Genome‐wide association study for frost tolerance in rapeseed/canola (<i>Brassica napus</i>) under simulating freezing conditions

Wrucke, Danielle F.; Talukder, Zahirul I.; Rahman, Mukhlesur

doi:10.1111/pbr.12771

Cited by 11 publications

(8 citation statements)

References 77 publications

(91 reference statements)

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“…To predict the functional insights of all DEGs, the MapMan pathway annotator was used for the metabolism overview of the DEGs. It was found that rapeseed responded to CS depending on the genetic background (Figures 4B-D), which is supported by previous reports (Lei et al, 2018;Zhang C. et al, 2019;Wrucke et al, 2020). A similar expression trend for up-and downregulated DEGs was mainly detected in the secondary metabolism, amino acids, lipids, cell wall, minor CHO, and light reaction pathways during the three comparisons.…”

Section: Analysis Based On Transcriptome Data Of C6 and C18 Under Cs Conditionssupporting

confidence: 89%

Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Raza

Hussain

et al. 2021

Front. Plant Sci.

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Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.

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Section: Analysis Based On Transcriptome Data Of C6 and C18 Under Cs Conditionssupporting

confidence: 89%

Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Raza

Hussain

et al. 2021

Front. Plant Sci.

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“…There is one marker (S1_306342432) very near the significant locus on C02 for freezing tolerance under field conditions that has low p-values in experiment one for both 2-week damage scores and Fv/Fo at 7 days. Likewise, there is a cluster of markers mapping to chromosome C04 between 23,260,477 and 23,260,521 bp that are closely linked to a marker associated with freezing tolerance under growth chamber conditions that mapped to 23,256,454 bp in a previous study [56]. Thus, although we did not find any highly significant loci previously identified by earlier studies, our study provides some additional support for freezing tolerance loci identified in those studies.…”

Section: Comparison To Other Association Mapping Studies Identify Add...supporting

confidence: 69%

“…There are two markers that have fairly low p-values in experimental run 2 for visual damage scores and for experimental run 1 for Fv/Fo at 7 days that are within 50 kb of a marker on A03 at position 20,587,761 bp associated with freezing tolerance under simulated conditions [38]. There is also a cluster of markers within 150 kb of the significant marker on chromosome A07 at 13,505,270 bp, another cluster near the marker on chromosome A09 at 8,152,488 bp, and one more near the marker on A09 at position 8,867,241 bp that were significant in a GWAS study of freezing tolerance under growth chamber freezing conditions [56]. There is one marker (S1_306342432) very near the significant locus on C02 for freezing tolerance under field conditions that has low p-values in experiment one for both 2-week damage scores and Fv/Fo at 7 days.…”

Section: Comparison To Other Association Mapping Studies Identify Add...mentioning

confidence: 91%

Genome-Wide Association Mapping of Freezing Tolerance Loci in Canola (Brassica napus L.)

et al. 2021

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Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we conducted a genome-wide association study (GWAS) using a genotyped diversity panel containing 399 accessions consisting primarily of winter canola. One-month-old greenhouse grown plants were subsequently cold-acclimated for two months in an environmental growth chamber prior to phenotyping for freezing survival using a visual damage scale and chlorophyll fluorescence (Fv/Fo). There was reasonable correlation observed between visual damage and chlorophyll fluorescence ratings among the top associated loci; the results indicated that some loci contributed to both freezing damage/tolerance and photosynthetic efficiency. The resulting numerical values for phenotypes were used for association analyses with the identified SNPs. Thirteen significant markers were identified on nine chromosomes for the phenotypes scored, with several showing significance for multiple phenotypes. Twenty-five candidate genes were identified as previously associated with freezing tolerance, photosynthesis, or cold-responsive in canola or Arabidopsis.

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“…Those regions might be suitable for selection to improve two or more desired traits, simultaneously, for example, to improve both abiotic stress response, seed component, and seed yield (A4:3.07–4.11 Mb). Several studies have already investigated on the co-location of QTLs from a different category of traits ( Shi et al, 2012 ; Zhao J. et al, 2012 ; Ding et al, 2014 ; Bouchet et al, 2016 ; Körber et al, 2016 ; Stein et al, 2017 ; Wan et al, 2017 ; Rahaman et al, 2018 ; Jan et al, 2019 ; Wrucke et al, 2019 ; Wu et al, 2019 ; Zhang K. et al, 2019 ). Those studies demonstrated the importance of analyzing multiple traits, at the same time, to target the loci for breeding cultivars with the most advantageous profile.…”

Section: Discussionmentioning

confidence: 99%

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Raboanatahiry

Chao

et al. 2022

Front. Plant Sci.

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Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

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Genome‐wide association study for frost tolerance in rapeseed/canola (Brassica napus) under simulating freezing conditions

Cited by 11 publications

References 77 publications

Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Genome-Wide Association Mapping of Freezing Tolerance Loci in Canola (Brassica napus L.)

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

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