Q-TARO: QTL Annotation Rice Online Database

Yonemaru, Jun‐ichi; Yamamoto, Tetsuro; Fukuoka, Shuichi; Uga, Yusaku; Hori, Kiyosumi; Yano, Masahiro

doi:10.1007/s12284-010-9041-z

Cited by 170 publications

(147 citation statements)

References 35 publications

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“…In this region, where SPIKE was identified, several QTLs for TSN have been detected, among which the alleles from japonica or tropical japonica cultivars increased TSN (30)(31)(32)(33)(34)(35)(36)(37)(38). Hitherto, no gene for TSN or grain yield in this cluster has been isolated (39). Through high-resolution mapping, we identified SPIKE, which influences TSN and FLW.…”

Section: Discussionmentioning

confidence: 97%

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Fujita

Trijatmiko

Tagle

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

268

253

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Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.qTSN4 | gene validation | pleiotropy | marker-assisted breeding

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Section: Discussionmentioning

confidence: 97%

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Fujita

Trijatmiko

Tagle

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

268

253

View full text Add to dashboard Cite

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“…The locations of genes and QTLs controlling heading date have been recently superimposed on the rice physical map by Yonemaru et al (2010). Based on the information from this database, the locations of the following candidate genes and QTLs are illustrated on the chromosome maps in Fig.…”

Section: Candidate Qtls For Heading Date Based On Substitution Analysismentioning

confidence: 99%

“…SSR marker locations were assigned by BLAST homology searches against IRGSP pseudomolecules Build 5 (http://rapdb.dna.affrc.go.jp/download/index.html). The locations of candidate genes and a QTL for days-to-heading are shown above each chromosome; data were obtained from the QTL annotation database constructed by Yonemaru et al (2010). Arrowheads under the chromosomes indicate the location of the RFLP markers nearest the QTLs previously detected by using RILs (Oda et al 2003).…”

Section: Usefulness Of Cssls For Future Genetic Studies and Breedingmentioning

confidence: 99%

Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65

2010

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We have developed two sets of chromosome segment substitution lines (CSSLs) of cultivated rice (Oryza sativa) carrying donor segments from indica cultivars DV85 and ARC10313. The lines in each set contain chromosomal segments that cover most of the donor genome in a uniform genetic background (ssp. japonica cv. Taichung 65). The starting materials were several recombinant inbred lines derived from the crosses Taichung 65 × DV85 and Taichung 65 × ARC10313. The CSSLs were generated by repeated backcrossing to Taichung 65 (pollen parent), with marker-assisted selection applied at several marker loci. The CSSLs of DV85 (TD-CSSLs) comprise 45 lines that cover 76.6% of the DV85 genome, and the CSSLs of ARC10313 (TA-CSSLs) comprise 44 lines that cover 74.4% of the ARC10313 genome. We investigated the genetic control of days-to-heading in both sets of CSSLs and demonstrated the genetic contribution of several chromosome regions. These CSSLs provide a valuable tool for rice germplasm enhancement, and we expect them to reveal the genetic basis of traits specific to the donor cultivars.

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“…Genes in rice involved in drought tolerance (A) and heat response (B) are shown in their corresponding chromosome locations. Gene data on drought and high temperature were generated from QTARO database (Yonemaru et al, 2010) and from (González-Schain et al, 2016), respectively.…”

Section: Gene Discovery and Regulatory Mechanismsmentioning

confidence: 99%

When water runs dry and temperature heats up: Understanding the mechanisms in rice tolerance to drought and high temperature stress conditions

Rabara¹,

Msanne²,

Ferrer³

et al. 2018

Preprint

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Rice production, owing to its high-water requirement for cultivation, is very vulnerable to the threat of changing climate, particularly prolonged drought and high temperature. Such threats heighten the need for abiotic stress-resilient rice varieties with better yield potential. This review examines the physiological and molecular mechanisms of rice varieties to cope with stress conditions of drought (DS), high temperature (HTS) and their combination (DS-HTS). It appraises research studies in rice about its various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for rice varieties with improved resilience to abiotic stresses. This review consolidates available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to climate-induced abiotic stresses. The development of new breeding and cultivation strategies for climate-resilient rice varieties is a challenging task. It requires a comprehensive understanding of the various morphological, biochemical, physiological, and molecular components governing yield under drought and high temperature, but possible by implementing cohesive approaches involving molecular and systems biology approaches in genomics and molecular breeding, including genetic engineering.

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Q-TARO: QTL Annotation Rice Online Database

Cited by 170 publications

References 35 publications

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65

<strong>When water runs dry and temperature heats up: </strong><strong>Understanding the mechanisms in rice tolerance to drought and </strong><strong>high temperature stress conditions</strong>

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