title: Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.
abstract: Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Hu
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] Department of Horticulture, Michigan State University, East Lansing, Michigan, USA.
authors.forename: Shujun
authors.initials: S
authors.lastname: Ou
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jiuyou
authors.initials: J
authors.lastname: Tang
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Ronghui
authors.initials: R
authors.lastname: Che
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: College of Life Science, Capital Normal University, Beijing, China.
authors.forename: Xuyang
authors.initials: X
authors.lastname: Chai
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Hongru
authors.initials: H
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yiqin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Chengzhen
authors.initials: C
authors.lastname: Liang
authors.affiliation: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Linchuan
authors.initials: L
authors.lastname: Liu
authors.affiliation: Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Zhongze
authors.initials: Z
authors.lastname: Piao
authors.affiliation: China National Hybrid Rice Research and Development Center, Changsha, China.
authors.forename: Qiyun
authors.initials: Q
authors.lastname: Deng
authors.affiliation: School of Agriculture, Henan University of Science and Technology, Luoyang, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Chi
authors.initials: C
authors.lastname: Xu
authors.affiliation: 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liang
authors.affiliation: School of Agriculture, Henan University of Science and Technology, Luoyang, China.
authors.forename: Lianhe
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Life Science, Capital Normal University, Beijing, China.
authors.forename: Legong
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Chengcai
authors.initials: C
authors.lastname: Chu
mesh_terms: D000483:Alleles; D000818:Animals; D027321:Anion Transport Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D002478:Cells, Cultured; D049810:Genetic Speciation; D014644:Genetic Variation; D000091285:Nitrate Transporters; D009566:Nitrates / Q000378:metabolism; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D014982:Xenopus laevis
chemical_list: D027321:Anion Transport Proteins; D000091285:Nitrate Transporters; D009566:Nitrates; D010940:Plant Proteins