title: QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativaL.).
abstract: Strong seedling vigor is desirable trait in dry direct-seeded rice (DSR) for enhancing crop establishment and the ability to compete against weeds. A set of 253 BC3F4lines derived from cross between Swarna and Moroberekan was phenotyped for early vigor (EV) and 8 related traitsviz., early uniform emergence (EUE), shoot length (SHL), stem length (SL), shoot fresh weight (SFW), total fresh weight (TFW), shoot dry weight (SDW), total dry weight (TDW), and root dry weight (RDW). Composite interval mapping analysis using genotypic data from 194 SNP markers identified six genomic regions associated with traits on chromosomes 3, 4, 5, and 6 with phenotypic variance ranging from 2.5 to 18.6%. Among them 2 QTL regions; one on chr3 (id3001701-id300833) and the other on chr5 (wd5002636-id5001470) were identified as QTL hotspots A and B respectively and expressed consistently in field as well as glasshouse condition. The majority of QTLs identified for early vigor, and related traits were clustered in the QTL hotspots A (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1) and QTL hotspot B (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1). Ten putative candidate genesviz., 1-alpha-amylase precursor, 2-glutamate decarboxylase, 1-ethylene-insensitive 3, 3-expansin precursor, and 3-phenylalanine ammonia-lyase associated with the target traits were identified in the selected QTL regions. Mutations were identified in the coding region of alpha-amylase precursor and ethylene-insensitive 3 gene between the parents which can be utilized in marker assisted breeding. Trait relationships among the agro-physiological traits were examined to select the best genotypes for the given traits for use in future breeding programs.
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISAT Patancheru, India.
authors.forename: Uma M
authors.initials: UM
authors.lastname: Singh
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISATPatancheru, India; Department of Plant Breeding, International Rice Research InstituteMetro Manila, Philippines.
authors.forename: Shailesh
authors.initials: S
authors.lastname: Yadav
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISAT Patancheru, India.
authors.forename: Shilpi
authors.initials: S
authors.lastname: Dixit
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISAT Patancheru, India.
authors.forename: P Janaki
authors.initials: PJ
authors.lastname: Ramayya
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISAT Patancheru, India.
authors.forename: M Nagamallika
authors.initials: MN
authors.lastname: Devi
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISAT Patancheru, India.
authors.forename: K Anitha
authors.initials: KA
authors.lastname: Raman
authors.affiliation: Department of Plant Breeding, International Rice Research Institute-South Asia Hub, ICRISATPatancheru, India; Department of Plant Breeding, International Rice Research InstituteMetro Manila, Philippines.
authors.forename: Arvind
authors.initials: A
authors.lastname: Kumar
keywords: QTL hotspots; candidate genes; direct-seeded rice; early vigor; quantitative trait loci; single nucleotide polymorphism