Construction of a high-density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing.

Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa "Hayward," is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis "Red5" reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.

Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple.

The apple dwarfing rootstock 'Malling9' ('M9') has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks. Progeny of 'M9' segregate for rootstock-induced dwarfing of the scion, indicating that this trait is controlled by one or more genetic factors. A quantitative trait locus (QTL) analysis of a rootstock population derived from the cross between 'M9' × 'Robusta5' (non-dwarfing) and grafted with 'Braeburn' scions identified a major QTL (Dw1) on linkage group (LG) 5, which exhibits a significant influence on dwarfing of the scion. A smaller-effect QTL affecting dwarfing (Dw2) was identified on LG11, and four minor-effect QTLs were found on LG6, LG9, LG10 and LG12. Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing, and that Dw1 has a stronger effect than Dw2. Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth. The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2. This suggests that most apple dwarfing rootstocks have been derived from the same genetic source.

Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci.

BACKGROUND: The vigour and precocity of trees highly influences their efficiency in commercial production. In apple, dwarfing rootstocks allow high-density plantings while their precocious flowering enables earlier fruit production. Currently, there is a lack of pear (Pyrus communis L.) rootstocks that are equivalent to the high yielding apple rootstock 'M9'. For the efficient breeding of new Pyrus rootstocks it is crucial to understand the genetic determinants of vigour control and precocity. In this study we used quantitative trait loci (QTLs) analysis to identify genetic loci associated with the desired traits, using a segregating population of 405 F1 P. communis seedlings from a cross between 'Old Home' and 'Louise Bonne de Jersey' (OHxLBJ). The seedlings were grafted as rootstocks with 'Doyenne du Comice' scions and comprehensively phenotyped over four growing seasons for traits related to tree architecture and flowering, in order to describe the growth of the scions. RESULTS: A high density single nucleotide polymorphism (SNP)-based genetic map comprising 597 polymorphic pear and 113 apple markers enabled the detection of QTLs influencing expression of scion vigour and precocity located on linkage groups (LG)5 and LG6 of 'Old Home'. The LG5 QTL maps to a position that is syntenic to the apple 'Malling 9' ('M9') Dw1 locus at the upper end of LG5. An allele of a simple sequence repeat (SSR) associated with apple Dw1 segregated with dwarfing and precocity in pear and was identified in other pear germplasm accessions. The orthology of the vigour-controlling LG5 QTL between apple and pear raises the possibility that the dwarfing locus Dw1 arose before the divergence of apple and pear, and might therefore be present in other Rosaceae species. CONCLUSION: We report the first QTLs associated with vigour control and flowering traits in pear rootstocks. Orthologous loci were found to control scion growth and precocity in apple and pear rootstocks. The application of our results may assist in the breeding process of a pear rootstock that confers both vigour control and precocity to the grafted scion cultivar.

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control.

BACKGROUND: Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. RESULTS: High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. CONCLUSIONS: The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

Rootstocks affect pear (Pyrus communis) tree growth through extent of node neoformation and flowering with key differences to apple.

Improved knowledge of rootstock effects on pear (Pyrus communis L.) tree development is required before early assessment of rootstock breeding populations can be improved. Two cultivars, 'Doyenné du Comice' and 'Concorde', were grafted on Pyrus calleryana Decne. (vigorous), Quince BA29 (semi-vigorous) and Quince C (semi-dwarfing) rootstocks. Growth of the compound trees was studied over 2 years after grafting and flowering was recorded in the spring of the third year. Using architectural analysis, annual shoot types common to all treatments and closely connected to the patterns of extension of preformed and neoformed metamers were identified and the differences among rootstock vigour treatments were quantified by proportions of these shoot types. Rootstock affected node neoformation, which was highest in the treatment with P. calleryana. The extent of sylleptic branching varied among the treatments, whereas the budbreak along the primary-axis in the second year of growth was unaffected, hence, the number of proleptic secondary axes was largely determined the primary-axis node number developed in year one. Spring flowering first occurred in the third year of tree growth and its intensity was influenced by rootstock. Quince C, the least vigorous rootstock, produced the highest number of floral buds. Flowering was delayed in young pear trees compared with apple, as shown in previous studies, so we conclude flowering does not play such a pivotal role in secondary axes development and early tree dwarfing by rootstock as has been observed in apple.

