1.
2.
3.
4.
5.
6.
7.
8.
Jiang, W.; Struik, P.C.; Lingna, J.; Van Keulen, H.; Ming, Z.; Stomph, T.J. Uptake and distribution of root-applied or foliar-applied
65Zn after flowering in aerobic rice. Ann. Appl. Biol. 2007, 150, 383–391. [CrossRef]
Ahn, S.; Anderson, J.A.; Sorrells, M.E.; Tanksley, S.D. Homoeologous relationships of rice, wheat and maize chromosomes. Mol.
Gen. Genet. 1993, 241, 483–490. [CrossRef]
Kurata, N.; Moore, G.; Nagamura, Y.; Foote, T.; Yano, M.; Minobe, Y.; Gale, M. Conservation of genome structure between rice
and wheat. Nat. Biotechnol. 1994, 12, 276–278. [CrossRef]
Buell, C.R.; Yuan, Q.; Ouyang, S.; Liu, J.; Zhu, W.; Wang, A.; Maiti, R.; Haas, B.; Wortman, J.; Pertea, M.; et al. Sequence, annotation,
and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 2005, 15, 1284–1291. [CrossRef]
[PubMed]
Goff, S.A.; Ricke, D.; Lan, T.-H.; Presting, G.; Wang, R.; Dunn, M.; Glazebrook, J.; Sessions, A.; Oeller, P.; Varma, H.; et al. A draft
sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296, 92–100. [CrossRef]
Yu, J.; Hu, S.; Wang, J.; Wong, G.K.S.; Li, S.; Liu, B.; Deng, Y.; Dai, L.; Zhou, Y.; Zhang, X.; et al. A draft sequence of the rice
genome (Oryza sativa L. ssp. indica). Science 2002, 296, 79–92. [CrossRef]
Abe, A.; Kosugi, S.; Yoshida, K.; Natsume, S.; Takagi, H.; Kanzaki, H.; Matsumura, H.; Yoshida, K.; Mitsuoka, C.; Tamiru, M.; et al.
Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol. 2012, 30, 174–178. [CrossRef]
Fekih, R.; Takagi, H.; Tamiru, M.; Abe, A.; Natsume, S.; Yaegashi, H.; Sharma, S.; Sharma, S.; Kanzaki, H.; Matsumura, H.; et al.
MutMap+: Genetic mapping and mutant identification without crossing in rice. PLoS ONE 2013, 8, e68529. [CrossRef]
Plants 2023, 12, 929
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
22 of 23
Takagi, H.; Abe, A.; Yoshida, K.; Kosugi, S.; Natsume, S.; Mitsuoka, C.; Uemura, A.; Utsushi, H.; Tamiru, M.; Takuno, S.; et al.
QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.
Plant J. 2013, 74, 174–183. [CrossRef]
Varshney, R.K.; Terauchi, R.; McCouch, S.R. Harvesting the promising fruits of genomics: Applying genome sequencing
technologies to crop breeding. PLoS Biol. 2014, 12, e1001883. [CrossRef]
Yamamoto, T.; Nagasaki, H.; Yonemaru, J.-I.; Ebana, K.; Nakajima, M.; Shibaya, T.; Yano, M. Fine definition of the pedigree
haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genom.
2010, 11, 267. [CrossRef] [PubMed]
Enoki, H.; Takeuchi, Y. New genotyping technology, GRAS-Di, using next generation sequencer. In Proceedings of the Plant and
Animal genome conference XXVI, San Diego, CA, USA, 13–17 January 2018. Available online: https://pag.confex.com/pag/
xxvi/meetingapp.cgi/Paper/29067 (accessed on 10 January 2023).
Hosoya, S.; Hirase, S.; Kikuchi, K.; Nanjo, K.; Nakamura, Y.; Kohno, H.; Sano, M. Random PCR-based genotyping by sequencing
technology GRAS-Di (genotyping by random amplicon sequencing-direct) reveals genetic structure of mangrove fishes. Mol. Ecol.
Resour. 2019, 19, 1153–1163. [CrossRef] [PubMed]
Enoki, H. The construction of pseudomolecules of a commercial strawberry by DeNovoMAGIC and new genotyping technology,
GRAS-Di. In Proceedings of the Plant and Animal genome conference XXVII, San Diego, CA, USA, 12–16 January 2019. Available
online: https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/37002 (accessed on 10 January 2023).
