Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing

Song, Jiayu; Li, Jinqun; Sun, Jian; Hu, Tao; Wu, Aiting; Liu, Sitong; Wang, Wenjia; Ma, Dianrong; Zhao, Mingzhu

doi:10.3389/fpls.2018.00875

Cited by 32 publications

(20 citation statements)

References 39 publications

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“…Most temperate or hardy plants have evolved specific strategies to survive low temperature, which involves a series of physiological, biochemical, molecular, and metabolic processes [3]. The multifaceted nature of the responses of the plant to cold stress and the intricate relationships between growth and response mechanisms, which in themselves are complex, dictate that cold tolerance is a highly complex, multigenic trait, as evidenced by a large number of quantitative trait locus (QTLs) that have been associated with cold tolerance [4,5]. Transcriptomic studies in model species under controlled conditions have indicated that the transcript abundances of hundreds of genes are altered under the imposition of cold stress [6,7].…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

Jiang

Zhang

Ren

et al. 2020

IJMS

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Plants tolerate cold stress by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. Identifying TFs related to cold tolerance contributes to cold-tolerant crop breeding. In this study, a comparative transcriptome analysis was carried out to investigate global gene expression of entire TFs in two peanut varieties with different cold-tolerant abilities. A total of 87 TF families including 2328 TF genes were identified. Among them, 445 TF genes were significantly differentially expressed in two peanut varieties under cold stress. The TF families represented by the largest numbers of differentially expressed members were bHLH (basic helix—loop—helix protein), C2H2 (Cys2/His2 zinc finger protein), ERF (ethylene-responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), NAC (NAM, ATAF1/2, CUC2) and WRKY TFs. Phylogenetic evolutionary analysis, temporal expression profiling, protein–protein interaction (PPI) network, and functional enrichment of differentially expressed TFs revealed the importance of plant hormone signal transduction and plant-pathogen interaction pathways and their possible mechanism in peanut cold tolerance. This study contributes to a better understanding of the complex mechanism of TFs in response to cold stress in peanut and provides valuable resources for the investigation of evolutionary history and biological functions of peanut TFs genes involved in cold tolerance.

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Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

Jiang

Zhang

Ren

et al. 2020

IJMS

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“…Therefore, it is of high interest to understand other putative roles, if there are any, of DNA markers associated with disease resistance. The significant association between a marker gene and a trait is widely applied using associa-tion mapping approach in many crops including rice (Song et al, 2018). Since the identification of R genes in Egyptian and Saudi Arabian rice has not been well-addressed, it is worthwhile to determine putative local rice genotypes that carry R gene(s).…”

Section: Introductionmentioning

confidence: 99%

Molecular identification of blast resistance genes in rice genotypes using gene-specific markers

Aldaej¹,

Ismail²,

Rezk³

et al. 2019

bta

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Molecular identification of major blast resistance (R ) genes in rice was performed in a group of 10 rice (Oryza sativa) genotypes from Egypt and Saudi Arabia using six DNA markers (T8042, NSB, YL153/YL154, RM3843, RM3330, and z4794) belonging to three classes: single-nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and insertion-deletions (InDels). The markers were chosen based on their linkage to six major R genes (Pit, Pib, Pi39 (t), Pi40 (t), Piz/Piz-t, and Pita /Pita2 ). The studied markers showed low allelic diversity, with the number of alleles identified in a single genotype ranging between two and nine alleles. The Egyptian genotype Eg-N-7 had two alleles of the Pi40 (t) gene, while the Saudi Arabian genotype Al-Ahsa1 had nine alleles that belonged to the seven R genes. The studied genotypes were also assessed for 19 agro-morphological traits.Analysis of variance of the studied traits showed significant differences among the genotypes. The putative associations between molecular markers and the agro-morphological traits were examined using associationmapping approach by employing the unified mixed model. Eight significant marker-trait associations were detected for eight agro-morphological traits (plant height, panicle length, sterility percentage, grain width, grain shape, elongation percentage, gelatinization temperature, and days to maturity). The phenotypic variance shown by each marker ranged between 43% and 65%. The findings of the current study will assist in identifying possible blast resistance genotypes for future rice breeding programs. Additionally, the results highlight the possible dual usage of specific markers in genotypic screening as well as in determining marker-trait associations.

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“…The SLAF sequencing were conducted based on the standard protocol from Beijing Biomarker Technologies Corporation (http://www.biomarker.com.cn) and the introduction by Sun et al (2013) and Song et al (2018). To simplify, the first step was to perform a SLAF pre-design experiment with 8 accessions of landraces and different enzymes combinations.…”

Section: Methodsmentioning

confidence: 99%

Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing

Zhao

Song

et al. 2018

Front. Plant Sci.

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Trivalent Aluminum (Al3+) in acidic soils is harmful to root growth and significantly reduce crop yields. Therefore, mining beneficial genes for Al tolerance is valuable for rice production. The objective of this research is to identify some beneficial genes for Al tolerance from rice landraces with high density SNP set from SLAF-seq (Specific-Locus Amplified Fragment sequencing). A total of 67,511 SNPs were obtained from SLAF-seq and used for genome-wide association study (GWAS) for Al tolerance with the 150 accessions of rice landraces in the Ting's rice core collection. The results showed that rice landraces in the Ting's rice core collection possessed a wide-range of variation for Al tolerance, measured by relative root elongation (RRE). With the mixed linear models, GWAS identified a total of 25 associations between SNPs and Al tolerant trait with p < 0.001 and false discovery rate (FDR) <10%. The explained percentage by quantitative trait locus (QTL) to phenotypic variation was from 7.27 to 13.31%. Five of twenty five QTLs identified in this study were co-localized with the previously cloned genes or previously identified QTLs related to Al tolerance or root growth/development. These results indicated that landraces are important sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.

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Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing

Cited by 32 publications

References 39 publications

Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

Molecular identification of blast resistance genes in rice genotypes using gene-specific markers

Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing

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