Abe A, Takagi H, Fujibe T, Aya K, Kojima M, Sakakibara H, Uemura A, Matsuoka M, Terauchi R (2012) OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice. Theor Appl Genet 125:647–657
Article
CAS
PubMed
Google Scholar
Barrett J, Fry B, Maller J, Daly M (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265
Article
CAS
PubMed
Google Scholar
Berens M, Wolinska K, Spaepen S, Ziegler J, Nobori T, Nair A, Krüler V, Winkelmüller T, Wang Y, Mine A, Becker D, Garrido-Oter R, Schulze-Lefert P, Tsuda K (2019) Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk. Proc Natl Acad Sci 116(6):2364–2373
Article
CAS
PubMed
PubMed Central
Google Scholar
Borjas A, De L, Subudhi P (2016) Genetic analysis of germinating ability and seedling vigor under cold stress in US weedy rice. Euphytica 208:251–264
Article
Google Scholar
Bostock R, Pye M, Roubtsova T (2014) Predisposition in plant disease: exploiting the nexus in abiotic and biotic stress perception and response. Annu Rev Phytopathol 52:517–549
Article
CAS
PubMed
Google Scholar
Caplan J, Padmanabhan M, Dinesh-Kumar S (2008) Plant NB-LRR immune receptors from recognition to transcriptional reprogramming. Cell Host Microbe 3(3):126–135
Article
CAS
PubMed
Google Scholar
Fujino K, Obara M, Shimizu T, Koyanagi K, Ikegaya T (2015) Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region. Breed Sci 65:403–410
Article
CAS
PubMed
PubMed Central
Google Scholar
Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci 105:12623–12628
Article
CAS
PubMed
PubMed Central
Google Scholar
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin S, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799
Article
CAS
PubMed
Google Scholar
Han L, Zhang Y, Qiao Y, Cao G, Zhang S, KIM J, Koh H (2006) Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genet Sin 33(11):998–1006
Article
CAS
PubMed
Google Scholar
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler E, Qian Q, Zhang Q, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
Article
CAS
PubMed
Google Scholar
Jiang L, Liu S, Hou M, Tang J, Chen L, Zhai H, Wan J (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res 98:68–75
Article
Google Scholar
Jiang N, Shi S, Shi H, Khanzada H, Wassan G, Zhu C, Peng X, Yu Q, Chen X, He X, Fu J, Hu L, Xu J, Ouyang L, Sun X, Zhou D, He H, Bian J (2017) Mapping QTL for seed germinability under low temperature using a new high-density genetic map of rice. Front Plant Sci 8:1223
Article
PubMed
PubMed Central
Google Scholar
Jiang S, Wang D, Yan S, Liu S, Liu B, Kang H, Wang G (2019) Dissection of the genetic architecture of rice tillering using a genome-wide association study. Rice 12:43
Article
PubMed
PubMed Central
Google Scholar
Kawahara Y, de la Bastide M, Hamilton J, Kanamori H, McCombie W, Ouyang S, Schwartz D, Tanaka T, Wu J, Zhou S, Childs K, Davidson R, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee S, Kim J, Numa H, Itoh T, Buell C, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4
Article
PubMed
PubMed Central
Google Scholar
Ke S, Liu X, Luan X, Yang W, Zhu H, Liu G, Zhang G, Wang S (2018) Genome-wide transcriptome profiling provides insights into panicle development of rice. Gene 675:285–300
Article
CAS
PubMed
Google Scholar
Ku Y, Sintaha M, Cheung M, Lam H (2018) Plant hormone signaling crosstalks between biotic and abiotic stress responses. Int J Mol Sci 19:3206
Article
PubMed Central
CAS
Google Scholar
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Article
CAS
PubMed
PubMed Central
Google Scholar
