title: Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.
abstract: Deep rooting is a very important trait for plants' drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding.
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China.
authors.forename: Qiaojun
authors.initials: Q
authors.lastname: Lou
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China cl@sagc.org.cn lijun@sagc.org.cn.
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Hanwei
authors.initials: H
authors.lastname: Mei
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wei
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Fangjun
authors.initials: F
authors.lastname: Feng
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Hui
authors.initials: H
authors.lastname: Xia
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China.
authors.forename: Tiemei
authors.initials: T
authors.lastname: Li
authors.affiliation: Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China cl@sagc.org.cn lijun@sagc.org.cn.
authors.forename: Lijun
authors.initials: L
authors.lastname: Luo
mesh_terms: D002874:Chromosome Mapping; D055106:Genome-Wide Association Study; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: Drought avoidance; genome-wide association study (GWAS); quantitative trait locus (QTL); ratio of deep rooting (RDR); rice; root architecture; selective sweep.