Outline of rice genetic stocks reservation project
(Plant Breeding Laboratory)

Kyushu University (Plant Breeding Lab)

  1. Features and management system of experimental strain groups
  2. Outlines of rice experimental strain groups
  3. Present status of system construction for seed multiplication, management and distribution
  4. Database construction and presentation to the public

1. Features and Management System of Experimental Strain Groups

Management is performed as rice genetic stocks reservation project by Plant Breeding Laboratory in cooperation with Genetic Resources Development Research, Graduate School of Agriculture. The rice experimental strain groups maintained in our laboratory have the following features.

  1. Strains holding genes recognized by classical genetics and distinctly located on the RFLP map.
  2. Unique collection of numerical and structural variants of chromosomes
  3. Recombinant inbred lines and chromosome segment introgression lines of subspecies and alien species created in the course of rice genome research are rich resources for genetic research and not seen in other place.

The strains of item (iii) will become more enriched since the present research work in our laboratory is concentrated on the item (iii). Management of strains of items (i) and (ii) is performed by the experts consisting of professors and associated professors.

2. Outlines of Rice Experimental Strain Groups

Plant Breeding Laboratory takes care of the following rice experimental strain groups under National Bioresource Project (as of May 2004). 95% of them are original product of our Laboratory and completed except chromosome substitution lines, which are under development and evaluation. Besides, there are about 1000 lines under development.

Gene preservation lines

SG Stock for genes 194 strains
FL F lines 587 strains
Fn(T65) T65 background 287 strains

Chromosome variation lines

T Triploid lines 250 strains (approx.)
RT Reciprocal translocation lines 288 strains

Recombinant inbred lines (RIL) derived from inter-subspecies hybrid

RIA RIL ("Asominori"/"IR24") 83 strains
RIB RIL ("Kinmaze"/"DV85") 83 strains
RIC RIL ("T65"/"DV85") 125 strains
RID RIL ("T65"/"DVC10313") 138 strains

Chromosome segment substitution lines derived from inter-subspecies hybrid

IAS “Asominori” chromosome segment on the "IR24" background 70 strains
AIS “IR24” chromosome segment on the "Asominori" background 98 strains
TACSSL ARC10313 chromosome segment on the T65 background 46 strains
TDCSSL DV85 chromosome segment on the T65 background 47 strains

Chromosome segment substitution lines derived from inter-species hybrid
(Genetic background: T65)

W1962ILs O. rufipogon introgression line
44 strains
IRGC105715ILs 0. nivara introgression line (T65 cytoplasm) 33 strains
GLU-ILs[T65] O. glumaepatula introgression line (T65 cytoplasm) 35 strains
GLU-ILs[GLU] O. glumaepatula introgression line (glumaepatula cytoplasm) 34 strains
MER-ILs[T65] O. meridionalis introgression line (T65 cytoplasm) 37 strains
MER-ILs[MER] O. meridionalis introgression line (meridionalis cytoplasm) 42 strains
W1508ILs O. longistaminata introgression line (T65 cytoplasm) 33 strains
GILs O. glaberrima introgression line
41 strains
IRGC103777[T65] O. glaberrima introgression line (T65 cytoplasm) 11 strains
IRGC103777[GILs] O. glaberrima introgression line (glaberrima cytoplasm) 17 strains

Details of each strain group are presented as follows:

Gene preservation lines

SG Strain Group or "Stock for genes"

  • Person in charge: Dr. Hideshi Yasui
  • Category: Marker gene stocks
  • Genetic background: japonica cultivars
  • No. of strains: 194(→strain List)
  • Use: They are used for gene mapping.
  • Origin & building procedure : They are based on the marker gene strains which have been used in our laboratory and the strains used for RFLP mapping of genes within these ten years.
  • Features: They maintain original strains as possible. Most genetic loci are known for the position on RFLP linkage map.
  • Reference: Yoshimura, A., O.Ideta and N. Iwata (1997) Linkage map of phenotype and RFLP markers in rice. Plant Mol. Biol. 35:49-60.

