Institute of Crop Science, NARO

Soybean and Field Crop Applied Genomics Research Unit

Soybean is one of the most important grain crops as a staple source of nutritious vegetable protein and oil for humans and livestock. In Japan, soybean is an important source of traditional foods such as tofu, natto, miso and soy sauce. We have developed new strategies for effective soybean breeding through 1) analysis of the genome structure of Japanese (domestic) soybean, 2) development of DNA markers serving as landmarks of agronomically important traits, 3) development of research resources for the identification of important genes in soybean, and 4) isolation of genes controlling important traits such as disease and pest resistance, productivity, seed quality and regional adaptability through maturity control.


Unit Leader

Akito KAGA
Research Topics :


Unit Members

Name
Position
Research Topics
Fumio TAGUCHI-SHIOBARA Principal Researcher Disease resistance, marker-assisted selection
Atsunori FUKUDA Principal Researcher Response to environment, mutant
Eri OGISO-TANAKA Researcher Applied genomics, gene expression, genomic selection

Research Publications

  • Yano R, Takagi K, Takada Y, Mukaiyama K, Tsukamoto C, Sayama T, Kaga A, Anai T, Sawai S, Ohyama K, Saito K, Ishimoto M (2016) Metabolic switching of astringent and beneficial triterpenoid saponins in soybean is achieved by a loss‐of‐function mutation in Cytochrome P450 72A69. Plant J in press
  • Jiang CJ, Sugano S, Kaga A, Lee SS, Sugimoto T, Takahashi M, Ishimoto M (2016) Evaluation of resistance to Phytophthora sojae in soybean mini core collections using an improved assay system. Phytopathology in press
  • Takeshima R, Hayashi T, Zhu J, Zu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J (2016) A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J Exp Bot 67(17):5247-5258.
  • Kato S, Takada Y, Shimamura S, Hirata K, Sayama T, Taguchi-Shiobara F, Ishimoto M, Kikuchi A, Nishio T (2016) Transfer of the Rsv3 locus from 'Harosoy' for resistance to soybean mosaic virus strains C and D in Japan. Breed Sci 66(2): 319-327
  • Takagi K, Kaga A, Ishimoto M, Hajika M, Matsunaga T (2015) Diversity of seed cesium accumulation in soybean mini-core collections. Breed Sci 65(5): 372-380
  • Tsuda M, Kaga A, Anai T, Shimizu T, Sayama T, Takagi K, Machita K, Aatanabe S, Nishimura M, Yamada N, Mori S, Sasaki H, Kanamori H, Katayose Y, Ishimoto M (2015) Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing. BMC Genomics 16:1014
  • Yamaguchi N, Taguchi-Shiobara F, Sayama T, Miyoshi T, Kawasaki M, Ishimoto M, Senda M (2015) Quantitative trait loci associated with tolerance to seed cracking under chilling temperatures in soybean. Crop Sci 55(5): 2100-2107
  • Shimomura M, Kanamori H, Komatsu S, Namiki N, Mukai Y, Kurita K, Kamatsuki K, Ikawa H, Yano R, Ishimoto M, Kaga A, Katayose Y (2015) The Glycine max cv. Enrei genome for improvement of Japanese soybean cultivars. International Journal of Genomics 2015: 358127
  • Kato S, Fujii K, Yumoto S, Ishimoto M, Shiraiwa T, Sayama T, Kikuchi A, Nishio T (2015) Seed yield and its components of indeterminate and determinate lines in recombinant inbred lines of soybean. Breed Sci 65(2): 154-160
  • Fujii K, Kato S, Sayama T, Tanaka Y, Nakazaki T, Ishimoto M, Shiraiwa T (2015) Stability verification of the effects of stem determination and earliness of flowering on green stem disorder of soybean against genetic background and environment. Plant Prod Sci 18(2): 166-179
