Stigmatic Transcriptome Analysis of Self-Incompatible and Compatible Pollination in Corylus heterophylla Fisch. × Corylus avellana L.

Hou, Sen; Zhao, Tengteng; Yang, Zhen; Liang, Lisong; Ma, Wenxu; Wang, Guixi; Ma, Qinghua

doi:10.3389/fpls.2022.800768

Cited by 8 publications

(13 citation statements)

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“…Corylus may harbor a novel SSI molecular mechanism that differs from Brassica (Hill et al, 2021;Hou et al, 2022). The analysis presented here provides additional evidence for independent evolution of a sporophytic self-incompatibility mechanism that is unique to Corylus, and not shared by other members of the Betulaceae, nor model species of SSI such as Brassica oleracea.…”

Section: Cross-genus Level Analysismentioning

confidence: 64%

“…The locus regulating sporophytic self-incompatibility (SSI) in hazelnut has been fine-mapped in C. avellana (Hill et al, 2021) and C. heterophylla x C. avellana interspecific hybrids (Hou et al, 2022). These studies identified three MIK2 homologues believed to be responsible for SSI in these two Corylus species.…”

Section: Phylogenetic Analysis Of Sporophytic Self-incompatibilitymentioning

confidence: 99%

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The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus

Brainard

Sanders

Brůna

et al. 2023

Preprint

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The native shrub American hazelnut (Corylus americana) is currently used in breeding programs that are aiming to develop commercially viable hazelnut varieties for the U.S. Upper Midwestern U.S. This species provides significant ecological benefits as it is a perennial crop and well-adapted to this region. Breeding cycles for perennial species are long, and may benefit from the use of predictive methods such as genomic selection to reduce cycle time and increase the efficiency of field trials. High-quality reference genome assemblies are very useful for the implementation marker-assisted selection and genomic prediction, and we therefore developed the first chromosome-scale reference assemblies for C. americana, using the accessions 'Rush' and 'Winkler'. Initial draft assemblies were created using HiFi PacBio reads and Arima Hi-C sequencing to assemble genomes into 11 pseudomolecules. We then utilized Oxford Nanopore reads and a high-density genetic map in order to perform error correction. N50 scores were calculated to be 31.9 Mb and 35.3 Mb for 'Rush' and 'Winkler', respectively, while 97.1% (for 'Winkler') and 90.2% (for 'Rush') of the total genome was assembled into the 11 pseudomolecules. Gene prediction was performed using both RNAseq libraries as well as protein homology data. 'Rush' had a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating extremely high-quality assemblies. These two independent, de novo assemblies enable unbiased assessment of structural variation across the genome, as well as patterns of syntenic relationships within C. americana and the Corylus genus. These assemblies are also an important first step in providing a resource for using next-generation sequencing data in the improvement of C. americana. We demonstrate this utility through the generation of high-density SNP marker sets from genotyping-by-sequencing data for 1,343 C. americana, C. avellana, and C. americana x C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing further evidence of unique molecular pathways governing self-incompatibility in Corylus not exhibited in other well-studied SSI systems. We hope these assemblies will aide in the application of modern breeding methods to the development of commercially viable hazelnut varieties for the U.S. Upper Midwest.

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Section: Cross-genus Level Analysismentioning

confidence: 64%

Section: Phylogenetic Analysis Of Sporophytic Self-incompatibilitymentioning

confidence: 99%

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus

Brainard

Sanders

Brůna

et al. 2023

Preprint

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“…It is a rather a complex genetic network containing multiple genes. It has been reported that TFs play an important role in plant biological processes by regulating relative gene expression, including plant growth, synthesis of secondary metabolites ( Song et al., 2022 ), stress/stimulus responses ( Luo et al., 2022 ), flower senescence ( Ji et al, 2022 ), SI reaction processes ( Hou et al., 2022 ), pollen tube growth ( Zou et al., 2010 ) and other important biological processes. In tomato, progressive mutation of TFs led to a transition from outcrossing to self-pollination ( Benoit, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Gene coexpression analysis reveals key pathways and hub genes related to late-acting self-incompatibility in Camellia oleifera

et al. 2023

Front. Plant Sci.

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IntroductionSelf-incompatibility (SI) is an important strategy for plants to maintain abundant variation to enhance their adaptability to the environment. Camellia oleifera is one of the most important woody oil plants and is widely cultivated in China. Late acting self-incompatibility (LSI) in C. oleifera results in a relatively poor fruit yield in the natural state, and understanding of the LSI mechanism remains limited. MethodsTo better understand the molecular expression and gene coexpression network in the LSI reaction in C. oleifera, we conducted self- and cross-pollination experiments at two different flower bud developmental stages (3–4 d before flowering and 1 d before flowering), and cytological observation, fruit setting rate (FSR) investigation and RNA-Seq analysis were performed to investigate the mechanism of the male −female interaction and identify hub genes responsible for the LSI in C. oleifera.ResultsBased on the 21 ovary transcriptomes, a total of 7669 DEGs were identified after filtering out low-expression genes. Weighted gene coexpression network analysis (WGCNA) divided the DEGs into 15 modules. Genes in the blue module (1163 genes) were positively correlated with FSR, and genes in the pink module (339 genes) were negatively correlated with FSR. KEGG analysis indicated that flavonoid biosynthesis, plant MAPK signaling pathways, ubiquitin-mediated proteolysis, and plant-pathogen interaction were the crucial pathways for the LSI reaction. Fifty four transcription factors (TFs) were obtained in the two key modules, and WRKY and MYB were potentially involved in the LSI reaction in C. oleifera. Network establishment indicated that genes encoding G-type lectin S-receptor-like serine (lecRLK), isoflavone 3’-hydroxylase-like (CYP81Q32), cytochrome P450 87A3-like (CYP87A3), and probable calcium-binding protein (CML41) were the hub genes that positively responded to the LSI reaction. The other DEGs inside the two modules, including protein RALF-like 10 (RALF), F-box and pectin acetylesterase (MTERF5), might also play vital roles in the LSI reaction in C. oleifera.DiscussionOverall, our study provides a meaningful resource for gene network studies of the LSI reaction process and subsequent analyses of pollen−pistil interactions and TF roles in the LSI reaction, and it also provides new insights for exploring the mechanisms of the LSI response.

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“…Sequences for three S-locus genes (MIK3 homologues) reported by Hou et al (2022) were obtained from the transcriptome reported in Zhao et al (2021). NCBI-BLAST v2.6.0+ (Altschul et al, 1990) was used to identify homologous sequences in all Corylus species, as well as B. pendula, M. domestica and Brassica oleracea.…”

Section: Phylogenetic Analysis Of Sporophytic Self-incompatibility (Ssi)mentioning

confidence: 99%

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Brainard,

Sanders,

Bruna

et al. 2023

Plant Biotechnology Journal

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SummaryThe native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus.

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Stigmatic Transcriptome Analysis of Self-Incompatible and Compatible Pollination in Corylus heterophylla Fisch. × Corylus avellana L.

Cited by 8 publications

References 69 publications

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus

Gene coexpression analysis reveals key pathways and hub genes related to late-acting self-incompatibility in Camellia oleifera

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

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