After initial invigoration by heading, young pear trees show reduction in axis vigour and increased propensity to flower.

Fast establishment of the canopy in young trees, followed by reduced vegetative vigour and precocity are desirable traits in fruit production. Severe heading (cutting back the primary axis of the tree after the first year of growth) to induce branching is a nursery practice to increase early fruit yield. Our aim was to provide a systematic study of the responses of young pear trees to severe heading. We used an experimental system with two scion genotypes and three rootstocks to create trees with contrasting branching habits and vigour. The trees' trunks were headed and a single bud was allowed to outgrow in the following season. Architectural analysis was used to quantify the development of regenerated trees. In the first year after heading, the growth of the primary axes and, depending on the scion genotype, the sylleptic branching of regenerating trees, were invigorated. In the second year, the percentage of budbreak was also increased, but the shoot growth was greatly reduced. Axis propensity to flower in spring of the third year of growth was increased. The new insights into the effects of heading on tree aging and flowering will be used for guiding the best approaches to managing young pear trees.

Fruit dry matter concentration: a new quality metric for apples.

BACKGROUND: In the fresh apple market fruit must be crisp and juicy to attract buyers to purchase again. However, recent studies have shown that consumer acceptability could be further enhanced by improving taste. This study evaluates the use of fruit dry matter concentration (DMC) as a new fruit quality metric for apple. RESULTS: Fruit samples collected at harvest, in the two main fruit growing regions of New Zealand, showed a variation in mean fruit DMC from 130 to 156 g kg(-1) with 'Royal Gala' and with 'Scifresh' from 152 to 176 g kg(-1). Individual fruit DMC showed a larger range, from 108 to 189 g kg(-1) with 'Royal Gala' and from 125 to 201 g kg(-1) with 'Scifresh'. Fruit DMC proved a more reliable predictor of total soluble solids after 12 weeks of air storage at 0.5 °C than TSS at harvest for both 'Royal Gala' and 'Scifresh'. Fruit DMC was also positively related to flesh firmness, although this relationship was not as strong as that seen with soluble solids and was more dependent on cultivar. Consumer studies showed that consumer preference was positively related to fruit DMC of 'Royal Gala' apples. CONCLUSION: Fruit DMC can therefore be measured before or at harvest, and be used to predict the sensory potential for the fruit after storage.

Apple dwarfing rootstocks and interstocks affect the type of growth units produced during the annual growth cycle: precocious transition to flowering affects the composition and vigour of annual shoots.

BACKGROUND AND AIMS: Precocious flowering in apple trees is often associated with a smaller tree size. The hypothesis was tested that floral evocation in axillary buds, induced by dwarfing rootstocks, reduces the vigour of annual shoots developing from these buds compared with shoots developing from vegetative buds. METHODS: The experimental system provided a wide range of possible tree vigour using 'Royal Gala' scions and M.9 (dwarfing) and MM.106 (non-dwarfing) as rootstocks and interstocks. Second-year annual shoots were divided into growth units corresponding to periods (flushes) of growth namely, vegetative spur, extension growth unit, uninterrupted growth unit, floral growth unit (bourse) and extended bourse. The differences between the floral and vegetative shoots were quantified by the constituent growth units produced. KEY RESULTS: The dwarfing influence was expressed, firstly, in reduced proportions of shoots that contained at least one extension growth unit and secondly, in reduced proportions of bicyclic shoots (containing two extension growth units) and shoots with an uninterrupted growth unit. In treatments where floral shoots were present, they were markedly less vigorous than vegetative shoots with respect to both measures. In treatments with M.9 rootstock, vegetative and floral shoots produced on average 0.52 and 0.17 extension growth units, compared with 0.77 extension growth units per shoot in the MM.106 rootstock treatment. Remarkably, the number of nodes per extension growth unit was not affected by the rootstock/interstock treatments. CONCLUSIONS: These results showed that rootstocks/interstocks affect the type of growth units produced during the annual growth cycle, reducing the number of extension growth units, thus affecting the composition and vigour of annual shoots. This effect is particularly amplified by the transition to flowering induced by dwarfing rootstocks. The division of annual shoot into growth units will also be useful for measuring and modelling effects of age on apple tree architecture.