First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit

Tahir, Jibran; Crowhurst, Ross N.; Deroles, Simon C.; Hilario, Elena; Deng, Cecilia; Schaffer, Robert J.; Lievre, Liam Le; Brendolise, Cyril; Chagné, David; Gardiner, Susan E.; Knaebel, Mareike; Catanach, Andrew; McCallum, John; Datson, P. M.; Thomson, Susan; Brownfield, Lynette; Nardozza, Simona; Pilkington, Sarah M.

doi:10.3389/fgene.2022.852161

Cited by 13 publications

(10 citation statements)

References 43 publications

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“…The eight kiwifruit pollen RNA-seq libraries were then aligned to the male Actinidia chinensis var. c hinensis acc “Russell” genome assembly ( Tahir et al., 2022 ). Sequencing data mapped to the assembly with a rate of approximately 90% for all samples ( Supplementary Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…The Arabidopsis TAIR10.1 (BioProject: PRJNA10719) or the male A. chinensis acc. ‘Russell’ genome (assembly and annotation files available online at https://figshare.com/s/c6ffcc5300533022cc5a ; Tahir et al., 2022 ) genome assemblies were used as appropriate. The tool featureCounts from the Subread 2.0.3 package ( Liao et al., 2014 ) was used with default parameters to determine expression level of genes for each sample, based on the feature annotations from the Araport11 gene model assembly ( Cheng et al., 2017 ) for Arabidopsis and the Russell gene models for kiwifruit ( Tahir et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…‘Russell’ genome (assembly and annotation files available online at https://figshare.com/s/c6ffcc5300533022cc5a ; Tahir et al., 2022 ) genome assemblies were used as appropriate. The tool featureCounts from the Subread 2.0.3 package ( Liao et al., 2014 ) was used with default parameters to determine expression level of genes for each sample, based on the feature annotations from the Araport11 gene model assembly ( Cheng et al., 2017 ) for Arabidopsis and the Russell gene models for kiwifruit ( Tahir et al., 2022 ). Quality control package Qualimap v2.2.2 ( García-Alcalde et al., 2012 ) was used to determine number of genomic alignments which fall into exonic, intronic or intergenic regions for the Arabidopsis data generated in this study.…”

Section: Methodsmentioning

confidence: 99%

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RNA-seq analysis of synchronized developing pollen isolated from a single anther

et al. 2023

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Pollen development, from unicellular microspores to anthesis, is a complex process involving the coordinated specification, differentiation and functions of different cell types. Key to understanding this development is identifying the genes expressed at precise stages of development. However, transcriptomic studies on pollen prior to anthesis are complicated by the inaccessible nature of pollen developing in the anther and the resistant pollen wall. To assist with understanding gene expression during pollen development we have developed a protocol to perform RNA-Seq on pollen isolated from a single anther (SA RNA-Seq). The protocol involves removing pollen from a single anther for analysis and viewing the remaining pollen to determine the developmental stage. The isolated pollen is chemically lysed and mRNA isolated from the lysate using an oligo-dT column before library preparation. Here, we report on the development and testing of our method and the generation of a transcriptome for three stages of pollen development from Arabidopsis (Arabidopsis thaliana) and two stages from male kiwifruit (Actinidia chinensis). This protocol enables the transcriptome of precise developmental stages of pollen to be analyzed, and uses a small number of plants, potentially facilitating studies that require a range of treatments or the analysis of the first generation of transgenic plants.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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RNA-seq analysis of synchronized developing pollen isolated from a single anther

et al. 2023

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“…Two sex‐determining genes have been identified: Shy Girl acts as a dominant suppressor of carpel development, while friendly boy acts as a male promoting factor for male fertility (Akagi et al ., 2019 ). Recent genome assembly of a male kiwifruit has confirmed that both genes are located in the SDR of chromosome 25 (Tahir et al ., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit

Wang¹,

Xing

Bourke

et al. 2022

Plant Biotechnology Journal

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Summary Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high‐throughput genotyping platform for genome‐wide DNA polymorphisms. In this study, we developed a high‐density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome‐wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high‐value crop.

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“…Resulting sequence reads were mapped against the A. chinensis var. chinensis 'Russell' reference genome (Tahir et al 2022). Alignments were generate using BWA-MEM (Li 2013) and SAMtools (Danecek et al 2021) using default parameters.…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

Implementation of different relationship estimate methodologies in Breeding Value prediction in kiwiberry (Actinidia arguta)

Mertten

Baldwin

Cheng³

et al. 2023

Preprint

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In dioecious crops such as Actinidia arguta(kiwiberries), some of the main challenges when breeding for fruit characteristics is the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of Genomic Best Linear Unbiased Prediction (BLUP), which does not rely exclusively on information of relatives, would allow direct estimation of sex-related traits and speed up kiwiberry breeding. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs, heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations.

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First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit

Cited by 13 publications

References 43 publications

RNA-seq analysis of synchronized developing pollen isolated from a single anther

RNA-seq analysis of synchronized developing pollen isolated from a single anther

Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit

Implementation of different relationship estimate methodologies in Breeding Value prediction in kiwiberry (Actinidia arguta)

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