Ahmadi N., Audebert A., Bennett M. J., Bishopp A., de Oliveira A. C., Courtois B. et al. 2014 The roots of future rice harvests. Rice 7, 1–9.

Article  Google Scholar 

Alexander D. H., Novembre J. and Lange K. 2009 Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Belanger E., Lucotte M., Gregoire B., Moingt M., Paquet S., Davidson R. et al. 2015 Lignin signatures of vegetation and soils in tropical environments. Adv. Environ. Res. 4, 247–262.

Article  Google Scholar 

Benjamini Y. and Hochberg Y. 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Stat. Methodol. 57, 289–300.

Google Scholar 

Bomba L., Nicolazzi E. L., Milanesi M., Negrini R., Mancini G., Biscarini F. et al. 2015 Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection. Genet. Sel. 47, 1–14.

Google Scholar 

Browning B. L., Zhou Y. and Browning S. R. 2018 A one-penny imputed genome from next-generation reference panels. Am. J. Hum. Genet. 103, 338–348.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen X., Shang J., Chen D., Lei C., Zou Y., Zhai W. et al. 2006 AB-lectin receptor kinase gene conferring rice blast resistance. Plant J. 46, 794–804.

Article  CAS  PubMed  Google Scholar 

Chiniquy D., Varanasi P., Oh T., Harholt J., Katnelson J., Singh S. et al. 2013 Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis. Front. Plant Sci. 4, 83.

Article  PubMed  PubMed Central  Google Scholar 

Chu G., Chen T., Wang Z., Yang J. and Zhang J. 2014 Reprint of Morphological and physiological traits of roots and their relationships with water productivity in water-saving and drought-resistant rice. Field Crops Res. 165, 36–48.

Article  Google Scholar 

Cook D. E. and Andersen E. C. 2017 VCF-kit: assorted utilities for the variant call format. Bioinformatics 33, 1581–1582.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cosgrove D. J. 2005 Growth of the plant cell wall. Nat. Rev. Mol. Cell Biol. 6, 850–861.

Article  CAS  PubMed  Google Scholar 

Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A. et al. 2011 The variant call format and VCFtools. Bioinformatics 27, 2156–2158.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Decker J. E., McKay S. D., Rolf M. M., Kim J., Molina A. A., Sonstegard T. S. et al. 2014 Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 10, e1004254.

Article  PubMed  PubMed Central  Google Scholar 

Dong N.-Q., Sun Y., Guo T., Shi C.-L., Zhang Y.-M., Kan Y. et al. 2020 UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat. Commun. 11, 1–16.

Article  CAS  Google Scholar 

Durinck S., Spellman P. T., Birney E. and Huber W. 2009 Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fageria N., Slaton N. and Baligar V. 2003 Nutrient management for improving lowland rice productivity and sustainability. Adv. Agron. 80, 63–152.

Article  CAS  Google Scholar 

Feuk L., Carson A. R. and Scherer S. W. 2006 Structural variation in the human genome. Nat. Rev. Genet. 7, 85–97.

Article  CAS  PubMed  Google Scholar 

Fukuda M., Soma D. M., Iwasaki S., Nakamura S., Kanda T., Ouattara K. and Nagumo F. 2021 Site-specific responses of lowland rice to acidulated and calcined phosphate rock fertilizers in the Center-West region of Burkina Faso. PLoS One 16, e0250240.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fuller D. Q., Sato Y.-I., Castillo C., Qin L., Weisskopf A. R., Kingwell-Banham E. J. et al. 2010 Consilience of genetics and archaeobotany in the entangled history of rice. Archaeol. Anthropol. Sci. 2, 115–131.

Article  Google Scholar 

Gamuyao R., Chin J. H., Pariasca-Tanaka J., Pesaresi P., Catausan S., Dalid C. et al. 2012 The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488, 535–539.

Article  CAS  PubMed  Google Scholar 

Grossman S. R., Shylakhter I., Karlsson E. K., Byrne E. H., Morales S., Frieden G. et al. 2010 A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327, 883–886.

Article  CAS  PubMed  Google Scholar 

He Z., Zou T., Xiao Q., Yuan G., Liu M., Tao Y. et al. 2021 An L-type lectin receptor-like kinase promotes starch accumulation during rice pollen maturation. Development 148, dev196378.