FL Strain Group or "F lines"

  • Person in charge: Dr. Hideshi Yasui
  • Category: Marker gene accumulation stocks
  • Genetic background: japonica cultivars
  • No. of strains: 587(→strain List)
  • Use: These strains have been used for "Mapping of rice genes", which is the main research theme of Plant Breeding Laboratory.
  • Origin & building procedure : From the offspring of hybridization between marker strains, the plants having multiple markers were chosen and self-propagated at least to the F16 generation.
  • Features: More than two markers are included.

Fn(T65) Strain Group or "Backcross Fn generation (T65)"

  • Person in charge: Dr. Hideshi Yasui
  • Category: Marker gene stocks
  • Genetic background: japonica cultivar "Taichung 65"
  • Donor parent: Mainly FL stocks
  • No. of strains: 287(→strain List)
  • Use: Gene mapping and a tester for various genetic experiments. "Taichung 65" is convenient material for the transformation experiment as its efficiency for callus differentiation and redifferentiation. Origin & building procedure: F1 between Taichung 65 and FL strain was backcrossed to Taichung 65.
  • Features: Uniformity of heading date is useful for genetic experiments.
  • Reference: Yoshimura, A., O. Ideta and N. Iwata (1997) Linkage map of phenotype and RFLP markers in rice. Plant Mol. Biol. 35: 49-60.

Chromosome variation lines

Triplo Strain Group

  • Person in charge: Dr. Hideshi Yasui
  • Category: Trisomics
  • Origin :
    1. Progeny of autotriploids x diploid ("Nipponbare")
    2. Progeny of desynapsis mutant x diploid ("Kinmaze” and "Taichung 65")
  • Use: Belonging chromosome is determined for marker genes and DNA markers.
  • Construction procedure :
    1. From the progeny of hybridization between autotriploid and diploid of "Nipponbare", trisomics having various morphological characteristics were chosen and trisomic analysis was performed by crossing to marker gene strains. Primary trisomic series with genetic background of "Nipponbare" was constructed.
    2. Desynaptic variants induced by MNU treatment on fertilized eggs of "Kinmaze" and "Taichung 65" were crossed to their diploid parent, and from their progeny, primary trisomics series having each variety as genetic background were established based on the morphological characteristics.
  • Features of strains: Distinctive characteristics of grain shape, panicle shape and plant type are associated with the concerning extra chromosome or area of extra chromosome.
  • Reference: Iwata, N., and Omura, T. 1984. Studies on the trisomics in rice plants (Oryza sativa L.). VI. An accomplishment of a trisomic series in japonica rice plants. Japan. J. Genet. 59: 199-204.
    Yasui, H., H. Satoh and N. Iwata 1989. Establishment of a trisomic series in rice by using a desynaptic mutant. Rice Genetics Newsletter 6: 50-51.
    Nonomura, K. I., A. Yoshimura and N. Iwata 1997. Cytogenetical gene mapping by reciprocal translocation and tertiary trisomic analyses in rice (Oryza sativa L.). Genes Genet. Syst. 72:41-49.

RT (Reciprocal Translocation) Strains

  • Person in charge: Dr. Hideshi Yasui
  • Category: Recombinant inbred lines.
  • Genetic background: japonica cultivars
  • No. of strains: 288(→strain List)
  • Use: These strains have been used for the source of various aneuploids and the materials of gene mapping. It is expected to be useful for a material of chromosome research.
  • Origin :
    1. RT strains identified in X-rayed and atomic bomb induced variants by Dr. Y. Nishimura: 29 strains.
    2. RT strains chosen from the atomic bomb induced rice variant progeny and identified for their participant chromosomes in our Laboratory: 9 strains.
    3. RT strains obtained from Dr. H.I. Oka and identified for their participant chromosomes in our Laboratory: 18 strains.
    4. RT strains obtained from the progeny of gamma ray (Co60) treated "Taichung 65" and "Nipponbare": 195 strains among which 38 strains are identified for their participant chromosomes.
    5. Isogenic RT strains having the "Taichung 65" background obtained from Dr. S. Sato, Ryukyu University: 40 strains.
  • Features: Many RT strains are identified for their participating chromosomes. Among them, the strains originated from the atomic bomb induced variants are of historical significance.
  • Reference: Yoshimura, A., N. Iwata, T. Kawasaki, M. Ali and T. Omura (1988) Identification of interchanged chromosomes in twenty-five reciprocal translocation lines newly established in rice cultivar Nipponbare. Rice Genetics Newsletter 5: 62-64.

