1 |
Su JJ, Pang CY, Wei HL, Li LB, Liang B, Wang CX, Song MZ, Wang HT, Zhao SQ, Jia XY, Mao GZ, Huang L, Geng DD, Wang CS, Fan SL, Yu SX (2016) Identification of favorable SNP alleles and candidate genes fortraits related to early maturity via GWAS in upland cotton. BMC Genomics 17:687
DOI
|
2 |
Dong Y, Kamiunten H, Ogawa T, Tsuzuki E, Terao H, Lin D, Matsuo M (2004) Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.). Euphytica 138:169-175
DOI
|
3 |
Feng Z, Wu C, Wang C, Roh J, Zhang L, Chen J, Zhang S, Zhang H, Yang C, Hu J, You X, Liu X, Yang X, Guo X, Zhang X, Wu F, Terzaghi W, Kim SK, Jiang L, Wan J (2016) SLG controls grain size and leaf angle by modulating brassinosteroid homeostasis in rice. Journal of Experimental Botany 16(14):4341-4253
|
4 |
Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M (2010) Molecular coloning of Sdr4, a regulator incolced in seed dormancy and domestication of rice. Preceedings of the National Academy of Sciences of the United States of America 107:5792-5797
|
5 |
Takagi H, Uemura A, Yaegashi H, Tamiru M, Abe A, Mitsuoka C, Utsushi H, et al. (2013) MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytoloist 200:276-283
|
6 |
Tanaka A, Nakagawa H, Tomita C, Shimatani Z, Ohtake M, Nomura T, Jiang CJ, Dubouzet JG, Kikuchi S, Sekimoto H (2009) BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice. Plant Physiology 151:669-680
DOI
|
7 |
Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15:1749-1770
DOI
|
8 |
Wallace C, Newhouse SJ, Braund P, Zhang F, Tobin M, Falchi M, Ahmadi K, et al. (2008) Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. American Journal of Human Genetics 82(1):139-149
DOI
|
9 |
Weedon MN, Lettre G, Freathy RM, Lindgren GM, Voight BF, Perry JR, Elliott KS, et al. (2007) A common variant of HMGA2 is associated with adult and childhood height in the general population. Nature Genetics 39(10):1245-1250
DOI
|
10 |
Garg AK, Kim JK, Owens TG, Ranwala AP, Choi YD, Kochian LV, Wu RJ (2002) Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proceedings of the National Academy of Sciences of the United States of America 99(25):15898-15903
DOI
|
11 |
Grandori G, Cowley SM, James LP, Eisenman RM (2000) The Myc/Max/Mad network and the transcriptional control of cell behavior. Annual Review of Cell and Developmental Biology 16:653-699
DOI
|
12 |
Heang D, Sassa H (2012) Antagonistic actions of HLH/bHLH proteins are involved in grain length and weight in rice. PLoS One 7:e31325
DOI
|
13 |
Hu WD, Zhang H, Jiang JH, Wang YY, Sun DY, Wang XS, Liang K, Hong DL (2012) Genetic analysis and QTL mapping of large flag leaf angle trait in Japonica rice. Rice Scienc 19(4):277-285
DOI
|
14 |
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Research 19:1068-1076
|
15 |
Fujino K, Obara M, Sato K (2014) Diversification of the plantspecific hybrid glycine-rich protein (HyGRP) genes in cereals. Plant Science 24:489
|
16 |
Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genetics 41:494-497
DOI
|
17 |
Hunter KW, Crawford NPS (2008) The future of mouse QTL mapping to diagnose disease in mice in the age of whole-genome association studies. Annual Review of Genetics 42:131-141
DOI
|
18 |
Jang S, An G, Li HY (2017) Rice leaf angle and grain size are affected by the OsBUL1 transcriptional activator complex. Plant Physiology 173(1):688-702
DOI
|
19 |
Zhang LY, Bai MY, Wu J, Zhu JY, Wang H, Zhang Z, Wang W, Sun Y, Zhao J, Sun X (2009) Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell 21:3767-3780
DOI
|
20 |
Y H, Feng J, Zhang L, Zhang J, Mispan MS, Cao Z, Yang J, Beighley DH, Gu X (2015) Map-based cloning of qSD1-2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice. Plant Physiology 169:152-165
|
21 |
Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355-360
DOI
|
22 |
Kruglyak L (2008) The road to genome-wide association studies. Nature Reviews Genetics 9(4):314-318
DOI
|
23 |
Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS ONE 3:e3337
DOI
|
24 |
Kim TS, He Q, Kim KW, Yoon MY, Ra WH, Li FP, Tong W, et al. (2016) Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics 17:408
DOI
|
25 |
Kobayashi S, Fukuta Y, Morita S, Sato T (2003) Quantitative trait loci affecting flag leaf development in rice (Oryza sativa L.). Breeding Science 53:255-262
DOI
|
26 |
