The<i>Glycine max</i>cv. Enrei Genome for Improvement of Japanese Soybean Cultivars

Shimomura, Michihiko; Kanamori, Hajime; Komatsu, Setsuko; Namiki, Nobukazu; Mukai, Yukinori; Kurita, Kanako; Kamatsuki, Kaori; Ikawa, Hiroshi; Yano, Ryoichi; Ishimoto, Masao; Kaga, Akito; Katayose, Yūichi

doi:10.1155/2015/358127

Cited by 43 publications

(32 citation statements)

References 37 publications

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“…naringenin chalcone and isoliquiritigenin) then undergo three successive enzymatic reactions catalyzed by chalcone isomerase (CHI or GmCHI), 2‐hydroxyisoflavanone synthase (IFS or GmIFS; a cytochrome P450), and 2‐hydroxyisoflavanone dehydratase (HID or GmHID) to produce genistein and daidzein, respectively (Figure ). These isoflavonoid enzymes are encoded by multigene families in the soybean genome (Schmutz et al ., ; Shimomura et al ., ). For example, there are at least nine paralogs encoding CHS (Schmutz et al ., ; Shimomura et al ., ), 12 encoding CHI (Shimada et al ., ; Ralston et al ., ; Dastmalchi and Dhaubhadel, ), two encoding IFS (Cheng et al ., ), and two encoding HID (Akashi et al ., ; Livingstone et al ., ).…”

Section: Introductionmentioning

confidence: 97%

“…These isoflavonoid enzymes are encoded by multigene families in the soybean genome (Schmutz et al ., ; Shimomura et al ., ). For example, there are at least nine paralogs encoding CHS (Schmutz et al ., ; Shimomura et al ., ), 12 encoding CHI (Shimada et al ., ; Ralston et al ., ; Dastmalchi and Dhaubhadel, ), two encoding IFS (Cheng et al ., ), and two encoding HID (Akashi et al ., ; Livingstone et al ., ). For each enzyme, different isozymes exert different physiological functions in soybean plants (Shimizu et al ., ; Tuteja et al ., ; Dhaubhadel et al ., ; Livingstone et al ., ).…”

Section: Introductionmentioning

confidence: 97%

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Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2‐hydroxyisoflavanone synthase

et al. 2018

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Soybean (Glycine max) 5-deoxyisoflavonoids (daidzein and its conjugates) are precursors of glyceollin phytoalexins. They are also converted to equol by microbes in the human intestine, resulting in health benefits. 5-Deoxyisoflavonoids accumulate in the roots (93% mol/mol of the total root isoflavonoids) and seeds of unstressed soybean plants. Chalcone reductase (CHR) is a key enzyme mediating 5-deoxyisoflavonoid biosynthesis because it catalyzes the production of 6'-deoxychalcone through its effects on the chalcone synthase (CHS)-catalyzed reaction. The soybean genome encodes at least 11 CHR-related homologs, but it is unclear which ones are functionally important for daidzein accumulation in unstressed plants. Among the CHR homologs, the temporal and spatial expression patterns of GmCHR5 were the most correlated with the distribution patterns of 5-deoxyisoflavonoids. The CHR activity of GmCHR5 was confirmed in vitro and in planta. In the in vitro assays, the ratio of CHR products (6'-deoxychalcone) to total CHS products (R value) was dependent on GmCHR5 and CHS concentrations, with higher concentrations resulting in higher R values (i.e. approaching 90%). Subcellular localization analyses revealed that GmCHR5 was present in the cytoplasm and nucleus. Protein-protein interaction assays indicated that GmCHR5, but not GmCHR1 and GmCHR6, interacted with 2-hydroxyisoflavanone synthase (IFS) isozymes. The CHS isozymes also interacted with IFS isozymes but not with GmCHR5. The proposed micro-compartmentalization of isoflavone biosynthesis through the formation of an IFS-mediated metabolon is probably involved in positioning GmCHR5 close to CHS, resulting in an R value that is high enough for the accumulation of abundant 5-deoxyisoflavonoids in soybean roots.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2‐hydroxyisoflavanone synthase

et al. 2018

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“…A second assembly, Wm82.a2, was released by DOE‐JGI in 2014 and comprised 949 Mbp in 20 pseudomolecules, plus 29.3 Mbp in 1170 unanchored scaffolds (Song et al ., ). Additional ab initio (Salamov and Solovyev, ) soybean genome assemblies have been released recently: Zhonghuang 13 (Shen et al ., ); Enrei (Shimomura et al ., ); a perennial relative of soybean, Glycine latifolia (Liu et al ., ); draft assemblies for seven wild soybean accessions (Li et al ., ); and a high‐quality G. soja assembly for accession W05 (Xie et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Construction and comparison of three reference‐quality genome assemblies for soybean

et al. 2019

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We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

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“…However, NILs of the Japanese cultivar 'Enrei' have now been developed through marker assisted selection (Yamada et al, 2012). 'Enrei' is so far the only Japanese soybean cultivar to have had its whole genome sequenced (Shimomura et al, 2015). It is used as a parent for breeding due to its higher protein content which is suitable for tofu production (Takahashi et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Effects of maturity genes E2 and E3 on yield formation in soybean cultivar Enrei in warm region, Fukuyama in Japan

Kawasaki

Yamazaki

Katayama

et al. 2018

Plant Production Science

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Understanding how maturity genes affect soybean yield formation will provide important information for crop management decisions. This study aimed to reveal how maturity genes E2 and E3 in the soybean cultivar 'Enrei' affect yields and yield formation in warm regions of Japan. 'Enrei' (e2e3) and three near-isogenic lines of 'Enrei' (e2E3, E2e3, and E2E3) were cultivated in 2016 and 2017 in Fukuyama, Japan (34°30′N, 133°23′E). Two sowing dates were set in each year (June sowing and July sowing). E2 extended the period from emergence to R1 and also the period from R1 to R7, whereas E3 extended only the period from emergence to R1. Interaction between E2 and E3 did not affect duration of the period from emergence to R1, but did affect the period from R1 to R7. Although seed yield did not differ between genotypes in the June sowings, the effects of E2 and E3 on seed yield in July sowing were both significant and interaction between E2 and E3 also observed. The total number of nodes increased in E3 genotypes in both sowing dates, especially in E2E3. Pod-set ratio was lower in E2 and E3 genotypes than in e2 and e3 genotypes in the June sowings, but did not differ between genotypes in the July sowings. The high yield of E2E3 genotypes in the July sowings was attributed to increased number of nodes and flower production while maintaining pod-set ratio. Appropriate choice of sowing date is suggested to be essential when using E3 genotypes.

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TheGlycine maxcv. Enrei Genome for Improvement of Japanese Soybean Cultivars

Cited by 43 publications

References 37 publications

Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2‐hydroxyisoflavanone synthase

Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2‐hydroxyisoflavanone synthase

Construction and comparison of three reference‐quality genome assemblies for soybean

Effects of maturity genes E2 and E3 on yield formation in soybean cultivar Enrei in warm region, Fukuyama in Japan

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