A major pleiotropic QTL identified for yield components and nitrogen content in rice (Oryza sativa L.) under differential nitrogen field conditions

To identify the genomic regions for yield and NUE of rice genotypes and lines with promising yield under low N, a recombinant inbred population (RIL) developed between BPT5204 (a mega variety known for its quality) and PTB1 (variety with high NUE) was evaluated for consecutive wet and dry seasons un...

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Bibliographic Details
Published in:PloS one 2020-10, Vol.15 (10), p.e0240854-e0240854
Main Authors: Vishnukiran, T, Neeraja, C N, Jaldhani, V, Vijayalakshmi, P, Raghuveer Rao, P, Subrahmanyam, D, Voleti, S R
Format: Article
Language:English
Subjects:
Agricultural production
Alleles
Analysis
Biology and Life Sciences
Biomass
Chromosome 2
Chromosome Mapping
Chromosomes
Chromosomes, Plant - genetics
Crop yield
Crop yields
Dry season
Edible Grain - growth & development
Edible Grain - metabolism
Efficiency
Gene mapping
Gene polymorphism
Genes, Plant
Genetic aspects
Genomics
Genotypes
Genotyping
Genotyping Techniques
Grain
Growth
Hybrid rice
Identification and classification
Inbreeding
Markers
Morphology
Nitrogen
Nitrogen - metabolism
Nitrogen content
Nitrogen in agriculture
Oryza - genetics
Oryza - metabolism
Physiology
Polymorphism
Polymorphism, Single Nucleotide
Population
Quantitative trait loci
Quantitative Trait Loci - genetics
Rainy season
Research and Analysis Methods
Rice
Seeds
Single-nucleotide polymorphism
Supervision
Variance analysis
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Summary:To identify the genomic regions for yield and NUE of rice genotypes and lines with promising yield under low N, a recombinant inbred population (RIL) developed between BPT5204 (a mega variety known for its quality) and PTB1 (variety with high NUE) was evaluated for consecutive wet and dry seasons under low nitrogen (LN) and recommended nitrogen (RN) field conditions. A set of 291 RILs were characterized for 24 traits related to leaf, agro-morphological, yield, N content and nitrogen use efficiency indices. More than 50 RILs were found promising with grain yield >10 g under LN. Parental polymorphism survey with 297 SSRs and selective genotyping revealed five genomic regions associated with yield under LN, which were further saturated with polymorphic SSRs. Thirteen promising SSRs were identified out of 144 marker trait associations under LN using single marker analysis. Composite interval mapping showed 37 QTL under LN with five pleiotropic QTL. A major stable pleiotropic (RM13201-RM13209) from PTB1 spanning 825.4 kb region associated with straw N % (SNP) in both treatments across seasons and yield and yield related traits in WS appears to be promising for the MAS. Another major QTL (RM13181-RM13201) was found to be associated with only relative trait parameters of biomass, grain and grain nitrogen. These two major pleiotropic QTL (RM13201-RM13209 and RM13181-RM13201) on chromosome 2 were characterized for their positive allele effect and could be deployed for the development of rice varieties with NUE.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0240854