title: Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.).
abstract: The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Chengsong
authors.initials: C
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Yunlu
authors.initials: Y
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Hongzhou
authors.initials: H
authors.lastname: An
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Weijie
authors.initials: W
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
authors.forename: Gaoming
authors.initials: G
authors.lastname: Chen
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Huqu
authors.initials: H
authors.lastname: Zhai
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China. wangchm@njau.edu.cn.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China. wangchm@njau.edu.cn.
authors.forename: Chunming
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China. wanjianmin@caas.cn.|National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. wanjianmin@caas.cn.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wan
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D056726:Genetic Association Studies; D008040:Genetic Linkage; D023281:Genomics; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics; D009584:Nitrogen / Q000378:metabolism*; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*
chemical_list: D009584:Nitrogen
keywords: Association mapping; Breeding value; NUE; Rice