QTLs for Seedling Growth of Direct Seeded Rice under Submerged and Low Temperature Conditions

Fukuda, Akari; Kataoka, Takao; Shiratsuchi, Hiroyuki; Fukushima, Akira; Yamaguchi, Hiromichi; Mochida, Hideyuki; Ogiwara, H.

doi:10.1626/pps.17.41

Cited by 10 publications

(16 citation statements)

References 21 publications

(29 reference statements)

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“…In addition, a near isogenic line of qAG-9-2 showed better seedling establishment under flooding stress compared with the background variety, showing a higher grain yield in the paddy field (Chamara et al, 2018;Lal et al, 2018). In high latitude areas such as in East Asia, seedling emergence were observed under low temperature conditions in addition to flooding stress (Fukuda et al, 2014;Iwata et al, 2010). Coleoptile elongation under anaerobic conditions is considered to be one of the most important traits associated with seedling establishment (Adachi et al, 2015;Ogiwara & Terashima, 2009).…”

Section: Introductionmentioning

confidence: 99%

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

Nishimura

Sasaki

Yamaguchi

et al. 2020

Plant Production Science

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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.

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Section: Introductionmentioning

confidence: 99%

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

Nishimura

Sasaki

Yamaguchi

et al. 2020

Plant Production Science

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“…In addition, Lee et al (2015) detected two colocalized QTLs for LTG and coleoptile length under a low-temperature condition (13 °C) [ 6 ]. Fukuda et al (2015) also identified two QTLs associated with coleoptile length under 16 °C conditions [ 23 ]. Using the genome-wide association (GWAS) method, two QTLs associated with germination under cold tolerance, qCTGERM8-1 and qCTGERM8-2 , were identified in 421 accessions from a rice diversity panel (RDP1) [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice

Akhtamov

Adeva

Shim

et al. 2020

Genes

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Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC3F8 lines derived from an interspecific cross between the Korean japonica cultivar “Hwaseong” and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F2 population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant, implying that the QTLs act in an additive manner. Near-isogenic line plants with the combination of favorable alleles from O. rufipogon and Hwaseong exhibited higher LTG than two introgression lines. With regard to coleoptile length, three QTLs observed on chromosomes 1, 3, and 8 were colocalized with QTLs for LTG, suggesting the pleiotropy of the single gene at each locus. According to the results, the introgression of favorable O. rufipogon alleles could hasten the development of rice with high LTG and high coleoptile elongation in japonica cultivars.

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“…Therefore, although seedling growth rate and other agronomical traits have been suggested to be regulated by complex genetic and environment interactions, it is important to elucidate the genetic factors involved in enhancing these traits, as this will allow selecting preferable traits during rice breeding to improve the efficacy of direct seeding. One tool used to identify genetic factors affecting agronomical traits is quantitative trait loci (QTLs) analysis, which was previously performed to evaluate traits affecting seedling vigor (Iwata et al, 2010; Abe et al, 2012; Yano et al, 2012; Fukuda et al, 2014). However, QTLs analysis is laborious, time consuming, and only reveals genomic mutations; in some cases, it also involves significant genetic bias.…”

Section: Introductionmentioning

confidence: 99%

Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data

et al. 2018

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Seedling growth is an important factor for direct seeding of rice. However, the genetic and transcriptomic factors involved in this process are largely unknown. In this study, transcripts affecting shoot weight were identified in rice (Oryza sativa L.) using RNA sequencing (RNA-Seq) data from 20 backcrossed inbred lines (BILs) and their parental cultivars. The selection frequency of the genes for the regression model was determined using repeated analysis of random subsets of the transcriptome. The qLTG3-1gene, controlling low-temperature germinability, and short grain 1 gene (SG1), known to decrease organ elongation, showed high frequency. The quantitative trait loci (QTLs) analysis performed for BILs revealed that qLTG3-1 was included in the QTLs for shoot weight but SG1 was not. No nucleotide polymorphisms were found in the coding region of SG1 in either of the parental cultivars. Quantitative real-time PCR showed that SG1 expression was negatively correlated with shoot weight for all 104 BILs analyzed in this study. Expression QTL (eQTLs) analysis showed an eQTL for SG1 expression located in the same region as the QTL for shoot weight. However, no eQTLs were detected on the same chromosome as SG1, suggesting that nucleotide polymorphisms around the gene do not affect its expression in analyzed growth stage. Overall, these results indicate that RNA-Seq is a useful tool for identifying transcripts that can be related to seedling growth rate.

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QTLs for Seedling Growth of Direct Seeded Rice under Submerged and Low Temperature Conditions

Cited by 10 publications

References 21 publications

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice

Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data

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