Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation.

Young-Ho Kwon,So-Myeong Lee,Dong-Jin Shin,Nkulu-Rolly Kabange,Ji-Yun Lee,Ju-Won Kang,Jin-Kyung Cha,Jong-Hee Lee,Jong-Min Ko,Jun-Hyeon Cho

doi:10.3390/genes12050745

Abstract

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

Highlights

The global population is increasing at a relatively high growth rate per annum, and is projected to reach about 9.8 billion people by 2050 [1]
The results revealed a normal distribution for plant height (Figure 1A,B, Table S3, under normal and low nitrogen cultivation), number of panicles (Figure 1I, Table S3, under normal nitrogen cultivation), and root length (Figure 1K,L, Table S3, under normal and low nitrogen cultivation)
A positive skewness was recorded for tiller number (Figure 1C,D, Table S3), culm length (Figure 1E, Table S3, under normal nitrogen cultivation), panicle length (Figure 1G,H, Table S3, under normal and low nitrogen cultivation), panicle number (Figure 1J, Table S3, under low nitrogen cultivation), shoot dry weight (Figure 1M,N, Table S3, under both normal and low nitrogen cultivation), and root dry weight (Figure 1O,P, Table S3, under normal and low nitrogen cultivation)

Summary

Introduction

The global population is increasing at a relatively high growth rate per annum, and is projected to reach about 9.8 billion people by 2050 [1]. Since the domestication of rice, this Poaceae is the second most important cereal crop after corn and remains today the only cereal crop solely cultivated for human consumption, in addition to being the staple food crop for more than half of the world’s population, despite the increasing preference for various foods and the diversification of diet. To achieve optimum plant growth and development, and realize their potential in terms of productivity and quality, plant crops require nitrogen (N), among other essential macronutrients [2]. Rice cultivation requires abundant use of nitrogenous fertilizers [7], in high yielding varieties [8]. Excessive application of nitrogenous fertilizers has been associated with the emission of greenhouse gases (GHG), such as methane (CH4) and nitrous oxide (N2O) [9,10,11,12]

Methods

Results

Discussion

Conclusion