Kump B, Javornik B (1996) Evaluation of genetic variability among common buckwheat (Fagopyrum esculentum Moench) population by RAPD markers. Plant Science 114:149-158
DOI
|
27 |
Li J (2008) A novel strategy for detecting multiple loci in Genome-Wide Association Studies of complex diseases. International Journal of Bioinformatics Research and Applications 4(2):150-163
DOI
|
28 |
Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397-2399
DOI
|
29 |
Massari ME, Murre C (2000) Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms. Molecular and Cellular Biology 20:429-440
DOI
|
30 |
Ma X, Fu Y, Zhao X, Jiang L, Zhu Z, Gu P, Xu W, Su Z, Sun C, Tan L (2016) Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing. Scientific Reports 6:27425
DOI
|
31 |
Peng B, Kong HL, Li YB, Wang LQ, Zhong M, Sun L, Gao GJ, Zhang QL, Luo LJ, Wang GW, Xie WB, Chen JX, Yao W, Peng Y, Lei L, Lian XM, Xiao JH, Xu CG, Li XH, He YQ (2014) OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nature Communications 5:4847
DOI
|
32 |
Abdula SE et al (2013) Development and identification of transgenic rice lines with abiotic stress tolerance by using a full-length overexpressor gene hunting system. Plant Breed Biotechnol 1:33-48
DOI
|
33 |
Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology 30:174-178
DOI
|
34 |
Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Sackville Hamilton R, McNally KL (2015) SNP-seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research 43(D1):1023-1027
DOI
|
35 |
Nicolae DL, Gamazon E, Zhang W, Duan S, Eileen Dolan M, Cox NJ (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genetics 6(4):e1000888
DOI
|
36 |
Park HS, Ha KY, Kim KY, Kim WJ, Nam JK, Baek MK, Kim JJ, Jeong JM, Cho YC, Lee JH, Kim BK, Ahn SN (2015) Development of high-yielding rice lines and analysis of panicle and yield-related traits using doubled haploid lines derived from the cross between Deuraechan and Boramchan, high-yielding japonica rice cultivars in Korea. Korean Journal of Breeding Science 47:384-402
DOI
|
37 |
Perez-de-Castro AM, Vilanova S, Canizares J, Pascual L, Blanca JM, Diez MJ, Prohens J, Pico B (2012) Application of genomic tools in plant breeding. Current Genomics 13:179-195
|
38 |
Sakai H, Kanamori H, Arai-Kichise Y, Shibata-Hatta M, Ebana K, Oono Y, Kurita K, et al. (2014) Construction of pseudomolecule sequences of the Aus rice cultivar kasalath for comparative genomics of asian cultivated rice. DNA research 21(4):397-405
DOI
|
39 |
Asano K, Takashi T, Miura K, Qian Q, Kitano H, Matsuoka M, Ashikari M (2007) Genetic and molecular analysis of utility of sd1 alleles in rice breeding. Korean Journal of Breeding Science 57:53-58
DOI
|
40 |
Altshule D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322:881-888.
|
41 |
Cai J, Zhang M, Guo LB, Li XM, Bao JS, Ma LY (2015) QTLs for rice flag leaf traits in doubled haploid populations in different environments. Genetics and Molecular Research 14(2): 6786-6795
DOI
|
42 |
Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, et al. (2014) New whole genome de nomo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica. bioRxiv doi:http://dx.doi.org/10.1101/003764
DOI
|
43 |
Shabalina SA, Spiridonov NA (2004) The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biology 5(4):105
DOI
|
44 |
Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445(7130):881-885
DOI
|
45 |
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741-745
DOI
|
46 |
Blawid R, Silva JMF, Nagata T (2017) Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline. Annals of Applied Biology 170:301-314
DOI
|
47 |
Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nature Genetics 31(4):415-418
DOI
|
48 |
Cheong HS, Yoon DH, Kim LH, Park BL, Lee HW, Park BL, Choi YH, Chung ER, Cho YM, Park EW, Cheong IC, Oh SJ, Yi SG, Park TS, Shin HD (2006) Growth hormone-releasing hormone (GHRH) polymorphisms associated with carcass traits of meat in Korean cattle. BMC Genetics 7:35-40
|
49 |
Cho DS (1975) Studies on the productivity of individual leaf blade of paddy rice. Korean Journal of Breeding Science 18:1-27
|
50 |
Cho YG, McCouch SR, Kuiper M, Kang MR, Pot J, Groenen JTM, Eun MY (1998) Integrated map of AFLP, SSLP, and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.). Theoretical and Applied Genetics 97:370-380
|