Identification of QTLs controlling low-temperature germination of the East European rice (Oryza sativa L.) variety Maratteli

Satoh, T.; Tezuka, Kazuhiko; Kawamoto, Tomohiko; Matsumoto, Shinichi; Satoh-Nagasawa, Namiko; Uéda, Kenji; Sakurai, Kazuo; Watanabe, Akio; Takahashi, Hidekazu; Akagi, Hiromori

doi:10.1007/s10681-015-1531-z

Cited by 38 publications

(34 citation statements)

References 22 publications

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“…Germination and early seedling growth traits are governed by a combination of multiple QTLs and genes. The complex inheritance and phenotypic expression are significantly affected by environmental factors (Cruz et al 2006;Satoh et al 2016;Shakiba et al 2017;Zhao et al 2017). Genetic dissection of potential chromosomal regions harboring QTLs related to LTS tolerance during germination and the early seedling stage is expected to reveal the genetic control of the trait.…”

Section: Discussionmentioning

confidence: 99%

“…LTS tolerance in rice is a very complex and polygenic trait that is genetically controlled by multiple QTLs. Several LTS tolerance QTLs have been mapped on different genomic regions distributed on all 12 rice chromosomes using various types of molecular markers such as RFLP, AFLP, SSR, STS, and SNP, which has facilitated the identification of chromosomal regions associated with tolerance of low temperature (Andaya and Tai 2006;Lou et al 2007;Ji et al 2010;Ye et al 2010;Jena et al 2012;Verma et al 2014;Satoh et al 2016;Wang et al 2016a;Jiang et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

et al. 2020

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An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BC I F 7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

et al. 2020

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“…Among the japonica gene pool, the European varieties Arroz da Terra and Italica Livorno have been employed as cold tolerant parents in breeding programs [ 30 , 31 ], and some advanced populations derived from these crosses have been used to map QTLs related to LTG [ 24 ]. The favourable qLTG3-1 allele of Italica Livorno detected in the chromosome 3 [ 19 ] has been cloned [ 32 ] and also detected in the cultivar Maratelli, which possesses other positive allele for LTG in chromosome 11, qLTG11-1 [ 33 ]. Using a population of recombinant inbred lines (RILs) derived from the Russian cultivar USSR5, Li et al [ 34 ] identified three QTLs associated to LTG in chromosomes 7, 9 and 12, and fine mapped the locus showing the largest effect, qLTG9.…”

Section: Introductionmentioning

confidence: 99%

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

et al. 2017

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A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

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“…During the seed development period, various factors, such as environment and genetic background, influence low-temperature germination [ 7 ]. In rice cultivating regions, in areas where rice is irrigated with cold water, weak seedling growth and slow growth reduce yield significantly [ 8 , 9 , 10 , 11 , 12 , 13 ].…”

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

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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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Identification of QTLs controlling low-temperature germination of the East European rice (Oryza sativa L.) variety Maratteli

Cited by 38 publications

References 22 publications

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

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

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