Recombinant inbred lines (RIL) derived from inter-subspecies hybrid

RIA (Recombinant Inbred Lines A)

  • Person in charge: Dr. Hideshi Yasui
  • Category: Recombinant inbred lines.
  • Origin: "Asominori" (japonica) x "IR24" (indica)
  • No. of strains: 83(→strain List)
  • Genotype : Excel(RFLP)
  • construction procedure : From the progeny of the cross between "Asominori" (japonica) and "IR24" (indica), selfing generation has been advanced by Single Seed Decent Method (SSD) to the F12 generation at present.
  • Features: RIA strains are genetically homozygous and can be used 7 for QTL analysis.
  • Reference : Tsunematsu, H, A. Yoshimura, Y. Harushima, Y. Nagamura, N. Kurata, M. Yano, T. Sasaki and N. Iwata (1996) RFLP Framework map using recombinant inbred lines in rice. Breed. Sci. 46:279-284. DOI: 10.1270/jsbbs1951.46.279

RIB Strain Group (Recombinant Inbred Lines B)

  • Person in charge: Dr. Hideshi Yasui
  • Category: Recombinant inbred lines.
  • Origin: "Kinmaze" (japonica) x "DV85" (indica)
  • No. of strains: 83(->strain List)
  • Genotype : Excel(RFLP)
  • Construction procedure : Based on the progeny of the crossing between "Kinmaze" and "DV85", selfing generation has been advanced .

RIC Strain Group (Recombinant Inbred Lines C)

  • Person in charge: Dr. H. Yasui
  • Category: Recombinant inbred lines.
  • Origin: "Taichung 65" (japonica) x "DV85" (indica)
  • No. of strains: 125(->strain List)
  • Genotype : Excel(RFLP),Excel(GBS)
  • Construction procedure : Based on the progeny of the crossing between "Taichung 65" and "DV85", selfing generation has been advanced .

RID Strain Group (Recombinant Inbred Lines D)

  • Person in charge: Dr. H. Yasui
  • Category: Recombinant inbred lines.
  • Origin: "Taichung 65" (japonica) x "ARC10313" (indica)
  • No. of strains: 138(->strain List)
  • Genotype : Excel(GBS)
  • Construction procedure: Based on the progeny of the crossing between “Taichung 65” and “ARC10313”, selfing generation has been advanced .

Chromosome segment substitution lines derived from inter-subspecies hybrid(CSSL)

IAS Strain Group

  • Person in charge: Dr. Hideshi Yasui
  • Category: Chromosome segment substitution line
  • Genetic background: "IR24" (indica)
  • Donor parent: "Asominori" (japonica)
  • No. of strains: 70(→strain List)
  • Genotype : Excel(RFLP)
  • Use: Detailed QTL analysis, gene mapping and isolation, analysis of gene interaction.
  • Construction procedure : In each backcross generation of 18 RIA strains to "IR24", RFLP marker selection was performed to establish chromosome segment substitution line. Substitution chromosome segments of donor parent “Asominori”, overlapping among strains, covers entire genome. From 888 candidate plants chosen at BC2F2 generation by marker selection, finally 70 chromosome segment substitution lines were established. They have been kept by selfing and reached to BC2F7 generation at present.
  • Features: IAS strains cover almost entire genome area with substitution segment of "Asominori" chromosome and their genetic background became essentially that of "IR24", recurrent parent. They are efficient experimental populations for the analysis of traits controlled by multiple genes. IAS is expected, together with its reciprocal counterpart AIS, to be used effectively for gene interaction analysis.
  • Reference: K Kubo, T., Y. Aida, K. Nakamura, H. Tsunematsu, K. Doi and A. Yoshimura (2002) Reciprocal chromosome segment substitution series derived from Japonica and Indica cross of rice (Oryza sativa L.). Breed. Sci. 52:319-325. DOI: 10.1270/jsbbs.52.319