Li L, Liu X, Xie K, Wang Y, Liu F, Lin Q, Wang W, Yang C, Lu B, Liu S, Chen L, Jiang L, Wan J (2013) qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.). Theor Appl Genet 126:2313–2322
Article
CAS
PubMed
Google Scholar
Love M, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550
Article
PubMed
PubMed Central
CAS
Google Scholar
Mahender A, Anandan A, Pradhan S (2015) Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers. Planta 241:1027–1050
Article
CAS
PubMed
Google Scholar
McCouch S, Wright M, Tung C, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev G, Naredo M, Harrington S, Shi Y, Branchini D, Kuser-Falcao P, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J (2016) Open access resources for genome-wide association mapping in rice. Nat Commun 7:10532
Article
CAS
PubMed
PubMed Central
Google Scholar
Minic Z (2008) Physiological roles of plant glycoside hydrolases. Planta 227(4):723–740
Article
CAS
PubMed
Google Scholar
Minic Z, Jouanin L (2006) Plant glycoside hydrolases involved in cell wall polysaccharide degradation. Plant Physiol Biochem 44:435–449
Article
CAS
PubMed
Google Scholar
Miura K, Lin S, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299
Article
CAS
Google Scholar
Olszewski N, Sun T, Gubler F (2002) Gibberellin signaling: biosynthesis, catabolism, and response pathways. Plant Cell 14:S61–S80
Article
CAS
PubMed
PubMed Central
Google Scholar
Pan Y, Zhang H, Zhang D, Li J, Xiong H, Yu J, Li J, Rehman R, Li G, Ma X, Cao G, Han L, Li Z (2015) Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping. PLoS One 10(3):e0120590
Article
PubMed
PubMed Central
CAS
Google Scholar
Pertea M, Kim D, Pertea G, Leek J, Salzberg S (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11(9):1650–1659
Article
CAS
PubMed
PubMed Central
Google Scholar
Ranawake A, Manangkilb O, Yoshidac S, Ishiid T, Morie N, Nakamurae C (2014) Mapping QTLs for cold tolerance at germination and the early seedling stage in rice (Oryza sativa L.). Biotechnol Biotechnol Equip 28(6):989–998
Article
PubMed
PubMed Central
CAS
Google Scholar
Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the rice cold tolerance gene Ctb1. Plant Sci 179(1–2):97–102
Article
CAS
Google Scholar
Sales E, Viruel J, Domingo C, Marque’s L (2017) Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties. PLoS One 12(8):e0183416
Article
PubMed
PubMed Central
CAS
Google Scholar
SAS Institute (2000) SAS/STAT user’s guide, version 8.1. SAS Institute Inc, Cary
Google Scholar
Satoh T, Tezuka K, Kawamoto T, Matsumoto S, Satoh N, Ueda K, Sakurai K, Watanabe A, Takahashi H, Akagi H (2016) Identification of QTLs controlling low-temperature germination of the east European rice (Oryza sativa L.) variety Maratteli. Euphytica 207:245–254
Article
Google Scholar
Schläppi M, Jackson A, Eizenga G, Wang A, Chu C, Shi Y, Shimoyama N, Boykin D (2017) Assessment of five chilling tolerance traits and GWAS mapping in rice using the USDA Mini-Core collection. Front Plant Sci 8:957
Article
PubMed
PubMed Central
Google Scholar
Shakiba E, Edwards J, Jodari F, Duke S, Baldo A, Korniliev P, McCouch S, Eizenga G (2017) Genetic architecture of cold tolerance in rice (Oryza sativa L.) determined through high resolution genome-wide analysis. PLoS One 12(3):e0172133
Article
PubMed
PubMed Central
CAS
Google Scholar
Shaun P, Benjamin N, Kathe T, Lori T, Manuel A, David B, Maller J, Pamela S, Paul I, Mark J, Pak C (2007) PLINK: a tool set for whole genome association and population based linkage analyses. Am J Hum Genet 81:559–575
Article
CAS
Google Scholar
