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

T Vishnukiran,D Subrahmanyam,V Jaldhani,P Vijayalakshmi,S R Voleti,C N Neeraja,P Raghuveer Rao,Ahmad Naeem Shahzad

doi:10.1371/journal.pone.0240854

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.

Highlights

Rice is one of the main cereal crops and staple food for more than half of the world population
Significant variation was observed between the parents (BPT5204 and PTB1) for 24 phenotype traits/parameters studied under low nitrogen (LN) (S5 Table)
There was overall reduction for the 24 traits/parameters of the study under LN in comparison to recommended nitrogen (RN) for both parents, the reduction of relatively less in PTB1 than BPT5204 (S6 Table)

Summary

Introduction

Rice is one of the main cereal crops and staple food for more than half of the world population. Despite the increase in world rice production since the past half century, rice yield improvement is still required to support the growing needs of the increasing world population. Nitrogen (N) is the key nutrient required in large quantities for rice production [1]. 60% of the applied N is lost to the environment through combinations of different processes causing negative effects to the climate [2, 3]. Selection of rice genotypes with efficiency in N.

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Discussion

Conclusion