title: A genomic perspective on the important genetic mechanisms of upland adaptation of rice.
abstract: BACKGROUND
  Cultivated rice consists of two important ecotypes, upland and irrigated, that have respectively adapted to either dry land or irrigated cultivation. Upland rice, widely adopted in rainfed upland areas in virtue of its little water requirement, contains abundant untapped genetic resources, such as genes for drought adaptation. With water shortage exacerbated and population expanding, the need for breeding crop varieties with drought adaptation becomes more and more urgent. However, a previous oversight in upland rice research reveals little information regarding its genetic mechanisms for upland adaption, greatly hindering progress in harnessing its genetic resources for breeding and cultivation.
  
  
  RESULTS
  In this study, we selected 84 upland and 82 irrigated accessions from all over the world, phenotyped them under both irrigated and dry land environments, and investigated the phylogenetic relations and population structure of the upland ecotype using whole genome variation data. Further comparative analysis yields a list of differentiated genes that may account for the phenotypic and physiological differences between upland and irrigated rice.
  
  
  CONCLUSIONS
  This study represents the first genomic investigation in a large sample of upland rice, providing valuable gene list for understanding upland rice adaptation, especially drought-related adaptation, and its subsequent utilization in modern agriculture.
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. lvu.jun@gmail.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Lyu
authors.forename: Baoye
authors.initials: B
authors.lastname: Li
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Shilai
authors.initials: S
authors.lastname: Zhang
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Gou
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Liyun
authors.initials: L
authors.lastname: Meng
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Dayun
authors.initials: D
authors.lastname: Tao
authors.forename: Wangqi
authors.initials: W
authors.lastname: Huang
authors.forename: Fengyi
authors.initials: F
authors.lastname: Hu
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D057914:Agricultural Irrigation; D060146:Ecotype; D017343:Genes, Plant; D005828:Genetics, Population; D018745:Genome, Plant; D005843:Geography; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D010641:Phenotype; D010802:Phylogeny; D018517:Plant Roots / Q000033:anatomy & histology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D019655:Quantitative Trait, Heritable; D013045:Species Specificity