  • Yamaguchi N, Kurosaki H, Ishimoto M, Kawasaki M, Senda M, Miyoshi T (2015) Early-maturing and chilling-tolerant soybean lines derived from crosses between Japanese and Polish cultivars. Plant Prod Sci 18(2): 234-239
  • Oki N, Komatsu K, Takahashi M, Takahashi M, Kono Y, Ishimoto M (2015) Field assessment of resistance QTL to common cutworm (Spodoptera litura Fabricius) in soybean. Crop Sci 55(2):624-630
  • Hirata K, Masuda R, Tsubokura Y, Yasui T, Yamada T, Takahashi K, Nagaya T, Sayama T, Ishimoto M, Hajika M (2014) Identification of quantitative trait loci associated with boiled seed hardness in soybean. Breed Sci 64(4):362-370
  • Yamada T, Shimada S, Hajika M, Hirata K, Takahashi K, Nagaya T, Hamaguchi H, Maekawa T, Sayama T, Hayashi T, Ishimoto M, Tanaka J (2014) Major QTLs associated with green stem disorder insensitivity of soybean (Glycine max (L.) Merr.). Breed Sci 64(4):331-338
  • Yamaguchi N, Sayama T, Yamazaki H, Miyoshi T, Ishimoto M, Funatsuki H (2014) Quantitative trait loci associated with lodging tolerance in soybean cultivar 'Toyoharuka'. Breed Sci 64(4):300-308
  • Funatsuki H, Suzuki M, Hirose A, Inaba H, Yamada T, Hajika M, Komatsu K, Katayama T, Sayama T, Ishimoto M, Fujino K (2014) Molecular basis of a shattering resistance boosting global dissemination of soybean. Proc Natl Acad Sci USA 111:17797-17802
  • Inoue Y, Kobae Y, Omoto E, Tanaka A, Banba M, Takai S, Tamura Y, Hirose A, Komatsu K, Otagaki S, Matsumoto S, Taniguchi M, Masuta C, Ishimoto M, Hata S (2014) The soybean mycorrhiza-inducible phosphate transporter gene, GmPT7, also shows localized expression at the tips of vein endings of senescent leaves. Plant Cell Physiol 55:2102-2111
  • Hayashi M, Shiro S., Kanamori H, Mori-Hosokawa S, Sasaki-Yamagata H, Sayama T, Nishioka M, Takahashi M, Ishimoto M, Katayose Y, Kaga A, Harada K, Kouchi H, Saeki Y, Umehara Y (2014) A thaumatin-like protein, Rj4, controls nodule symbiotic specificity in soybean. Plant Cell Physiol 55:1679-1689
  • Sakazono S, Nagata T, Matsuo R, Kajihara S, Watanabe M, Ishimoto M, Shimamura S, Harada K, Takahashi R, Mochizuki T (2014) Variation in root development response to flooding among 92 soybean lines during early growth stages. Plant Prod Sci 17:228-236
  • Maruyama N, Fujiwara K, Yokoyama K, Cabanos C, Hasegawa H, Takagi K, Nishizawa K, Uki Y, Kawarabayashi T, Shouji M, Ishimoto M, Terakawa T (2014) Stable accumulation of seed storage proteins containing vaccine peptides in transgenic soybean seeds. Journal of Bioscience and Bioengineering 118:441-447
  • Yamaguchi N, Sayama T, Sasama H, Yamazaki H, Miyoshi T, Tanaka Y, Ishimoto M (2014) Mapping of quantitative trait loci (QTLs) associated with terminal raceme length in soybean. Crop Sci 54(6): 2461-2468
  • Kato S, SayamaT, Fujii K, Yumoto S, Kono Y, Hwang TY, Kikuchi A, Takada Y, Tanaka Y, Shiraiwa T, Ishimoto M (2014) A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. Theor Appl Genet 127(6): 1365-1374
  • Tsubokura Y, Watanabe S, Xia Z, Kanamori H, Yamagata H, Kaga A, Katayose Y, Abe J, Ishimoto M, Harada K (2014) Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Annals of Botany 113(3): 429-441
  • Xia Z, Wu H, Watanabe S, Harada K (2014) Construction and targeted retrieval of specific clone from a non-gridded soybean bacterial artificial chromosome library. Analytical Biochemistry 444: 38-40
  • Takagi K., Nishizawa, K., Hirose, A., Kurauchi, T., Senda, M., Masuta, C., Ishimoto, M. (2013) Seed coat pigmentation in transgenic soybean expressing the silencing suppressor 2b gene of Cucumber mosaic virus. Plant Cell Rep 32(12): 1903-1912
  • Xu M, Xu Z, Liu B, Kong F, Tsubokura Y, Watanabe S, Xia Z, Harada K, Kanazawa A, Yamada T, Abe J (2013) Genetic variation in four maturity genes affects photoperiod insensitivity and PHYA-regulated post-flowering responses of soybean. BMC Plant Biol 13:91
  • Takada Y, Sasama H, Sayama T, Kikuchi A, Kato S, Ishimoto M, Tsukamoto C (2013) Genetic and chemical analysis of a key biosynthetic step for soyasapogenol A, an aglycone of group A saponins that influence soymilk flavor. Theor Appl Genet 126(3): 721-731
  • Hanafy MS, Rahman SM, Nakamoto Y, Fujiwara T, Naito S, Wakasa K, Ishimoto M (2013) Differential response of methionine metabolism in two grain legumes, soybean and azuki bean, expressing a mutated form of Arabidopsis cystathionine γ-synthase. J Plant Physiol 170(3): 338-345
  • Ishimoto M, Kuroda M, Yoza K, Nishizawa K, Teraishi M, Mizutani N, Ito K, Moriya S (2012) Heterologous expression of corn cystain in soybean and effect on growth of the stink bug. Biosci. Biotechnol Biochem 76(11): 2142-2145
  • Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Toyoaki A, Sato S, Yamazaki T, Lu S, Wu H, Tabata S, Harada K (2012) Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci USA 109(32): 2155-2164
  • Sayama T, Ono E, Takagi K, Takada Y, Horikawa M., Nakamoto, Y., Hirose, A., Sasama, H., Ohashi, M., Hasegawa, H., Terakawa, T., Kikuchi, A., Kato, S., Tatsuzaki, N., Tsukamoto, C., Ishimoto M (2012) The Sg-1 glycosyltransferase locus regulates structural diversity of triterpenoid saponins of soybean. Plant Cell 24: 2123-2138
  • Yamada T, Takagi K, Ishimoto M (2012) Recent advances in soybean transformation and their application to molecular breeding and genomic analysis. Breed Sci 61(5): 480-494
  • Sugimoto T, Kato M, Yoshida S, Matsumoto I, Kobayashi T, Kaga A, Hajika M, Yamamoto R, Watanabe K, Aino M, Matoh T, Walker DR, Biggs AR, Ishimoto M (2012) Pathogenic diversity of Phytophthora sojae and breeding strategies to develop Phytophthora-resistant soybeans. Breed Sci 61(5): 511-522
  • Watanabe S, Harada K, Abe J (2012) Genetic and molecular bases of photoperiod responses of flowering in soybean. Breed Sci 61(5): 531-543
  • Funatsuki H, Hajika M, Yamada T, Suzuki M, Hagihara S, Tanaka Y, Fujita S, Ishimoto M, Fujino K (2012) Mapping and use of QTLs controlling pod dehiscence in soybean. Breed Sci 61(5): 554-558
  • Kaga A, Shimizu T, Watanabe S, Tsubokura Y, Katayose Y, Harada K, Vaughan DA, Tomooka N (2012) Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections. Breed Sci 61(5): 566-592
  • Hirota T, Sayama T, Yamasaki M., Sasama H, Sugimoto T, Ishimoto M, Yoshida S (2012) Diversity and population structure of black soybean landraces originating from Tanba and neighboring regions. Breed Sci 61(5): 593-601
  • Oki N, Komatsu K, Sayama T, Ishimoto M, Takahashi M (2012) Genetic analysis of antixenosis resistance to the common cutworm (Spodoptera litura Fabricius)and its relationship with pubescence characteristics in soybean (Glycine max (L.) Merr.). Breed Sci 61(5): 608-617