AIS Strain Group

  • Person in charge: Dr. Hideshi Yasui
  • Category: Chromosome segment substitution line(CSSL)
  • Genetic background: "Asominori" (japonica)
  • Donor parent: "IR24" (indica)
  • No. of strains: 98(→strain List)
  • Genotype : Excel(RFLP)
  • Use: Detailed QTL analysis, gene mapping and isolation, analysis of gene interaction.
  • Construction procedure : In the fourth backcross generation to "Asominori", BC3F1, and its selfing generation, BC3F2, RFLP marker selection was performed to establish chromosome segment substitution line. Substitution chromosome segments of donor parent "IR24", overlapping among strains, covers entire genome. Candidate plants were chosen in respect of uniformity of background. In BC3F1 generation 66 plants were chosen based on 116 RFLP markers. From their 400 selfed progeny plants, finally 91 chromosome segment substitution lines were established. They have been kept by selfing and reached to BC3F6 generation at present.
  • Features: AIS strains cover almost entire genome area except a part of Chromosome 3 with substitution segment of "IR24" chromosome and their genetic background became essentially that of "Asominori", recurrent parent. They are efficient experimental populations for the analysis of traits controlled by multiple genes. They may be used for construction of NIL and map based cloning. Using this material, principal genes concerning hybrid sterility have been identified. AIS is expected, together with its reciprocal counterpart IAS, to be used effectively for gene interaction analysis.
  • Reference: Kubo, T., Y. Aida, K. Nakamura, H. Tsunematsu, K. Doi and A. Yoshimura (2002) Reciprocal chromosome segment substitution series derived from Japonica and Indica cross of rice (Oryza sativa L.). Breed. Sci. 52:319-325. DOI: 10.1270/jsbbs.52.319

TACSSL

  • Person in charge: Dr. H. Yasui
  • Category: Chromosome segment substitution line.(CSSL)
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: ARC10313(japonica)
  • No. of strains: 46(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure
  • Reference: Yasui, H., Yamagata, Y., Yoshimura, A. 2010. Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65. Breed. Sci. 60: 620 628.

TDCSSL

  • Person in charge: Dr. H. Yasui
  • Category: Chromosome segment substitution line.(CSSL)
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: DV85(japonica)
  • No. of strains: 47(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure
  • Reference: Yasui, H., Yamagata, Y., Yoshimura, A. 2010. Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65. Breed. Sci. 60: 620 628.

Chromosome segment substitution lines derived from inter-species hybrid(wCCSL)
(Genetic background: T65)

W1962ILs Strain Group (O. rufipogon Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. rufipogon (W1962 from China)
  • No. of strains: 44(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure :
  • Features:
  • Reference:

IRGC105715ILs Strain Group (0. nivara Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. nivara (IRGC105715 from Cambodia)
  • No. of strains: 33(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure :
  • Features:
  • Reference:

GLU-ILs Strain Group (O. glumaepatula Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. glumaepatula (IRGC 105668)
  • No. of strains:
    (1) glumaepatula cytoplasm series: 34(→strain List)
    (2) T65 cytoplasm series: 35(→strain List)
  • Genotype : GLU-ILs(GLU) Excel(SSR),GLU-ILs(T65) Excel(SSR)
  • Construction procedure : BC4F1 was obtained by backcrossing each of reciprocal F1’s of T65 x O. glumaepatula to pollen parent "Taichung 65" repeatedly. In BC3F1 and BC4F1, candidate plants were chosen by whole genome selection using 106 RFLP markers. In total, 72 lines were selected for T65 cytoplasmic series and 63 lines for O. glumaepatula cytoplasmic series.
  • Features: GLU-ILs covers almost entire nuclear genome of O. glumaepatula in both cytoplasmic groups, though there are some lacks in chromosomal area. There is strong hybrid weakness found in O. glumaepatula cytoplasm, but the introduction of weakness recovery gene (Rhw) on Chromosome 8 makes the maintenance of lines possible. In the process of GLU-ILs establishment, gene loci were identified for several seed shattering and heading date genes. They benefit the gene analysis of specific traits to O. glumaepatula. These strains may be useful to analyze the cytoplasmic genomes as they have both of different cytoplasms.
  • Reference
    Sobrizal, K. Ikeda, P. L. Sanchez, K. Doi, E. R. Angeles, G. S. Khush and A. Yoshimura (1999) Development of Oryza glumaepatula introgression lines in rice, Oryza sativa L. Rice Genet. Newsl. 16:107-108.
    Yoshimura, A., Nagayama, H., Sobrizal, Kurakazu, T., Sanchez, P. L., Doi, K., Yamagata, Y., et al. (2010). Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng. Breed. Sci., 60(5), 597 603. DOI:10.1270/jsbbs.60.597