Zhang, Q.; Maroof, M.A.S.; Lu, T.Y.; Shen, B.Z. Genetic diversity and differentiation of indica and japonica rice detected by RFLP
analysis. Theor. Appl. Genet. 1992, 83, 495–499. [CrossRef] [PubMed]
Gupta, P.K.; Rustgi, S.; Kulwal, P.L. Linkage disequilibrium and association studies in higher plants: Present status and prospects.
Plant Mol. Biol. 2005, 57, 461–485. [CrossRef] [PubMed]
Terauchi, R.; Abe, A.; Takagi, H.; Tamiru, M.; Fekih, R.; Natsume, S.; Yaegashi, H.; Kosugi, S.; Kanzaki, H.; Matsumura, H.; et al.
Whole genome sequencing to identify genes and QTL in rice. In Advances in the Understanding of Biological Sciences Using Next
Generation Sequencing (NGS) Approaches; Springer: Berlin/Heidelberg, Germany, 2015; pp. 33–42. ISBN 9783319171579.
Fekih, R.; Tamiru, M.; Kanzaki, H.; Abe, A.; Yoshida, K.; Kanzaki, E.; Saitoh, H.; Takagi, H.; Natsume, S.; Undan, J.R.; et al. The
rice (Oryza sativa L.) LESION MIMIC RESEMBLING, which encodes an AAA-type ATPase, is implicated in defense response.
Mol. Genet. Genom. 2015, 290, 611–622. [CrossRef]
Nagata, K.; Ando, T.; Nonoue, Y.; Mizubayashi, T.; Kitazawa, N.; Shomura, A.; Matsubara, K.; Ono, N.; Mizobuchi, R.; Shibaya, T.;
et al. Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. Breed.
Sci. 2015, 65, 308–318. [CrossRef]
Tamiru, M.; Takagi, H.; Abe, A.; Yokota, T.; Kanzaki, H.; Okamoto, H.; Saitoh, H.; Takahashi, H.; Fujisaki, K.; Oikawa, K.; et al.
A chloroplast-localized protein lesion and lamina bending affects defence and growth responses in rice. New Phytol. 2016,
210, 1282–1297. [CrossRef]
Yamasaki, M.; Ideta, O. Population structure in Japanese rice population. Breed Sci. 2013, 63, 49–57. [CrossRef]
Yokoo, M.; Hirao, M.; Imai, T. Annual change in leading rice varieties between 1956 and 2000 in Japan. Bull. Natl. Inst. Crop Sci.
2005, 7, 19–125.
Kobayashi, A.; Hori, K.; Yamamoto, T.; Yano, M. Koshihikari: A premium short-grain rice cultivar - its expansion and breeding in
Japan. Rice 2018, 11, 15. [CrossRef]
Hori, K.; Ogiso-Tanaka, E.; Matsubara, K.; Yamanouchi, U.; Ebana, K.; Yano, M. Hd16, a gene for casein kinase I, is involved in
the control of rice flowering time by modulating the day-length response. Plant J. 2013, 76, 36–46. [CrossRef] [PubMed]
Yu, J.; Holland, J.B.; McMullen, M.D.; Buckler, E.S. Genetic design and statistical power of nested association mapping in maize.
Genetics 2008, 178, 539–551. [CrossRef] [PubMed]
McMullen, M.D.; Kresovich, S.; Villeda, H.S.; Bradbury, P.; Li, H.; Sun, Q.; Flint-Garcia, S.; Thornsberry, J.; Acharya, C.;
Bottoms, C.; et al. Genetic properties of the maize nested association mapping population. Science 2009, 325, 737–740. [CrossRef]
[PubMed]
Bajgain, P.; Rouse, M.N.; Tsilo, T.J.; Macharia, G.K.; Bhavani, S.; Jin, Y.; Anderson, J.A. Nested association mapping of stem rust
resistance in wheat using genotyping by sequencing. PLoS ONE 2016, 11, e0155760. [CrossRef]
Maurer, A.; Draba, V.; Jiang, Y.; Schnaithmann, F.; Sharma, R.; Schumann, E.; Kilian, B.; Reif, J.C.; Pillen, K. Modelling the genetic
architecture of flowering time control in barley through nested association mapping. BMC Genom. 2015, 16, 290. [CrossRef]
Takita, T.; Solis, R.O. Rice Breeding at the National Agricultural Research Center for the Tohoku Region (NARCT) and Rice
Varietal Recommendation Process in Japan. Bull. Natl. Agric. Res. Cent. Tohoku Reg. 2002, 100, 93–117. (in Japanese).
