. Zabrotes subfasciatus, a South and Central American bruchid that is a storage pest of common bean, develops normally on the transgenic azuki bean.

Bruchid resistance of transgenic azuki bean expressing seed α‐amylase inhibitor of common bean

https://www.jstage.jst.go.jp/article/aez1966/24/3/24_3_281/_pdf

Growth Inhibitory Effects of an α-Amylase Inhibitor from the Kidney Bean, Phaseolus vulgaris (L.) on Three Species of Bruchids (Coleoptera : Bruchidae)

[alpha]-Amylase inhibitor ([alpha]AI) protects seeds of the common bean (Phaseolus vulgaris) against predation by certain species of bruchids such as the cowpea weevil (Callosobruchus maculatus) and the azuki bean weevil (Callosobruchus chinensis), but not against predation by the bean weevil (Acanthoscelides obtectus) or the Mexican bean weevil (Zabrotes subfasciatus), insects that are common in the Americas. We characterized the interaction of [alpha]AI-1 present in seeds of the common bean, of a different isoform, [alpha]AI-2, present in seeds of wild common bean accessions, and of two homologs, [alpha]AI-Pa present in seeds of the tepary bean (Phaseolus acutifolius) and ([alpha]AI-Pc in seeds of the scarlet runner bean (Phaseolus coccineus), with the midgut extracts of several bruchids. The extract of the Z. subfasciatus larvae rapidly digests and inactivates [alpha]AI-1 and [alpha]AI-Pc, but not [alpha]AI-2 or [alphha]AI-Pa. The digestion is caused by a serine protease. A single proteolytic cleavage in the [beta] subunit of [alpha]AI-1 occurs at the active site of the protein. When degradation is prevented, [alpha]AI-1 and [alpha]AI-Pc do not inhibit the [alpha]-amylase of Z. subfasciatus, although they are effective against the [alpha]-amylase of C. chinensis. [alpha]AI-2 and [alpha]AI-Pa, on the other hand, do inhibit the [alpha]-amylase of Z. subfasciatus, suggesting that they are good candidates for genetic engineering to achieve resistance to Z. subfasciatus.

/pdf/protective-mechanism-of-the-mexican-bean-weevil-against-high-56yzskps3a.pdf

Protective mechanism of the Mexican bean weevil against high levels of alpha-amylase inhibitor in the common bean.

A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding.

/pdf/high-density-integrated-linkage-map-based-on-ssr-markers-in-466furtx2r.pdf

Masao Ishimoto

Papers

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

Bruchid resistance of transgenic azuki bean expressing seed α‐amylase inhibitor of common bean

Growth Inhibitory Effects of an α-Amylase Inhibitor from the Kidney Bean, Phaseolus vulgaris (L.) on Three Species of Bruchids (Coleoptera : Bruchidae)

Protective mechanism of the Mexican bean weevil against high levels of alpha-amylase inhibitor in the common bean.

High-density Integrated Linkage Map Based on SSR Markers in Soybean