  • Ohnishi S, Miyake N., Takeuchi T., Kousaka F., Hiura S., Kanehira O., Saito, M., Sayama, T., Higashi, A., Ishimoto, M., Tanaka, Y., Fujita, S. (2012) Fine mapping of foxglove aphid (Aulacorthum solani) resistance gene Raso1 in soybean and its effect on tolerance to soybean dwarf virus transmitted by foxglove aphid. Breed Sci 61(5): 618-624
  • Saruta M, Takada Y, Kikuchi A, Yamada T, Komatsu K, Sayama T, Ishimoto M, Okabe A (2012) Screening and genetic analysis of resistance to peanut stunt virus in soybean: identification of putative Rpsv1 resistance gene. Breed Sci 61(5): 625-630
  • Takada Y, Tayama I, Sayama T, Sasama H, Saruta M, Kikuchi A, Ishimoto M, Tsukamoto C (2012) Genetic analysis of variations in the sugar chain composition at the C-3 position of soybean seed saponins. Breed Sci 61(5): 639-645
  • Komatsu K, Hwang TY, Takahashi M, Sayama T, Funatsuki H, Oki N, Ishimoto M (2012) Identification of QTL controlling post-flowering period in soybean. Breed Sci 61(5): 646-652
  • Yamada T, Hajika M, Yamada N, Hirata, K., Okabe, A., Oki, N., Takahashi, K., Seki, K., Okano, K., Fujita, Y., Kaga, A., Shimizu, T., Sayama, T., Ishimoto M (2012) Effects on flowering and seed yield of dominant alleles at maturity loci E2 and E3 in a Japanese cultivar, Enrei. Breed Sci 61(5): 653-660
  • Katayose Y, Kanamori H, Shimomura M, Ohyanagi H, Ikawa, H., Minami, H., Shibata, M., Ito, T., Kurita, K., Ito, K., Tsubokura, Y., Kaga, A., Wu, J., Matsumoto, T., Harada, K., Sasaki T (2012) DaizuBase, an integrated soybean genome database including BAC-based physical maps. Breed Sci 61(5): 661-664
  • Wadahama H, Iwasaki K, Matsusaki M, Nishizawa K, Ishimoto M, Arisaka F, Takagi K, Urade R (2012) Accumulation of β-conglycinin in soybean cotyledon through formation of disulfide bonds between α'-and α-subunits. Plant Physiol 158(3): 1395-1405
  • Tsubokura Y, Hajika M, Kanamori H, Xia, Z., Watanabe, S., Kaga, A., Katayose, Y., Ishimoto, M., Harada, K. (2012) The β-conglycinin deficiency in wild soybean is associated with the tail-to-tail inverted repeat of the α-subunit genes. Plant Mol Biol 78(3): 301-309
  • Sugimoto T, Yoshida, S., Kaga, A., Hajika, M., Watanabe, K., Aino, M., Tatsuda, K., Yamamoto, R., Matoh, T., Walker, D.R., Biggs, A.R., Ishimoto, M. (2011) Genetic analysis and identification of DNA markers linked to a novel Phytophthora sojae resistance gene in the Japanese soybean cultivar Waseshiroge. Euphytica 182(1): 133-145
  • Takagi K, Nishizawa K, Hirose A, Kita A, Ishimoto M (2011) Manipulation of saponin biosynthesis by RNA interference-mediated silencing of β-amyrin synthase gene expression in soybean. Plant Cell Rep 30(10): 1835-1846
  • Watanabe S, Xia Z, Hideshima, R., Tsubokura, Y., Sato, S., Yamanaka, N., Takahashi, R., Anai, T.,Tabata, S., Kitamura, K., Harada K (2011) A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 188: 395-407
  • Sayama T, Hwang TY, Komatsu K, Takada Y, Takahashi M, Kato S, Sasama H, Higashi A, Nakamoto Y, Funatsuki H, Ishimoto M (2011) Development and application of a whole-genome simple sequence repeat panel for high-throughput genotyping in soybean. DNA Research 18(2): 107-115
  • Onda R, Watanabe S, Sayama T, Komatsu K, Okano K, Ishimoto M, Harada K (2011) Genetic and molecular analysis of fasciation mutation in Japanese soybeans. Breed Sci 61(1): 26-34