title: Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci.
abstract: BACKGROUND
  Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits.
  
  
  RESULTS
  Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY 3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM.
  
  
  CONCLUSIONS
  Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. s.dixit@irri.org.
authors.forename: Shalabh
authors.initials: S
authors.lastname: Dixit
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. a.grondin@irri.org.|Present address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA. a.grondin@irri.org.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Grondin
authors.affiliation: Department of Biology, Duke University, Durham, NC, 27708, USA. cheng-ruei.lee@gmi.oeaw.ac.at.|Present address: Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria. cheng-ruei.lee@gmi.oeaw.ac.at.
authors.forename: Cheng-Ruei
authors.initials: CR
authors.lastname: Lee
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. a.henry@irri.org.
authors.forename: Amelia
authors.initials: A
authors.lastname: Henry
authors.affiliation: Department of Biology, Duke University, Durham, NC, 27708, USA. tmo1@duke.edu.
authors.forename: Thomas-Mitchell
authors.initials: TM
authors.lastname: Olds
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. a.kumar@irri.org.
authors.forename: Arvind
authors.initials: A
authors.lastname: Kumar
mesh_terms: D000220:Adaptation, Biological; D044822:Biodiversity; D017753:Ecosystem; D004777:Environment; D004843:Epistasis, Genetic; D012275:Oryza / Q000502:physiology*; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable