Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach

Deng, Qingyan; Kong, Zhongxin; Wu, Xiaoxia; Ma, Shengwei; Yuan, Yang; Jia, Haiyan; Ma, Zhengqiang

doi:10.1016/j.plantsci.2019.05.011

Cited by 15 publications

(8 citation statements)

References 76 publications

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“…The COBLs members have been found to mediate diverse physiological and developmental processes such as stem strength [ 6 ], pollen tube growth [ 12 ], pathogen resistance [ 13 ], and root-hair growth [ 4 ]. Silencing a COBL member, such as BRITTLE CULM1 (OsBC1) in rice, Brittle stalk 2 (ZmBk2) in maize, BRITTLE CULM1 (SbBC1) in sorghum, and TmBr1 in diploid wheat, caused plants to exhibit the brittle phenotype [ 6 , 7 , 14 , 15 ]. Cuticle lacking, abnormal shape, and irregular size distribution were observed in the epidermal cells of a tomato mutant in which the SlCOBRA-like gene was repressed.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

et al. 2021

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The COBRA-like (COBL) genes play key roles in cell anisotropic expansion and the orientation of microfibrils. Mutations in these genes cause the brittle stem and induce pathogen responsive phenotypes in Arabidopsis and several crop plants. In this study, an in silico genome-wide analysis was performed to identify the COBL family members in Brassica. We identified 44, 20 and 23 COBL genes in B. napus and its diploid progenitor species B. rapa and B. oleracea, respectively. All the predicted COBL genes were phylogenetically clustered into two groups: the AtCOB group and the AtCOBL7 group. The conserved chromosome locations of COBLs in Arabidopsis and Brassica, together with clustering, indicated that the expansion of the COBL gene family in B. napus was primarily attributable to whole-genome triplication. Among the BnaCOBLs, 22 contained all the conserved motifs and derived from 9 of 12 subgroups. RNA-seq analysis was used to determine the tissue preferential expression patterns of various subgroups. BnaCOBL9, BnaCOBL35 and BnaCOBL41 were highly expressed in stem with high-breaking resistance, which implies these AtCOB subgroup members may be involved in stem development and stem breaking resistance of rapeseed. Our results of this study may help to elucidate the molecular properties of the COBRA gene family and provide informative clues for high stem-breaking resistance studies.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

et al. 2021

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“…As disease resistance always gives rise to transcription factor responses, BSR can not only the map the function but can also help us screen DEGs and transcription factors in mapping regions, especially for regions with limited combinations. Similarly, TmBr1, a gene responsible for stem brittleness, was isolated by the MapRseq approach and was present in recombinant cold spots (Deng et al, 2019). Therefore, we believe that combining BSR-Seq analysis and KASP in the primary mapping region in a large F 2:3 population can considerably accelerate the isolation of the genes responsible for stress-related traits, such as disease resistance and resistance to abiotic stresses (drought stress, temperature stress, or mineral deficiency stress).…”

Section: 3mentioning

confidence: 99%

RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat

et al. 2021

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Powdery mildew causes considerable yield losses in common wheat (Triticum aestivum L.) production. Mapping and cloning powdery mildew-resistant quantitative trait loci can benefit stable yield production by facilitating the breeding of resistant varieties. In this study, we used the powdery mildew resistance introgression line 'CH7087' (harboring the resistance gene PmCH7087) and developed a large F 2 population and a corresponding F 2:3 segregation population containing 2,000 family lines for molecular mapping of PmCH7087. Genetic analysis demonstrated that the resistance phenotype was controlled by a single dominant gene. According to the performance exhibited by the F 2:3 lines, 50 resistant lines and 50 susceptible lines without phenotype segregation were chosen for pooling and bulked segregant RNA sequencing (BSR-Seq) analysis. A region spanning 42.77 Mb was identified, and genotyping of an additional 183 F 2:3 lines with extreme phenotypes using 20 kompetitive allele-specific polymerase chain reaction (KASP) markers in the BSR-Seq mapping regions confirmed this region and narrowed it to 9.68 Mb, in which 45 genes were identified and annotated. Five of these transcripts harbored nonsynonymous single nucleotide polymorphisms between the two parents, with the transcripts of TraesCS2B01G302800 being involved in signal transduction. Furthermore, TraesCS2B01G302800.2 was annotated as the closest homologue of serine/threonine-protein kinase PBS1, a typical participant in the plant disease immune response, indicating that TraesCS2B01G302800 was the candidate gene of PmCH7087. Our results may facilitate future research attempting to improve powdery mildew resistance in wheat and to identify candidate genes for further verification and gene cloning.

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“…The characterization of mutants is an effective method to identify the functions of brittle stalk genes and individual components of cell walls. Functions of some brittle stalk genes have been characterized using the mutations in the orthologous genes of Arabidopsis , rice, maize, wheat, and barley ( Kokubo et al, 1989 ; Li et al, 2003 ; Ching et al, 2006 ; Burton et al, 2010 ; Deng et al, 2019 ; Jiao et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…AtCOBL4 from Arabidopsis and its orthologs, OsBC1 from rice, TmBr1 from wheat, and SbBC1 from sorghum are associated with the mechanical strength of stalks. The loss-of - function mutations of these genes also result in the brittle stalk phenotype ( Li et al, 2003 , 2019 ; Brown et al, 2005 ; Persson et al, 2005 ; Sindhu et al, 2007 ; Sato et al, 2010 ; Deng et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize

Sun

Guo

et al. 2022

Front. Plant Sci.

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The mechanical strength of the stalk affects the lodging resistance and digestibility of the stalk in maize. The molecular mechanisms regulating the brittleness of stalks in maize remain undefined. In this study, we constructed the maize brittle stalk mutant (bk5) by crossing the W22:Mu line with the Zheng 58 line. The brittle phenotype of the mutant bk5 existed in all of the plant organs after the five-leaf stage. Compared to wild-type (WT) plants, the sclerenchyma cells of bk5 stalks had a looser cell arrangement and thinner cell wall. Determination of cell wall composition showed that obvious differences in cellulose content, lignin content, starch content, and total soluble sugar were found between bk5 and WT stalks. Furthermore, we identified 226 differentially expressed genes (DEGs), with 164 genes significantly upregulated and 62 genes significantly downregulated in RNA-seq analysis. Some pathways related to cellulose and lignin synthesis, such as endocytosis and glycosylphosphatidylinositol (GPI)-anchored biosynthesis, were identified by the Kyoto Encyclopedia of Gene and Genomes (KEGG) and gene ontology (GO) analysis. In bulked-segregant sequence analysis (BSA-seq), we detected 2,931,692 high-quality Single Nucleotide Polymorphisms (SNPs) and identified five overlapped regions (11.2 Mb) containing 17 candidate genes with missense mutations or premature termination codons using the SNP-index methods. Some genes were involved in the cellulose synthesis-related genes such as ENTH/ANTH/VHS superfamily protein gene (endocytosis-related gene) and the lignin synthesis-related genes such as the cytochrome p450 gene. Some of these candidate genes identified from BSA-seq also existed with differential expression in RNA-seq analysis. These findings increase our understanding of the molecular mechanisms regulating the brittle stalk phenotype in maize.

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Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach

Cited by 15 publications

References 76 publications

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat

Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize

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