Arteca RN (1996) Flowering. In: Plant growth substances. Springer, Boston, MA. pp 177–187 https://doi.org/10.1007/978-1-4757-2451-6_8.
Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S (2019) Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor Appl Genet 132(1):1–25. https://doi.org/10.1007/s00122-018-3219-y
Article
CAS
PubMed
Google Scholar
Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, Cheng Z, Liu X, Xu M (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20(7):1850–1861. https://doi.org/10.1105/tpc.108.058917
Article
CAS
PubMed
PubMed Central
Google Scholar
Doi K, Iwata N, Yoshimura A (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of Japonica rice (O. sativa L.). Rice Genet Newslett 14:39–41
CAS
Google Scholar
Eshed Y, Zamir D (1994) A genomic library of Lycopersicon pennellii in L. esculentum: A tool for fine mapping of genes. Euphytica 79(3):175–179. https://doi.org/10.1007/BF00022516
Article
CAS
Google Scholar
Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141(3):1147–1162. https://doi.org/10.1093/genetics/141.3.1147
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao H, Jin M, Zheng XM, Chen J, Yuan D, Xin Y, Wang M, Huang D, Zhang Z, Zhou K, Sheng P, Ma J, Ma W, Deng H, Jiang L, Liu S, Wang H, Wu C, Yuan L, Wan J (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. Proc Natl Acad Sci USA 111(46):16337–16342. https://doi.org/10.1073/pnas.1418204111
Article
CAS
PubMed
PubMed Central
Google Scholar
Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298(5602):2345–2349. https://doi.org/10.1126/science.1076641
Article
CAS
PubMed
Google Scholar
Hao W, Jin J, Sun SY, Zhu MZ, Lin HX (2006) Construction of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome and identification of quantitative trait loci for rice quality. J Plant Physiol Mol Biol 32(3):354–362
CAS
Google Scholar
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 Res 19(6):1068–1076. https://doi.org/10.1101/gr.089516.108
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang X, Yang S, Gong J, Zhao Q, Feng Q, Zhan Q, Zhao Y, Li W, Cheng B, Xia J, Chen N, Huang T, Zhang L, Fan D, Chen J, Zhou C, Lu Y, Weng Q, Han B (2016) Genomic architecture of heterosis for yield traits in rice. Nature 537(7622):629–633. https://doi.org/10.1038/nature19760
Article
CAS
PubMed
Google Scholar
Jiang N, Shi S, Shi H, Khanzada H, Wassan GM, 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. https://doi.org/10.3389/fpls.2017.01223
Article
PubMed
PubMed Central
Google Scholar
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40(11):1365–1369. https://doi.org/10.1038/ng.247
Article
CAS
PubMed
Google Scholar
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S et al (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 6(1):4. https://doi.org/10.1186/1939-8433-6-4
Article
PubMed
PubMed Central
Google Scholar
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43(10):1096–1105. https://doi.org/10.1093/pcp/pcf156
Article
CAS
PubMed
Google Scholar
Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K (2008) Hd3a and RFT1 are essential for flowering in rice. Development 135(4):767–774. https://doi.org/10.1242/dev.008631
Article
CAS
PubMed
Google Scholar
Komiya R, Yokoi S, Shimamoto K (2009) A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development 136(20):3443–3450. https://doi.org/10.1242/dev.040170
Article
CAS
PubMed
Google Scholar
Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang Z, Li J, Li Z, Paek NC (2013) Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. Mol Plant 6(6):1877–1888. https://doi.org/10.1093/mp/sst088
Article
CAS
PubMed
Google Scholar
Kubo T, Aida Y, Nakamura K, Tsunematsu H, Doi K, Yoshimura A (2002) Reciprocal chromosome segment substitution series derived from Japonica and Indica cross of rice (Oryza sativa L.). Breeding Sci 52(4):319–325. https://doi.org/10.1270/jsbbs.52.319
Article
CAS
Google Scholar
Lee S, Kim J, Han JJ, Han MJ, An G (2004) Functional analyses of the flowering time gene OsMADS50, the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20 (SOC1/AGL20) ortholog in rice. Plant J 38(5):754–764. https://doi.org/10.1111/j.1365-313X.2004.02082.x
Article
CAS
PubMed
Google Scholar
