title: qRT9, a quantitative trait locus controlling root thickness and root length in upland rice.
abstract: Breeding for strong root systems is an important strategy for improving drought avoidance in rice. To clone genes responsible for strong root traits, an upland rice introgression line IL392 with thicker and longer roots than the background parent lowland rice Yuefu was selected. A quantitative trait locus (QTL), qRT9, controlling root thickness and root length was detected under hydroponic culture using 203 F(2:3) populations derived from a cross between Yuefu and IL392. The qRT9 locus explained 32.5% and 28.1% of the variance for root thickness and root length, respectively. Using 3185 F2 plants, qRT9 was ultimately narrowed down to an 11.5 kb region by substitution mapping. One putative basic helix-loop-helix (bHLH) transcription factor gene, LOC_Os09g28210 (named OsbHLH120), is annotated in this region. Sequences of OsbHLH120 in 11 upland rice and 13 lowland rice indicated that a single nucleotide polymorphism (SNP) at position 82 and an insertion/deletion (Indel) at position 628-642 cause amino acid changes and are conserved between upland rice and lowland rice. Phenotypic analysis indicated that the two polymorphisms were significantly associated with root thickness and root length under hydroponic culture. Quantitative real-time PCR showed that OsbHLH120 was strongly induced by polyethylene glycol (PEG), salt, and abscisic acid, but higher expression was present in IL392 roots than in Yuefu under PEG and salt stress. The successfully isolated locus, qRT9, enriches our knowledge of the genetic basis for drought avoidance and provides an opportunity for breeding drought avoidance varieties by utilizing valuable genes in the upland rice germplasm.
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Junzhou
authors.initials: J
authors.lastname: Li
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Han
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Yipeng
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Yanxiu
authors.initials: Y
authors.lastname: Du
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Hongzheng
authors.initials: H
authors.lastname: Sun
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China qzzhaoh@126.com.
authors.forename: Quanzhi
authors.initials: Q
authors.lastname: Zhao
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D056726:Genetic Association Studies; D008969:Molecular Sequence Data; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D000069600:Plant Breeding; D018517:Plant Roots / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D016415:Sequence Alignment; D013312:Stress, Physiological
keywords: Oryza sativa; qRT9; quantitative trait locus; root length; root thickness; upland rice.