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

Abstract

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.

Fig 1. Schematic outline of phenotyping, parental polymorphism survey, selective genotyping, local linkage map construction and mapping.

SPAD: SPAD value, LL: leaf length (cm), LW: leaf width (cm), LA: leaf area (cm), DFF: days to 50% flowering, PH: plant height (cm), TNO: tiller number, PNO: panicle number: GRNO: grain number, HSW: hundred seed weight (g), GY: grain yield per plant (g/plant), TDM: total dry matter (g/plant), GNP: grain nitrogen percent, SNP: straw nitrogen percent, GNPP: grain nitrogen/ plant, SNPP: straw nitrogen/ plant, NHI: nitrogen harvest index, RGY: relative grain yield, RBM: relative biomass yield, RGN: relative grain nitrogen, RBN: relative biomass nitrogen, PNUE: physiological nitrogen use efficiency, ANUE: agronomic nitrogen use efficiency, APE: agro- physiological efficiency.

Fig 2

A. Correlation matrix under low N in wet season; B. Correlation matrix under low N in dry season. SPAD: SPAD value, LL: leaf length (cm), LW: leaf width (cm), LA: leaf area (cm), DFF: days to 50% flowering, PH: plant height (cm), TNO: tiller number, PNO: panicle number: GRNO: grain number, HSW: hundred seed weight (g), GY: grain yield per plant (g/plant), TDM: total dry matter (g/plant), GNP: grain nitrogen percent, SNP: straw nitrogen percent, GNPP: grain nitrogen/ plant, SNPP: straw nitrogen/ plant.

Fig 3. Local linkage map of chromosomes 1 and 2 with identified QTL under LN.

WS: Wet season, DS: Dry season, SPAD: SPAD value, LL: leaf length (cm), LW: leaf width (cm), DFF: days to 50% flowering, PH: plant height (cm), GRNO: grain number, HSW: hundred seed weight (g), GY: grain yield per plant (g/plant), TDM: total dry matter (g/plant), SNP: straw nitrogen percent, RBM: relative biomass yield, RGN: relative grain nitrogen, RBN: relative biomass nitrogen.