title: Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.
abstract: BACKGROUND
  Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.
  
  
  RESULTS
  Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the -QTL BILs and IR64, four major-effect QTL--one each on chromosomes 2, 4, 9, and 10--were identified. Meta-analysis of transcriptome data from the +QTL/-QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia.
  
  
  CONCLUSIONS
  Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.
authors.affiliation: International Rice Research Institute-IRRI, Los Baños, Laguna, Philippines.
authors.forename: B P Mallikarjuna
authors.initials: BP
authors.lastname: Swamy
authors.forename: Helal Uddin
authors.initials: HU
authors.lastname: Ahmed
authors.forename: Amelia
authors.initials: A
authors.lastname: Henry
authors.forename: Ramil
authors.initials: R
authors.lastname: Mauleon
authors.forename: Shalabh
authors.initials: S
authors.lastname: Dixit
authors.forename: Prashant
authors.initials: P
authors.lastname: Vikram
authors.forename: Ram
authors.initials: R
authors.lastname: Tilatto
authors.forename: Satish B
authors.initials: SB
authors.lastname: Verulkar
authors.forename: Puvvada
authors.initials: P
authors.lastname: Perraju
authors.forename: Nimai P
authors.initials: NP
authors.lastname: Mandal
authors.forename: Mukund
authors.initials: M
authors.lastname: Variar
authors.forename: S
authors.initials: S
authors.lastname: Robin
authors.forename: Ranganath
authors.initials: R
authors.lastname: Chandrababu
authors.forename: Onkar N
authors.initials: ON
authors.lastname: Singh
authors.forename: Jawaharlal L
authors.initials: JL
authors.lastname: Dwivedi
authors.forename: Sankar Prasad
authors.initials: SP
authors.lastname: Das
authors.forename: Krishna K
authors.initials: KK
authors.lastname: Mishra
authors.forename: Ram B
authors.initials: RB
authors.lastname: Yadaw
authors.forename: Tamal Lata
authors.initials: TL
authors.lastname: Aditya
authors.forename: Biswajit
authors.initials: B
authors.lastname: Karmakar
authors.forename: Kouji
authors.initials: K
authors.lastname: Satoh
authors.forename: Ali
authors.initials: A
authors.lastname: Moumeni
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Hei
authors.initials: H
authors.lastname: Leung
authors.forename: Arvind
authors.initials: A
authors.lastname: Kumar
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000383:Agriculture / Q000379:methods*; D003433:Crosses, Genetic; D055864:Droughts; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D040641:Quantitative Trait Loci / Q000235:genetics*; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*