Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies

Kumar, Satish; Bink, M.C.A.M.; Volz, Richard K.; Bus, Vincent G. M.; Chagné, David

doi:10.1007/s11295-011-0425-z

Cited by 105 publications

(68 citation statements)

References 95 publications

(98 reference statements)

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“…Such studies have shown that using these breeding values in association with the phenotype resulted in higher accuracy when selecting new superior genotypes, supporting the approach used in our study (Kumar et al, 2012b;Iwata et al, 2013).…”

Section: Implementing Genomic Selection In Table Grape Breeding Programssupporting

confidence: 81%

Genome selection in fruit breeding: application to table grapes

Viana

Resende

Riaz³

et al. 2016

Sci. agric. (Piracicaba, Braz.)

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Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger nematode and Pierce's disease (PD), and 'B90-116', a susceptible Vitis vinifera cultivar with desirable fruit characteristics. Our aim was to enhance the knowledge on the genomic variation of agronomical traits in table grape populations for future use in marker-assisted selection (MAS) and GS, by discovering a set of molecular markers associated with genomic regions involved in this variation. A number of Quantitative Trait Loci (QTL) were discovered but this method is inaccurate and the genetic architecture of the studied population was better captured by the BLasso method of genomic selection, which allowed for efficient inference about the genetic contribution of the various marker loci. The technology of genomic selection afforded greater efficiency than QTL analysis and can be very useful in speeding up the selection procedures for agronomic traits in table grapes.

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Section: Implementing Genomic Selection In Table Grape Breeding Programssupporting

confidence: 81%

Genome selection in fruit breeding: application to table grapes

Viana

Resende

Riaz³

et al. 2016

Sci. agric. (Piracicaba, Braz.)

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“…A total of 442 own-rooted seedlings were planted in four rows at 0.5-m Kumar et al, 2012) were used for QTL validation and fine-mapping. The three QTL validation families were grafted on M.9 rootstock and planted in a Plant and Food Research orchard in 2008.…”

Section: Plant Materialsmentioning

confidence: 99%

An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes

et al. 2012

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Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus 3 domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.

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“…GWS has rarely been applied to fruit trees, being restricted to apples (Kumar et al, 2012), pears (Iwata et al, 2013), and grapes (Viana et al, 2016). To our knowledge, the present study represents the first attempt to investigate the feasibility of genomic selection in Citrus.…”

Section: Introductionmentioning

confidence: 99%

Genome wide selection in Citrus breeding

et al. 2016

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ABSTRACT. Genome wide selection (GWS) is essential for the genetic improvement of perennial species such as Citrus because of its ability to increase gain per unit time and to enable the efficient selection of characteristics with low heritability. This study assessed GWS efficiency in a population of Citrus and compared it with selection based on phenotypic data. A total of 180 individual trees from a cross between Pera sweet orange (Citrus sinensis Osbeck) and Murcott tangor (Citrus sinensis Osbeck x Citrus reticulata Blanco) were evaluated for 10 characteristics related to fruit quality. The hybrids were genotyped using 5287 DArT_seq TM (diversity arrays technology) molecular markers and their effects on phenotypes were predicted using the random regression -best linear unbiased predictor (rr-BLUP) method. The predictive ability, prediction bias, and accuracy of GWS were estimated to verify its effectiveness for phenotype prediction. The proportion of genetic variance explained by the markers was also computed. The heritability of the traits, as determined by markers, was 16-28%. The predictive ability of these markers ranged from 0.53 to 0.64, and the regression coefficients between predicted and observed phenotypes were close to unity. Over 35% of the genetic variance was accounted for by the markers. Accuracy estimates with GWS were lower than those obtained by phenotypic analysis; however, GWS was superior in terms of genetic gain per unit time. Thus, GWS may be useful for Citrus breeding as it can predict phenotypes early and accurately, and reduce the length of the selection cycle. This study demonstrates the feasibility of genomic selection in Citrus.

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Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies

Cited by 105 publications

References 95 publications

Genome selection in fruit breeding: application to table grapes

Genome selection in fruit breeding: application to table grapes

An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes

Genome wide selection in Citrus breeding

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