William R. Okie

Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica).

*Chilling requirement, together with heat requirement, determines the bloom date, which has an impact on the climatic distribution of the genotypes of tree species. The molecular basis of floral bud chilling requirement is poorly understood, despite its importance to the adaptation and production of fruit trees. In addition, the genetic nature of heat requirement and the genetic interrelationships among chilling requirement, heat requirement and bloom date remain unclear. *A peach (Prunus persica) F(2) population of 378 genotypes developed from two genotypes with contrasting chilling requirements was used for linkage map construction and quantitative trait loci (QTL) mapping. The floral bud chilling and heat requirements of each genotype were evaluated over 2 yr and the bloom date was scored over 4 yr. *Twenty QTLs with additive effects were identified for three traits, including one major QTL for chilling requirement and two major QTLs for bloom date. The majority of QTLs colocalized with QTLs for other trait(s). In particular, one genomic region of 2 cM, pleiotropic for the three traits, overlapped with the sequenced peach EVG region. *This first report on the QTL mapping of floral bud chilling requirement will facilitate marker-assisted breeding for low chilling requirement cultivars and the map-based cloning of genes controlling chilling requirement. The extensive colocalization of QTLs suggests that there may be one unified temperature sensing and action system regulating chilling requirement, heat requirement and bloom date together.

Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [ Prunus persica (L.) Batsch]

Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many ‘specialty crops’ such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family. Our F2 mapping population of 57 genotypes segregates for bloom time (BD) and chilling requirement (CR) and we have extensively phenotyped this population. The population derives from a selfed F1 progeny of a cross between ‘Hakuho’ (high CR) and ‘UFGold’ (low CR). We were able to successfully employ GBS and the TASSEL GBS pipeline without modification of the original methodology using the ApeKI restriction enzyme and multiplexing at an equivalent of 96 samples per Illumina HiSeq 2000 lane. We obtained hundreds of SNP markers which were then used to construct a genetic linkage map and identify quantitative trait loci (QTL) for BD and CR.

Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population

Chilling requirement (CR) for floral bud dormancy release is one of the major limiting factors for geographical adaptation of fruiting trees. Using a whole genome sequencing approach (Illumina platform), we explored polymorphism underlying phenotypic differences among individuals in a peach F2 cross segregating for chilling requirement and bloom date. Allelic configuration of individuals, which represented phenotypic extremes in the cross (300 vs. 1,100 chill hours) allowed reconstruction of low- and high-chill haplotypes within three most significant quantitative trait locus (QTL) intervals on the Prunus G1, G4, and G7. We detected single nucleotide polymorphic sites (SNPs), small deletions and insertions (DIPs), and large structural variants (SVs) associated with low-chill haplotypes and created a prioritized list of candidate genes based on functionally characterized homologs from Arabidopsis thaliana. Two dormancy associated genes PpeDAM5 and PpeDAM6 are the strongest candidate genes for the major QTL signal at the lower end of G1. Also, key functional genes involved in the Polycomb repressive mechanism, cell cycle progression, and hormone regulation were evident as strong candidate genes underlying QTL intervals in this peach cross.

The distribution of peach scab lesions on the surface of diseased peaches

The aim of the study was to quantify peach scab (Fusicladosporium carpophilum) lesion distribution relative to the point of maximum lesion number on the fruit surface, the relationship between lesion count and distance from the point of maximum lesion density, and establish whether the distribution of lesions was consistent with a splash dispersed pathogen, and to assess the effect of lesion number on fruit size. Fruit of four cultivars, Jerseyqueen, Jefferson, BY07-6428r and Dixiland were collected and the fruit (assumed spherical) sliced taking three horizontal planes across the axis from the point of maximum disease, such that each horizontal zone (Z1-Z4) had the same vertical height, and thus equal surface areas. Lesion counts were analysed using general linear modeling with a Poisson distribution and a log-link function. Zones on the fruit had different numbers of lesions (P < 0.0001), with most lesions found on Z1. Cvs differed in the number of lesions per fruit (P = 0.0042–<0.0001). An analysis of covariance showed that although fruit size varied among most cvs (P = 0.1614–<0.0001), the number of lesions on a fruit did not affect fruit size (P = 0.5654). Measurements of the point of maximum disease relative to the peduncle-flower scar axis of the fruit suggest that fruit are not always held upright when infection occurs, such that up to 40% of fruit showed maximum infection at an angle >90° to the peduncle. This pattern of disease is consistent with observations of the splash-borne nature of conidia, with the most exposed, easily wetted, uppermost portion of fruit developing most disease.