Article  CAS  PubMed  Google Scholar 

Hill W. and Robertson A. 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226–231.

Article  CAS  PubMed  Google Scholar 

Huang L., Wang W., Zhang N., Cai Y., Liang Y., Meng X. et al. 2021 LAZY2 controls rice tiller angle through regulating starch biosynthesis in gravity-sensing cells. New Phytol. 231, 1073–1087.

Article  CAS  PubMed  Google Scholar 

Huang X., Kurata N., Wang Z.-X., Wang A., Zhao Q., Zhao Y. et al. 2012 A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Islam T., Manna M., Kaul T., Pandey S., Reddy C. S. and Reddy M. 2015 Genome-wide dissection of Arabidopsis and rice for the identification and expression analysis of glutathione peroxidases reveals their stress-specific and overlapping response patterns. Plant Mol. Biol. Rep. 33, 1413–1427.

Article  CAS  Google Scholar 

Jensen J. D., Kim Y., DuMont V. B., Aquadro C. F. and Bustamante C. D. 2005 Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170, 1401–1410.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jing Q., Spiertz J., Hengsdijk H., Van Keulen H., Cao W. and Dai T. 2010 Adaptation and performance of rice genotypes in tropical and subtropical environments. NJAS-Wagen. J. Life Sci. 57, 149–157.

Article  Google Scholar 

Joshi T., Pandey S. C., Maiti P., Tripathi M., Paliwal A., Nand M. et al. 2021 Antimicrobial activity of methanolic extracts of Vernonia cinerea against Xanthomonas oryzae and identification of their compounds using in silico techniques. Plos One 16, e0252759.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ju C., Buresh R. J., Wang Z., Zhang H., Liu L., Yang J. and Zhang J. 2015 Root and shoot traits for rice varieties with higher grain yield and higher nitrogen use efficiency at lower nitrogen rates application. Field Crops Res. 175, 47–55.

Article  Google Scholar 

Kim I. A., Kim B.-G., Kim M. and Ahn J.-H. 2012 Characterization of hydroxycinnamoyltransferase from rice and its application for biological synthesis of hydroxycinnamoyl glycerols. Phytochemistry 76, 25–31.

Article  CAS  PubMed  Google Scholar 

Kiple K. F., Ornelas K. 2000 The Cambridge world history of food. Cambridge University Press.

Book  Google Scholar 

Kiryu M., Hamanaka M., Yoshitomi K., Mochizuki S., Akimitsu K. and Gomi K. 2018 Rice terpene synthase 18 (OsTPS18) encodes a sesquiterpene synthase that produces an antibacterial (E)-nerolidol against a bacterial pathogen of rice. J. Genet. Plant Pathol. 84, 221–229.

Article  CAS  Google Scholar 

Koiwa H., Li F., McCully M. G., Mendoza I., Koizumi N., Manabe Y. et al. 2003 The STT3a subunit isoform of the Arabidopsis oligosaccharyltransferase controls adaptive responses to salt/osmotic stress. Plant Cell 15, 2273–2284.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kondo M., Aguilar A., Abe J. and Morita S. 2000 Anatomy of nodal roots in tropical upland and lowland rice varieties. Plant Prod. Sci. 3(4), 437–445.

Article  Google Scholar 

Kushwaha H. R., Joshi R., Pareek A. and Singla-Pareek S. L. 2016 MATH-domain family shows response toward abiotic stress in Arabidopsis and rice. Front. Plant Sci. 7, 923.

Article  PubMed  PubMed Central  Google Scholar 

La Camera S., Gouzerh G., Dhondt S., Hoffmann L., Fritig B., Legrand M. and Heitz T. 2004 Metabolic reprogramming in plant innate immunity: the contributions of phenylpropanoid and oxylipin pathways. Immunol. Rev. 198, 267–284.

Article  PubMed  Google Scholar 

Lavarenne J., Gonin M., Champion A., Javelle M., Adam H., Rouster J. et al. 2020 Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice. PLoS One 15, e0238736.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee G. W., Lee S., Chung M.-S., Jeong Y. S. and Chung B. Y. 2015 Rice terpene synthase 20 (OsTPS20) plays an important role in producing terpene volatiles in response to abiotic stresses. Protoplasma 252, 997–1007.