Singh K, Kumar V, Saharawat Y, Gathala M, Ladha J, Chauhan B (2013) Weedy rice: an emerging threat for direct-seeded rice production systems in India. J Rice Res 1:106
Article
Google Scholar
Tang Y, Liu X, Wang J, Li M, Wang Q, Tian F, Su Z, Pan Y, Liu D, Lipkai A, Buckler E, Zhang Z (2016) GAPIT version 2: an enhanced integrated tool for genomic association and prediction. Plant Genome 9:2
Article
CAS
Google Scholar
Turner SD (2018) qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. J Open Source Softw 3(25):731
Article
Google Scholar
Wang H, Lee A, Park S, Jin S, Lee J, Ham T, Park Y, Zhao W, Kwon S (2018b) Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa L.) during germination. 3 Biotech 8:235
Article
PubMed
PubMed Central
Google Scholar
Wang X, Zou B, Shao Q, Cui Y, Lu S, Zhang Y, Huang Q, Huang J, Hua J (2018a) Natural variation reveals that OsSAP16 controls low-temperature germination in rice. J Exp Bot 69(3):413–421
Article
CAS
PubMed
Google Scholar
Wang Z, Wang F, Zhou R, Wang J, Zhang H (2011) Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.). Euphytica 181:405–413
Article
Google Scholar
Xi Z, He F, Zeng R, Zhang Z, Ding X, Li W, Zhang G (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49(5):476–484
Article
CAS
PubMed
Google Scholar
Xiong H, Yang J, Li Y. (2012) Identication of submergence-responsive genes in two indica rice genotypes carrying SUB1A- but exhibiting differential tolerance. J Plant Biol 55:233–41
Article
CAS
Google Scholar
Yamaguchi S, Kamiya Y (2000) Gibberellin biosynthesis: its regulation by endogenous and environmental signals. Plant Cell Physiol 41(3):251–257
Article
CAS
PubMed
Google Scholar
Yang T, Zhang S, Wang X, Dong J, Huang Z, Zhao J, Liu Q, Mao X, Zhang G, Liu B (2017) Evaluation of cold tolerance at four growth stages and analysis of relationship between cold tolerance and indica-japonica differentiation in a diverse rice collection (Oryza Sativa L.). Mol Plant Breed 15(2):763–773 (In Chinese with English abstract)
Google Scholar
Yang T, Zhang S, Zhao J, Liu Q, Huang Z, Mao X, Dong J, Wang X, Zhang G, Liu B (2016) Identification and pyramiding of QTLs for cold tolerance at the bud bursting and the seedling stages by use of single segment substitution lines in rice (Oryza sativa L.). Mol Breed 36:96
Article
CAS
Google Scholar
Ye H, Feng J, Zhang L, Zhang J, Mispan M, Cao Z, Beighley D, Yang J, Gu X (2015) Map-based cloning of Seed Dormancy1-2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice. Plant Physiol 169(3):2152–2165
CAS
PubMed
PubMed Central
Google Scholar
Yu J, Buckler E (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160
Article
CAS
PubMed
Google Scholar
Zhang G, Zeng R, Zhang Z, Ding X, Li W, Liu G, He F, Talukdar A, Huang C, Xi Z, Qin L, Shi J, Zhao F, Feng M, Shan Z, Chen L, Guo X, Zhu H, Lu Y (2004) The construction of a library of single segment substitution lines in rice (Oryza sativa L.). Rice Genet Newsl 21:85–87
Google Scholar
Zhang H, Li M, He D, Wang K, Yang P (2020) Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice. PLoS Genet 16(1):e1008562
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang M, Ye J, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Wei X, Yang Y (2018) Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage. Plant Cell Rep 37:529–539
Article
CAS
PubMed
Google Scholar
Zhao J, Yang W, Zhang S, Yang T, Liu Q, Dong J, Fu H, Mao X, Liu B (2018) Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection. Rice 11:61
Article
PubMed
PubMed Central
Google Scholar