Bulked Segregant RNA-Seq Reveals Distinct Expression Profiling in Chinese Wheat Cultivar Jimai 23 Responding to Powdery Mildew

Zhu, Tong; Wu, Liru; He, Huagang; Song, Jiancheng; Jia, Mengshu; Liu, Liancheng; Wang, Xiaolu; Han, Ran; Niu, Liping; Du, Wei; Zhang, Xu; Wang, Wenrui; Xiao, Liang; Li, Haosheng; Liu, Jing; Xu, Hongxing; Liu, Cheng; Ma, Pengtao

doi:10.3389/fgene.2020.00474

Cited by 11 publications

(15 citation statements)

References 63 publications

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“…Over the past decade, RNA-seq has become indispensable for transcriptome-wide analyses of DEGs [63]. Several studies have used RNA-seq to identify candidate genes and QTLs controlling specific traits and processes in wheat [64][65][66][67][68]. However, the utility of RNA-seq for identifying Rf genes has not been explored.…”

Section: Discussionmentioning

confidence: 99%

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Tyrka

Bakera

Szeliga

et al. 2021

IJMS

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Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.

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Section: Discussionmentioning

confidence: 99%

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Tyrka

Bakera

Szeliga

et al. 2021

IJMS

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“…Using RNA samples with Integrity Number (RIN) ≥ 7, cDNA libraries of YD588, YN21, and the resistant and susceptible bulks were constructed. RNA integrity assessment and cDNA libraries construction were performed based on the previous studies ( Zhu et al, 2020 ). Then, using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, United States), the quality of the cDNA libraries was assessed.…”

Section: Methodsmentioning

confidence: 99%

“…To improve host resistance, the R genes were commonly identified and used in breeding. To date, more than 100 formally designated powdery mildew resistance ( Pm ) genes at 63 loci are reported in common wheat and its relatives ( Li G. et al, 2019 ; Maccaferri et al, 2019 ; Tan et al, 2019 ; Li Y. et al, 2020 ; Zhu et al, 2020 ; Wu et al, 2021 ). These resistance genes could be classified into two categories: qualitative resistance and quantitative resistance.…”

Section: Introductionmentioning

confidence: 99%

“…These resistance genes could be classified into two categories: qualitative resistance and quantitative resistance. Most reported Pm genes belonged to qualitative resistance and follow Mendel’s law of segregation ( Ma et al, 2014 ; Zhu et al, 2020 ). Owing to their high resistance to different virulent isolates, qualitative resistance genes have been widely utilized in wheat cultivars, such as Pm8 and Pm21 ( Hurni et al, 2014 ; Xing et al, 2018 ; Li H. et al, 2020 ; Wu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Especially, bulked segregant analysis-RNA-Seq (BSR-Seq), combined RNA-Seq, and bulked segregant analysis (BSA) are advanced strategies for both holistic studies of the expression profile of complex genome and gene/quantitative trait locus (QTL) mapping ( Michelmore et al, 1991 ; Pearce et al, 2015 ; Pankievicz et al, 2016 ). According to this method, mutant candidate genes and a large amount of SNP markers can be identified, and subsequently, comparative genomics analyses and high-density genetic linkage maps can also be carried out ( Liu S. et al, 2012 ; Trick et al, 2012 ; Li L. et al, 2014 ; Ramirez-Gonzalez et al, 2014 ; Wang et al, 2017 ; Wu et al, 2018 ; Zhu et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Bulked Segregant RNA-Seq Provides Distinctive Expression Profile Against Powdery Mildew in the Wheat Genotype YD588

et al. 2021

Front. Plant Sci.

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Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a destructive disease leading to huge yield losses in production. Host resistance can greatly contribute to the control of the disease. To explore potential genes related to the powdery mildew (Pm) resistance, in this study, we used a resistant genotype YD588 to investigate the potential resistance components and profiled its expression in response to powdery mildew infection. Genetic analysis showed that a single dominant gene, tentatively designated PmYD588, conferred resistance to powdery mildew in YD588. Using bulked segregant RNA-Seq (BSR-Seq) and single nucleotide polymorphism (SNP) association analysis, two high-confidence candidate regions were detected in the chromosome arm 2B, spanning 453,752,054-506,356,791 and 584,117,809-664,221,850 bp, respectively. To confirm the candidate region, molecular markers were developed using the BSR-Seq data and mapped PmYD588 to an interval of 4.2 cM by using the markers YTU588-004 and YTU588-008. The physical position was subsequently locked into the interval of 647.1–656.0 Mb, which was different from those of Pm6, Pm33, Pm51, Pm52, Pm63, Pm64, PmQ, PmKN0816, MlZec1, and MlAB10 on the same chromosome arm in its position, suggesting that it is most likely a new Pm gene. To explore the potential regulatory genes of the R gene, 2,973 differentially expressed genes (DEGs) between the parents and bulks were analyzed using gene ontology (GO), clusters of orthologous group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the data, we selected 23 potential regulated genes in the enriched pathway of plant-pathogen interaction and detected their temporal expression patterns using an additional set of wheat samples and time-course analysis postinoculation with Bgt. As a result, six disease-related genes showed distinctive expression profiles after Bgt invasion and can serve as key candidates for the dissection of resistance mechanisms and improvement of durable resistance to wheat powdery mildew.

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Deciphering the genomic hotspots in wheat for key breeding traits using comparative and structural genomics

Singh¹,

Vyas²,

Negi³

et al. 2022

Bioinformatics in Agriculture

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Bulked Segregant RNA-Seq Reveals Distinct Expression Profiling in Chinese Wheat Cultivar Jimai 23 Responding to Powdery Mildew

Cited by 11 publications

References 63 publications

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Bulked Segregant RNA-Seq Provides Distinctive Expression Profile Against Powdery Mildew in the Wheat Genotype YD588

Deciphering the genomic hotspots in wheat for key breeding traits using comparative and structural genomics

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