Collaborative project to identify direct and distant pedigree relationships in apple

Pedigree information is fundamentally important in breeding programs, enabling breeders to know the source of valuable attributes and underlying alleles and to enlarge genetic diversity in a directed way. Many apple cultivars are related to each other through both recent and distant common ancestors. As apple trees are clonally propagated, long-lived, and widely adapted, many of the ancestors of modern cultivars are still present in global germplasm collections. Use of apple SNP arrays enables identification of direct and distant pedigree relationships with precision. An example is the elucidation of the \u27Honeycrisp\u27 pedigree using the 8K SNP array, which enabled further findings regarding the inheritance of important alleles for traits including scab resistance and soft scald susceptibility. To facilitate more discoveries across apple germplasm, a large-scale collaborative apple pedigree reconstruction project has been initiated. This project utilizes output from the Illumina Infinium 20K and Affymetrix Axiom 480K apple SNP arrays, a high quality genetic linkage map for the 20K array SNPs, and a data curation pipeline developed through the FruitBreedomics and RosBREED projects. Techniques using shared haplotype length statistics will be used alongside historical information to deduce distant pedigree relationships. The project involves various experts, germplasm collections, and academic institutions around the world and is open for further extension. It will provide findings useful for breeding programs, germplasm collections, geneticists, and historians

A multifaceted investigation to unravel apple fruit texture physiology

Fruit texture plays a major role in apple fruit quality, and it has been the major driving factor in the selection process carried out by breeders. The economic importance of texture relies on the fact that some aspects of this multi-trait feature (crispness in particular) are the reason for not liking a particular fruit, and thus it represents the principal aspect sensorially perceived by consumers. Texture, which changes significantly during storage, can only be evaluated many years after from the crossing, and it has been established that it is regulated by a considerable number of genes. In this work a candidate gene driven association mapping approach has been employed in order to define valuable new markers suitable to predict the dissected fruit texture subtraits in apple. LD mapping was carried out in an apple collection, ad hoc assembled, and a candidate gene was targeted over a comprehensive QTL investigation based on two bi-parental maps. Finally we also present a preliminary functional genomic investigation addressed to target novel putative candidate genes to further unravel the complex control of fruit texture in apple

A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry

Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established

A candidate gene based approach validates Md-PG1 as the main responsible for a QTL impacting fruit texture in apple (Malus x domestica Borkh)

Background: Apple is a widely cultivated fruit crop for its quality properties and extended storability. Among the several quality factors, texture is the most important and appreciated, and within the apple variety panorama the cortex texture shows a broad range of variability. Anatomically these variations depend on degradation events occurring in both fruit primary cell wall and middle lamella. This physiological process is regulated by an enzymatic network generally encoded by large gene families, among which polygalacturonase is devoted to the depolymerization of pectin. In apple, Md-PG1, a key gene belonging to the polygalacturonase gene family, was mapped on chromosome 10 and co-localized within the statistical interval of a major hot spot QTL associated to several fruit texture sub-phenotypes. Results: In this work, a QTL corresponding to the position of Md-PG1 was validated and new functional alleles associated to the fruit texture properties in 77 apple cultivars were discovered. 38 SNPs genotyped by gene full length resequencing and 2 SSR markers ad hoc targeted in the gene metacontig were employed. Out of this SNP set, eleven were used to define three significant haplotypes statistically associated to several texture components. The impact of Md-PG1 in the fruit cell wall disassembly was further confirmed by the cortex structure electron microscope scanning in two apple varieties characterized by opposite texture performance, such as ‘Golden Delicious’ and ‘Granny Smith’. Conclusions: The results here presented step forward into the genetic dissection of fruit texture in apple. This new set of haplotypes, and microsatellite alleles, can represent a valuable toolbox for a more efficient parental selection as well as the identification of new apple accessions distinguished by superior fruit quality features

QTL mapping of pomological traits in peach and related species breeding germplasm

Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in marker-assisted breeding

Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit : breeding insights from a multi-family study

Acidity is a critical component of the apple fruit consumption experience. In previous biparental family studies, two large-effect acidity QTLs were reported using freshly harvested fruit. Objectives of this study were to determine the number and location of QTLs for acidity variation in a large apple breeding program and ascertain the quantitative effects and breeding relevance of QTL allelic combinations at harvest and after commercially relevant periods of cold storage. Pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents, genotyped for the 8K SNP array, was assessed for titratable acidity at harvest and after 10- and 20-week storage treatments, for three successive seasons. Using pedigree-based QTL mapping software, FlexQTL™, evidence was found for only two QTLs, on linkage groups 16 (the reported Ma locus) and LG 8 (here called Ma3) that jointly explained 66 ± 5% of the phenotypic variation. An additive allele dosage model for the two QTLs effectively explained most acidity variation, with an average of + 1.8 mg/L at harvest per high-acidity allele. The more high-acidity alleles, the faster the depletion with storage, with all combinations appearing to eventually converge to a common baseline. All parent cultivars and selections had one or two of the four possible high-acidity alleles. Each QTL had a rare second high-acidity allele with stronger or reduced effect. Diagnostic SNP markers were identified for QTL alleles derived from distinct sources. Combined QTL effects highlighted utility of the DNA-based information in new cultivar development for targeting desired fruit acidity levels before or after storage.</p

RosBREED: Enabling marker-assisted breeding in Rosaceae

Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including EST libraries, genetic and physical maps, QTLs, and whole genome sequences. The potential of genomics approaches to enhance crop improvement, particularly through marker-assisted breeding (MAB), is enormous, but unfulfilled. The U.S. Rosaceae genomics, genetics, and breeding community, with strong international involvement, has united behind the goal of translational genomics and collaborated on the development of large-scale USDA grant proposals. RosBREED, funded for four years from September 2009, incorporates eight teams (Breeding, Socio-Economics, Pedigree-Based Analysis, Breeding Information Management System, Genomics, Genotyping, MAB Pipeline, and Extension) in a transdisciplinary framework that involves significant educational and outreach activities and stakeholder participation. Objectives are to (1) enhance the likelihood of new cultivar adoption, enlarge market potential, and increase consumption of Rosaceae fruits with socio-economics knowledge objectively used in breeding decisions; (2) establish a sustainable technical infrastructure for an efficient MAB Pipeline in Rosaceae; (3) integrate breeding and genomics resources with a standardized breeding information management system incorporating Pedigree-Based Analysis; (4) implement MAB in core RosBREED breeding programs with a common focus on fruit quality traits; and (5) enhance sustainability of cultivar development with MAB technology transfer to current and future U.S. Rosaceae breeders and engagement of key stakeholder groups. Coordinated action is now required to make RosBREED a reality and fulfill the promise of genomics