Genomic predictions in diploid Actinidia chinensis (kiwifruit)

Cheng, Canhong; Datson, P. M.; Hilario, Elena; Deng, Canhui; Manako, K.I.; McNeilage, M.A.; Bomert, M.; Hoeata, K.

doi:10.17660/ejhs.2019/84.4.3

Cited by 6 publications

(3 citation statements)

References 27 publications

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“…In this study, we have shown the potential of using different variance co-variance relationship methodologies in A. arguta breeding programmes. Overall, the results of six traits considered in a marker-based relationship matrix showed a positive correlation of predictions to mean observations, indicating a better representative genetic architecture of genome-wide marker coverage using a multiplex PCR and new generation sequencing combination approach, compared with previous studies of other Actinidia species (Datson et al 2017 ; Cheng et al 2019 ). We were able to differentiate the effects of different relationship methodologies and ploidy to the best linear unbiased prediction in the parental generation and the progeny population, progeny both with and without phenotypic observation.…”

Section: Discussionmentioning

confidence: 61%

“…In particular, the selection of male parents requires progeny testing, as they do not provide phenotypic information on their genetic background, for the breeder. Recently, genomic methods have been developed to enable this prediction (Testolin 2011 ; Datson et al 2017 ; Cheng et al 2019 ). In polyploids with their multiple homologous chromosome sets, allele dosage information is crucial to estimating marker-based additive variance–covariance relationships between individuals to predict breeding values.…”

Section: Introductionmentioning

confidence: 99%

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Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

Mertten,

Baldwin,

Cheng

et al. 2023

Mol Breeding

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In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are 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 best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. 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. 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. 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. This study innovates the breeding programme of autotetraploid kiwiberries. 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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Section: Discussionmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

Mertten,

Baldwin,

Cheng

et al. 2023

Mol Breeding

View full text Add to dashboard Cite

show abstract

“…In this study we have shown the potential of using different variance co-variance relationship methodologies in A. arguta breeding programmes. Overall, the results of six traits considered in a markerbased relationship matrix showed a positive correlation of predictions to mean observations, indicating a better representative genetic architecture of genome-wide marker coverage using a multiplex PCR and new generation sequencing combination approach, compared with previous studies of other Actinidia species (Datson et al 2017;Cheng et al 2019). We were able to differentiate the effects of different relationship methodologies and ploidy to the best linear unbiased prediction in the parental generation and the progeny population, progeny both with and without phenotypic observation.…”

Section: )mentioning

confidence: 73%

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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Genomic selection for crop improvement in fruits and vegetables: a systematic scoping review

Lee,

Foong,

Song

et al. 2024

Mol Breeding

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Genomic predictions in diploid Actinidia chinensis (kiwifruit)

Cited by 6 publications

References 27 publications

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

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

Genomic selection for crop improvement in fruits and vegetables: a systematic scoping review

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