Li XM, Chao DY, Wu Y, Huang X, Chen K, Cui LG, Su L, Ye WW, Chen H, Chen HC, Dong NQ, Guo T, Shi M, Feng Q, Zhang P, Han B, Shan JX, Gao JP, Lin HX (2015) Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice. Nat Genet 47(7):827–833. https://doi.org/10.1038/ng.3305
Article
CAS
PubMed
Google Scholar
Liu B, Liu Y, Wang B, Luo Q, Shi J, Gan J, Shen WH, Yu Y, Dong A (2019) The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment. Nat Commun 10(1):2999. https://doi.org/10.1038/s41467-019-10850-5
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma X, Han B, Tang J, Zhang J, Cui D, Geng L, Zhou H, Li M, Han L (2019) Construction of chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of the japonica rice cultivar Nipponbare (Oryza sativa L.). Plant Physiol Biochem 144:274–282. https://doi.org/10.1016/j.plaphy.2019.09.041
Article
CAS
PubMed
Google Scholar
Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124(3):735–742. https://doi.org/10.1093/genetics/124.3.735
Article
CAS
PubMed
PubMed Central
Google Scholar
Price AH (2006) Believe it or not, QTLs are accurate! Trends Plant Sci 11(5):213–216. https://doi.org/10.1016/j.tplants.2006.03.006
Article
CAS
PubMed
Google Scholar
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y et al (2013) Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 54(2):e6. https://doi.org/10.1093/pcp/pcs183
Article
CAS
PubMed
PubMed Central
Google Scholar
Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10(6):297–304. https://doi.org/10.1016/j.tplants.2005.04.008
Article
CAS
PubMed
Google Scholar
Schaart JG, van de Wiel CCM, Lotz LAP, Smulders MJM (2016) Opportunities for products of new plant breeding techniques. Trends Plant Sci 21(5):438–449. https://doi.org/10.1016/j.tplants.2015.11.006
Article
CAS
PubMed
Google Scholar
Song S, Chen Y, Liu L, Wang Y, Bao S, Zhou X, Teo ZW, Mao C, Gan Y, Yu H (2017) OsFTIP1-Mediated regulation of Florigen transport in rice is negatively regulated by the ubiquitin-like domain kinase OsUbDKγ4. Plant Cell 29(3):491–507. https://doi.org/10.1105/tpc.16.00728
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K (2009) Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc Natl Acad Sci 106(11):4555–4560. https://doi.org/10.1073/pnas.0812092106
Article
PubMed
PubMed Central
Google Scholar
Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K (2007) Hd3a protein is a mobile flowering signal in rice. Science 316(5827):1033–1036. https://doi.org/10.1126/science.1141753
Article
CAS
PubMed
Google Scholar
Tamaki S, Tsuji H, Matsumoto A, Fujita A, Shimatani Z, Terada R, Sakamoto T, Kurata T, Shimamoto K (2015) FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice. Proc Natl Acad Sci USA 112(8):E901-910. https://doi.org/10.1073/pnas.1417623112
Article
CAS
PubMed
PubMed Central
Google Scholar
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40(11):1360–1364. https://doi.org/10.1038/ng.197
Article
CAS
PubMed
Google Scholar
Taoka K, Ohki I, Tsuji H, Furuita K, Hayashi K, Yanase T, Yamaguchi M, Nakashima C, Purwestri YA, Tamaki S, Ogaki Y, Shimada C, Nakagawa A, Kojima C, Shimamoto K (2011) 14–3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature 476(7360):332–335. https://doi.org/10.1038/nature10272
Article
CAS
PubMed
Google Scholar
Tsuji H (2017) Molecular function of florigen. Breed Sci 67(4):327–332. https://doi.org/10.1270/jsbbs.17026
Article
CAS
PubMed
PubMed Central
Google Scholar
Turck F, Fornara F, Coupland G (2008) Regulation and identity of florigen: flowering locus T moves center stage. Annu Rev Plant Biol 59:573–594. https://doi.org/10.1146/annurev.arplant.59.032607.092755
Article
CAS
PubMed
Google Scholar
Wang L, Wang A, Huang X, Zhao Q, Dong G, Qian Q, Sang T, Han B (2011) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 122(2):327–340. https://doi.org/10.1007/s00122-010-1449-8
Article
PubMed
Google Scholar
Wang S, Basten C, Zeng Z (2012b) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012a) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44(8):950–954. https://doi.org/10.1038/ng.2327
Article
CAS
PubMed
Google Scholar
Wei X, Qiu J, Yong K, Fan J, Zhang Q, Hua H, Liu J, Wang Q, Olsen KM, Han B, Huang X (2021) A quantitative genomics map of rice provides genetic insights and guides breeding. Nat Genet 53(2):243–253. https://doi.org/10.1038/s41588-020-00769-9
Article
CAS
PubMed
Google Scholar
Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153(4):1747–1758. https://doi.org/10.1104/pp.110.156943
Article
CAS
PubMed
PubMed Central
Google Scholar
Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (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. https://doi.org/10.1139/g06-005
Article
CAS
PubMed
Google Scholar
Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genom 11:656. https://doi.org/10.1186/1471-2164-11-656
Article
CAS
Google Scholar
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40(6):761–767. https://doi.org/10.1038/ng.143
Article
CAS
PubMed
Google Scholar
Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd71 plays an important role in grain yield and adaptation in rice. Cell Res 23(7):969–971. https://doi.org/10.1038/cr.2013.43
Article
CAS
PubMed
PubMed Central
Google Scholar
Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4(2):319–330. https://doi.org/10.1093/mp/ssq070
Article
CAS
PubMed
Google Scholar
Yano M, Harushima Y, Nagamura Y, Kurata N, Minobe Y, Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95(7):1025–1032. https://doi.org/10.1007/s001220050658
Article
CAS
Google Scholar
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12(12):2473–2484. https://doi.org/10.1105/tpc.12.12.2473
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, Xie D, Sun C (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52(5):891–898. https://doi.org/10.1111/j.1365-313X.2007.03284.x
Article
CAS
PubMed
Google Scholar
Yuan R, Zhao N, Usman B, Luo L, Liao S, Qin Y, Nawaz G, Li R (2020) Development of chromosome segment substitution lines (CSSLs) derived from guangxi wild rice (Oryza rufipogon Griff) under rice (Oryza sativa L) background and the identification of QTLS for plant architecture, agronomic traits and cold tolerance. Genes. https://doi.org/10.3390/genes11090980
Article
PubMed
PubMed Central
Google Scholar
Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2(12):983–989. https://doi.org/10.1038/35103590
Article
CAS
PubMed
Google Scholar
Zeng D, Tian Z, Rao Y, Dong G, Yang Y, Huang L, Leng Y, Xu J, Sun C, Zhang G, Hu J, Zhu L, Gao Z, Hu X, Guo L, Xiong G, Wang Y, Li J, Qian Q (2017) Rational design of high-yield and superior-quality rice. Nature Plants 3:17031. https://doi.org/10.1038/nplants.2017.31
Article
PubMed
Google Scholar
Zhang B, Shang L, Ruan B, Zhang A, Yang S, Jiang H, Liu C, Hong K, Lin H, Gao Z, Hu J, Zeng D, Guo L, Qian Q (2019) Development of three sets of high-throughput genotyped rice chromosome segment substitution lines and qtl mapping for eleven traits. Rice 12(1):33. https://doi.org/10.1186/s12284-019-0293-y
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang G, Zeng RZ, Zhang Z, Ding XH, Li WT, Liu GM, He F-H, Tulukdar A, Huang CF, Xi ZY, Qin LJ, Shi JQ, Zhao FM, Feng MJ, Shan ZL, Chen L, Guo XQ, Zhu HT, Lu YG (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 Q (2007) Strategies for developing green super rice. Proc Natl Acad Sci USA 104(42):16402–16409. https://doi.org/10.1073/pnas.0708013104
Article
PubMed
PubMed Central
Google Scholar
Zhang Y, Luo L, Xu C, Zhang Q, Xing Y (2006) Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor Appl Genet 113(2):361–368. https://doi.org/10.1007/s00122-006-0305-3
Article
CAS
PubMed
Google Scholar
Zhao J, Chen H, Ren D, Tang H, Qiu R, Feng J, Long Y, Niu B, Chen D, Zhong T, Liu YG, Guo J (2015) Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa). New Phytol 208(3):936–948. https://doi.org/10.1111/nph.13503
Article
CAS
PubMed
Google Scholar
Zhao Q, Huang X, Lin Z, Han B (2010) SEG-map: a novel software for genotype calling and genetic map construction from next-generation sequencing. Rice 3(2):98–102. https://doi.org/10.1007/s12284-010-9051-x
Article
Google Scholar
Zhu J, Niu Y, Tao Y, Wang J, Jian J, Tai S, Li J, Yang J, Zhong W, Zhou Y, Liang G (2015) Construction of high-throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading date. Plant Breed 134(2):156–163. https://doi.org/10.1111/pbr.12248
Article
CAS
Google Scholar
Zhu W, Lin J, Yang D, Zhao L, Zhang Y, Zhu Z, Chen T, Wang C (2009) Development of chromosome segment substitution lines derived from backcross between two sequenced rice cultivars, Indica recipient 93–11 and Japonica donor nipponbare. Plant Mol Biol Report 27(2):126–131. https://doi.org/10.1007/s11105-008-0054-3
Article
CAS
Google Scholar