Abstract
ABSTRACT Low oxygen concentrations in flooded paddy fields cause poor seedling establishment in wet direct seeded rice. We aimed to identify novel genomic regions associated with coleoptile elongation under anaerobic conditions in order to improve seedling establishment. Chromosome segment substitution lines (CSSLs), substituted with Koshihikari (Japonica-type) in the IR 64 genetic background (Indica-type) were evaluated. These lines were imbibed with a hydroponic solution containing Oxyrase to create a stable anaerobic condition and coleoptile lengths were measured six days after incubation at 30°C. Among the CSSLs, only SL2111 had a significantly longer coleoptile (23.9 mm) than that of IR 64 (14.3 mm). From genotype and phenotype analyses, a novel QTL, referred to as qACE3.1, for coleoptile elongation under anaerobic conditions was detected on chromosome 3. To explore the molecular mechanism of qACE3.1, the expression levels of genes encoding enzymes involved in starch degradation and fermentation were assessed. In SL2111 coleoptiles, the expression levels of pyruvate decarboxylase were significantly higher than in IR 64 coleoptiles whereas those of alcohol dehydrogenase were lower. In contrast, no differences were observed in the expression levels of genes associated with starch degradation. These results imply that qACE3.1 may specifically affect fermentative metabolism. In addition, we evaluated the impact of qACE3.1 on seedling establishment under flooded conditions in a paddy field.
Highlights
Direct seeded rice (DSR) helps meet the challenges caused by water and labor shortages, and time and cropping area conflicts
We evaluated coleoptile elongation under anaerobic conditions by adding the enzyme Oxyrase into the hydroponic solution to reduce the oxygen concentration. qACE3.1 was successfully detected on the short arm of chromosome 3 in the population of Chromosome segment substitution lines (CSSLs) which have part of their chromosome segment substituted with Koshihikari in the IR 64 genetic background
Two genetic loci for coleoptile elongation under anaerobic conditions have been detected by genome wide association studies (GWAS) (Hsu & Tung, 2015; Nghi et al, 2019) and quantitative trait locus (QTL) analyses (Jiang et al, 2006; Manangkil et al, 2013)
Summary
Direct seeded rice (DSR) helps meet the challenges caused by water and labor shortages, and time and cropping area conflicts. Soil waterlogging or flooding occurs when the land is not well-levelled in irrigated areas (Kirk et al, 2014) These problems of poor seedling emergence and establishment in flooded soils is further compounded by the subsequent invasion of weeds (Ismail et al, 2012). To overcome these problems, developing of new varieties can emerge their shoot from flooded soils would be beneficial way for DSR in these areas (Ismail et al, 2012). It is important to develop breeding materials that can withstand flooding during seedling emergence
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