Saka, N. A Rice (Oryza sativa L.) Breeding for Field Resistance to Blast Disease (Pyricularia oryzae) in Mountainous Region
Agricultural Research Institute, Aichi Agricultural Research Center of Japan. Plant Prod. Sci. 2006, 9, 3–9. [CrossRef]
Okada, S.; Suehiro, M.; Ebana, K.; Hori, K.; Onogi, A.; Iwata, H.; Yamasaki, M. Genetic dissection of grain traits in Yamadanishiki,
an excellent sake-brewing rice cultivar. Theor. Appl. Genet. 2017, 130, 2567–2585. [CrossRef]
Inoue, H.; Nishida, H.; Okumoto, Y.; Tanisaka, T. Identification of an early heading time gene found in the Taiwanese rice cultivar
Taichung 65. Breed. Sci. 1998, 48, 103–108. [CrossRef]
Ebana, K.; Kojima, Y.; Fukuoka, S.; Nagamine, T.; Kawase, M. Development of mini core collection of Japanese rice landrace.
Breed. Sci. 2008, 58, 281–291. [CrossRef]
Plants 2023, 12, 929
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.
45.
46.
47.
48.
23 of 23
Redoña, E.D.; Mackill, D.J. Mapping quantitative trait loci for seedling vigor in rice using RFLPs. Theoret. Appl. Genet. 1996,
92, 395–402. [CrossRef] [PubMed]
McCouch, S.R.; Zhao, K.; Wright, M.; Tung, C.-W.; Ebana, K.; Thomson, M.; Reynolds, A.; Wang, D.; DeClerck, G.; Ali, L.; et al.
Development of genome-wide SNP assays for rice. Breed. Sci. 2010, 60, 524–535. [CrossRef]
Nagasaki, H.; Ebana, K.; Shibaya, T.; Yonemaru, J.I.; Yano, M. Core single-nucleotide polymorphism —A tool for genetic analysis
of the Japanese rice populationn. Breed. Sci. 2010, 60, 648–655. [CrossRef]
Okumoto, Y.; Yoshimura, A.; Tanisaka, T.; Yamagata, H. Analysis of a rice variety Taichung 65 and its Isogenic early-heading lines
for late-heading genes E1, E2 and E3. Jpn. J. Breed. 1992, 42, 415–429, (in Japanese with English summary). [CrossRef]
Wang, L.; Hao, L.; Li, X.; Hu, S.; Ge, S.; Yu, J. SNP deserts of Asian cultivated rice: Genomic regions under domestication. J. Evol.
Biol. 2009, 22, 751–761. [CrossRef] [PubMed]
Takahashi, Y.; Shomura, A.; Sasaki, T.; Yano, M. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes
the alpha subunit of protein kinase CK2. Proc. Natl. Acad. Sci. USA 2001, 98, 7922–7927. [CrossRef]
Matsubara, K.; Kono, I.; Hori, K.; Nonoue, Y.; Ono, N.; Shomura, A.; Mizubayashi, T.; Yamamoto, S.; Yamanouchi,
U.; Shirasawa, K.A.; et al. Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from
crosses between japonica rice cultivars. Theor. Appl. Genet. 2008, 117, 935–945. [CrossRef]
Yano, M.; Katayose, Y.; Ashikari, M.; Yamanouchi, U.; Monna, L.; Fuse, T.; Baba, T.; Yamamoto, K.; Umehara, Y.; Nagamura, Y.;
et al. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time
gene CONSTANS. Plant Cell. 2000, 12, 2473–2484. [CrossRef]
Yano, M.; Harushima, Y.; Nagamura, Y.; Kurata, N.; Minobe, Y.; Sasaki, T. Identification of quantitative trait loci controlling
heading date in rice using a high-density linkage map. Theor. Appl. Genet. 1997, 95, 1025–1032. [CrossRef]
Doyle, J.J.; Doyle, J.J. A rapid procedure for DNA purification from small quantities of fresh leaf tissue. Phytochem. Bull. 1987,
19, 11–15.
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 2005, 436, 793–800. [CrossRef]
Kosambi, D.D. The estimation of map distances from recombination values. Ann. Hum. Genet. 1943, 12, 172–175. [CrossRef]
´ Churchill, G.A. R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003, 19, 889–890.
Broman, K.W.; Wu, H.; Sen, S.;
[PubMed]
Zeng, Z.B. A composite interval mapping method for locating multiple QTLs. In Proceedings of the 5th World Congress on
Genetics Applied to Livestock Production, Guelph, ON, Canada, 7–12 August 1994; University of Guelph: Guelph, ON, Canada,
1994; Volume 7.
Churchill, G.A.; Doerge, R.W. Empirical threshold values for quantitative trait mapping. Genetics 1994, 138, 963–971. [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.
...
論文の公開元へ
