Abstract
Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l(-1) for 7h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height -1.0%, shoot dry weight -15.9%, tiller number -8.3%, grain weight -9.3%, total panicle weight -19.7%, single panicle weight -5.5%) and biochemical/physiological traits (symptom formation, SPAD value -4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism (SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance.
Highlights
Due to anthropogenic gas emissions, the tropospheric ozone concentration is increasing and negatively affects natural vegetation and crop production (Ainsworth et al, 2012)
We tested the effect of ozone on nine traits, including leaf cell death as represented by leaf bronzing score (LBS); growth parameters such as plant height, shoot dry weight (DW), and tiller number; grain yield component parameters such as Thousand-kernel weight (TKW), total panicle weight (TPW), and single panicle weight (SPW); and biochemical parameters such as chlorophyll content (SPAD value) and foliar lignin content
Plant height decreased by 1.0%, DW decreased by 15.9%, tiller number decreased by 8.3%, TKW decreased by 9.3%, TPW decreased by 19.7%, SPW decreased by 5.5%, SPAD value decreased by 4.4%, and lignin content increased by 3.4%
Summary
Due to anthropogenic gas emissions, the tropospheric ozone concentration is increasing and negatively affects natural vegetation and crop production (Ainsworth et al, 2012). Some typical symptoms of ozone stress in plants are directly related to crop quality and yield: (i) chlorosis and pale colour of leaves; (ii) necrotic dark brown spots or dead regions on leaves; and (iii) reduced growth rate and a stunted phenotype, leading to reduced yield. Among those traits, necrotic dark brown spots are closely related to acute ozone stress and are caused either by direct oxidative damage or by programmed cell death, which involves plant hormonal pathways (Kangasjärvi et al, 2005). Little correlation was observed between the extent of leaf damage and growth reduction (Frei et al, 2008) or grain yield (Sawada and Kohno, 2009) in screening experiments with rice
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