Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

Yang, Liuqing; Lei, Lei; Wang, Jingguo; Wang, Chao; Yang, Fan; Chen, Jiahui; Liu, Hualong; Zheng, Hongliang; Wei, Xin; Zou, Detang

doi:10.3389/fpls.2021.647239

Cited by 21 publications

(10 citation statements)

References 73 publications

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“…Cold stress seriously affects the growth, development, yield, and quality of crops, and is a key limiting factor for rice production at higher altitudes and colder agricultural regions [ 23 ]. Many molecular studies have been performed on reference rice cultivars, providing important insights into the response to stress, although variability leads to the notion that conclusions are not always translatable to other cultivars with agronomic relevance.…”

Section: Discussionmentioning

confidence: 99%

An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

et al. 2022

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Background Rice (Oryza sativa L.) is one of the most widely grown food crops, and its yield and quality are particularly important for a warm-saturated diet. Cold stress restricts rice growth, development, and yield; however, the specific mechanism of cold tolerance in rice remains unknown. Results The analysis of leaf physiological and photosynthetic characteristics showed that the two rice varieties were significantly affected by cold stress, but the cold-tolerant variety KY131 had more stable physiological characteristics, maintaining relatively good photosynthetic capacity. To better explore the transcriptional regulation mechanism and biological basis of rice response to cold stress, a comprehensive analysis of the rice transcriptome and lipidome under low temperature and control temperature conditions was carried out. The transcriptomic analysis revealed that lipid metabolism, including membrane lipid and fatty acid metabolism, may be an important factor in rice cold tolerance, and 397 lipid metabolism related genes have been identified. Lipidomics data confirmed the importance of membrane lipid remodeling and fatty acid unsaturation for rice adaptation to cold stress. This indicates that the changes in the fluidity and integrity of the photosynthetic membrane under cold stress lead to the reduction of photosynthetic capacity, which could be relieved by increased levels of monogalactosyldiacylglycerol that mainly caused by markedly increased expression of levels of 1,2-diacylglycerol 3-beta-galactosyltransferase (MGD). The upregulation of phosphatidate phosphatase (PAP2) inhibited the excessive accumulation of phosphatidate (PA) to produce more phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), thereby preventing of membrane phase transition under cold stress. In addition, fatty acid β-oxidation is worth further study in rice cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of cold tolerance in rice, in which the advanced lipid metabolism system plays a central role. Conclusions Lipidome analysis showed that membrane lipid composition and unsaturation were significantly affected, especially phospholipids and galactolipids. Our study provides new information to further understand the response of rice to cold stress.

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Section: Discussionmentioning

confidence: 99%

An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

et al. 2022

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“…QTL-seq analysis allows rapid detection of the homozygous variants of a given phenotype by whole-genome resequencing of two bulked populations [18,27]. QTL-seq makes use of combined benefits of bulk-segregating analysis (BSA) and whole-genome resequencing, which can be used to identify the genomic regions responsible for the mutant phenotype in a single step [18,[28][29][30]. The QTL-seq technique was recently applied to the cucumber population to identify the putative variants closely linked to causal genes responsible for subgynoecy, powdery mildew resistance, and light-green immature fruit skin traits in cucumber [13,31,32].…”

Section: Discussionmentioning

confidence: 99%

Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (Cucumis sativus L.) Using QTL-seq and Marker Analyses

Kishor

Alavilli

Lee

et al. 2021

Plants

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Despite various efforts in identifying the genes governing the white immature fruit skin color in cucumber, the genetic basis of the white immature fruit skin color is not well known. In the present study, genetic analysis showed that a recessive gene confers the white immature fruit skin-color phenotype over the light-green color of a Korean slicer cucumber. High-throughput QTL-seq combined with bulked segregation analysis of two pools with the extreme phenotypes (white and light-green fruit skin color) in an F2 population identified two significant genomic regions harboring QTLs for white fruit skin color within the genomic region between 34.1 and 41.67 Mb on chromosome 3, and the genomic region between 12.2 and 12.7 Mb on chromosome 5. Further, nonsynonymous SNPs were identified with a significance of p < 0.05 within the QTL regions, resulting in eight homozygous variants within the QTL region on chromosome 3. SNP marker analysis uncovered the novel missense mutations in Chr3CG52930 and Chr3CG53640 genes and showed consistent results with the phenotype of light-green and white fruit skin-colored F2 plants. These two genes were located 0.5 Mb apart on chromosome 3, which are considered strong candidate genes. Altogether, this study laid a solid foundation for understanding the genetic basis and marker-assisted breeding of immature fruit skin color in cucumber.

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“…(2020) Bulk segregant analysis SNP; SNP; SSR Castor bean; Rice ( Oryza sativa ); Soybean Wang et al. (2021) ; Yang et al. (2021) ; Sreenivasa et al.…”

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

105

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The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

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Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

Cited by 21 publications

References 73 publications

An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (Cucumis sativus L.) Using QTL-seq and Marker Analyses

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

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