A Unique haplotype found in apple accessions exhibiting early bud-break could serve as a marker for breeding apples with low chilling requirements

Trainin, Taly; Zohar, Matat; Shimoni-Shor, Einav; Doron‐Faigenboim, Adi; Bar-Ya’akov, Irit; Hatib, Kamel; Sela, Noa; Holland, Doron; Isaacson, Tal

doi:10.1007/s11032-016-0575-7

Cited by 12 publications

(22 citation statements)

References 39 publications

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“…An extended interval of ~360 kb was nevertheless proposed to take into account the results of the re-sampling analysis, thus generating a final set of 66 candidate gene models. Interestingly, Trainin et al ( 2016 ) identified a common haplotype on the top of chromosome 9 shared by a small subset of mostly Israeli apple cultivars adapted to low-chill conditions such as the well-known “Anna.” They defined an interval of about 1.7 Mb but suggested that the genetic factor/s responsible for early bud-break could be located in a region of about only 190 kb (between SNP-A6-2 and SNP-A4). Mapping these SNPs on the GDDH13 genome, we found the corresponding interval to be 730,978–923,844 bp, which overlaps the extended interval accounting for SNP.9-5 (451,830–811,891 bp).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

et al. 2017

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Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

et al. 2017

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“…where n is the mean number of replicates per genotype, r 2 g is the genetic variance, and r 2 e is the residual error variance as described LG9 (Allard et al, 2016;Celton et al, 2011;van Dyk et al, 2010) were selected for QTL mapping. An additional six SSRs, which were generated based on a comparison between the resequenced genome of the 'Anna' apple to the published apple genome (Trainin et al, 2016) as well as four markers from the HiDRAS (http://www.hidras.unimi.it/) and 15 markers from the equivalent genomic regions in pear, were selected (Chen et al, 2014). All markers tested are listed in Table S2.…”

Section: Statistical Analysesmentioning

confidence: 99%

“…In previous apple genetics studies using fullsib families, quantitative trait loci (QTL) for CR were identified (Allard et al, 2016;Celton et al, 2011;van Dyk et al, 2010). However, the only common QTL was located in linkage group (LG) 9, suggesting its stability over different families, climate regions and years (Allard et al, 2016;van Dyk et al, 2010;Trainin et al, 2016).…”

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confidence: 99%

Identification of QTLs associated with spring vegetative budbreak time after dormancy release in pear (Pyrus communis L.)

et al. 2017

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Dormancy release is greatly affected by chilling unit (CU) accumulation. Lack of CU has a major impact on spring vegetative budbreak (VB). To understand the genetic mechanism governing the chilling requirement (CR), we conducted a QTL analysis of VB date in F1 population, derived from a cross between ‘Spadona’ (low CR) and ‘Harrow Sweet’ (high CR). Using a unique methodology of tree mobility, replicates of the same genotypes were exposed during the winter, over two consecutive years, to climates that differ greatly in their CU and to the same heat conditions to induce VB, in order to evaluate CR genetic impact and to distinguish it from the heat factor. Broad‐sense heritability within locations ranged from 0.62 to 0.66. Due to a strong impact of GxE interaction, it was reduced to 0.46 for the overall mean. We examined the previously discovered apple QTLs detected in linkage groups (LG) 9 and 8, based on the synteny between the species. Our analysis confirms significant QTLs in LG8 (R2 = 12%–24%) and LG9 (R2 = 20%–38%) for all locations and years

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“…Recently, the chromosome location of early bud break of “Anna” has been discovered including several SNPs in several genes ( Trainin et al, 2016 ), however, so far, it is not clear if the low storage capacity of “Anna” is also localized to the same site. Taken together, this study provides new understanding on pre-climacteric events in “Anna” that might affect its ripening behavior and storage capacity.…”

Section: Discussionmentioning

confidence: 99%

“…Apple cultivars vary considerably in their physico-chemical characteristics, texture, and storage performance ( Hoehn et al, 2003 ; Johnston et al, 2009 ). The spring or summer apple cultivars like “Anna” ( Pre-Aymard et al, 2003 ; Trainin et al, 2016 ), “Sunrise” ( Wiersma et al, 2007 ), “McIntosh” ( Harb et al, 2012 ), and “Gala” ( Jenny et al, 1995 ) are prone to fast ripening and softening, however, mid-late season cultivars such as “Honeycrisp” ( Harb et al, 2012 ), “Golden Delicious (GD)” ( Wiersma et al, 2007 ), and “Fuji” ( Wakasa et al, 2006 ; Wei et al, 2010 ) have long storage capacity and slow softening. “Anna,” an early maturating apple cultivar, which was developed in Israel, is becoming increasingly popular because of its low chilling requirement for flowering and a short fruit developmental period ( Trainin et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Different Preclimacteric Events in Apple Cultivars with Modified Ripening Physiology

2017

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“Anna” is an early season apple cultivar exhibiting a fast softening and juiciness loss during storage, in comparison to two mid-late season cultivars “Galaxy” and “GD.” The poor storage capacity of “Anna” was correlated with high lipid oxidation-related autoluminescence, high respiration and ethylene production rates, associated with high expression of MdACO1, 2, 4, 7, and MdACS1. All cultivars at harvest responded to exogenous ethylene by enhancing ethylene production, typical of system-II. The contribution of pre-climacteric events to the poor storage capacity of “Anna” was examined by comparing respiration and ethylene production rates, response to exogenous ethylene, expression of genes responsible for ethylene biosynthesis and response, and developmental regulators in the three cultivars throughout fruit development. In contrast to the “Galaxy” and “GD,” “Anna” showed higher ethylene production and respiration rates during fruit development, and exhibited auto-stimulatory (system II-like) effect in response to exogenous ethylene. The higher ethylene production rate in “Anna” was correlated with higher expression of ethylene biosynthesis genes, MdACS3a MdACO2, 4, and 7 during early fruit development. The expression of negative regulators of ripening (AP2/ERF) and ethylene response pathway, (MdETR1,2 and MdCTR1) was lower in “Anna” in comparison to the other two cultivars throughout development and ripening. Similar pattern of gene expression was found for SQUAMOSA promoter binding protein (SBP)-box genes, including MdCNR and for MdFUL. Taken together, this study provides new understanding on pre-climacteric events in “Anna” that might affect its ripening behavior and physiology following storage.

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A Unique haplotype found in apple accessions exhibiting early bud-break could serve as a marker for breeding apples with low chilling requirements

Cited by 12 publications

References 39 publications

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Identification of QTLs associated with spring vegetative budbreak time after dormancy release in pear (Pyrus communis L.)

Different Preclimacteric Events in Apple Cultivars with Modified Ripening Physiology

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