MER-ILs Strain Group (O. meridionalis Introgression Lines)

  • Person in charge:Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. meridionalis (W1625)
  • No. of strains:
    (1) T65 cytoplasm series: 37(→strain List)
    (2) meridionalis cytoplasm series: 42(→strain List)
  • Genotype : MER-ILs(T65) Excel(SSR),MER-ILs(MER) Excel(SSR)
  • Construction procedure : BC4F1 was obtained by backcrossing each of reciprocal F1’s of T65 x O. meridionalis to pollen parent “Taichung 65” repeatedly. In BC4F1, candidate plants were chosen by whole genome selection using 110 RFLP markers. In total, 26 lines were selected for T65 cytoplasmic series and 35 lines for O. glumaepatula cytoplasmic series.
  • Features: MER-ILs covers almost entire nuclear genome of O. meridionalis in both cytoplasmic groups, though there are some lacks in chromosomal area. In the process of GLU-ILs establishment, gene loci were identified for several awned and shattering genes. These strains may be useful to analyze the cytoplasmic genomes as they have both of different cytoplasms.
  • Reference
    Yoshimura, A., Nagayama, H., Sobrizal, Kurakazu, T., Sanchez, P. L., Doi, K., Yamagata, Y., et al. (2010). Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng. Breeding Science, 60(5), 597–603.
    Kurakazu, T., Sobrizal, K. Ikeda, P. L. Sanchez, K. Doi, E. R. Angeles, G. S. Khush and A. Yoshimura (2001) Oryza meridionalis chromosomal segment introgression lines in cultivated rice, O. sativa L. Rice Genetics Newsletter 18:81-82.

W1508ILs Strain Group (O. longistaminata Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. longistaminata (W1508 from Madagascar)
  • No. of strains: 33(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure :
  • Features:
  • Reference:

GILs Strain Group (O. glaberrima Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. glaberrima (IRGC 104038)
  • No. of strains: 41(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure : BC3F1 was obtained by backcrossing of F1 to "Taichung 65" three times. From BC3F1 and its selfed progeny BC3F2, chromosome segment introgression lines was established by marker selection. Substitution chromosome segments of donor parent O. glaberrima, overlapping among lines, cover entire genome. Strains have been kept by selfing and reached to BC3F7 at present.
  • Features: GILs successfully introduced chromosome segments originating in O. glaberrima to "Taichung 65", except a part of Chromosomes 1,7, 5, 10 and 12. The QTL analysis of major traits of O. glaberrima is in progress now. Heading date genes and hybrid pollen sterility genes have been clearly identified and located on the genetic map.
  • Reference:
    Doi, K., N. Iwata and A. Yoshimura (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of Japonica rice (O. sativa L.). Rice Genetics Newsletter 14 :39-41.
    Doi, K., A. Yoshimura and N. Iwata (1998) RFLP mapping and QTL analysis of heading date and pollen sterility using backcross populations between Oryza sativa L. and O. glaberrima Steud. Breed. Sci. 48: 395-399.

IRGC103777 Strain Group (O. glaberrima Introgression Lines)

  • Person in charge: Dr. Hideshi Yasui, Dr. Yoshiyuki Yamagata
  • Genetic background: "Taichung 65" (japonica)
  • Donor parent: O. glaberrima (IRGC 103777)
  • No. of strains:
    (1) glumaepatula cytoplasm series: 17(→strain List)
    (2) T65 cytoplasm series:  11(→strain List)
  • Genotype : Excel(SSR)
  • Construction procedure :
  • Features:
  • Reference:

3. Present Status of System Construction for Seed Multiplication, Management and Distribution

The present situation of system construction for above mentioned rice resources possessed by Plant Breeding Laboratory, Kyushu University is as follows:

4. Database Construction and Presentation to The Public

Results of the research performed in our Laboratory, i.e. the mutant gene loci determined on the RFLP map and the morphological photograph pictures of various mutants will be presented to the public. They are to be accessed at http://www.agr.kyushu-u.ac.jp/lab/plantbreed/mutant/

/rice/oryzabase