Simple Sequence Repeat (SSR) markers differentiate Turkish sour cherry germplasm

Eighty-one tetraploid cherry selections, including sour cherry (Prunus cerasus L.) and its progenitor species P. fruticosa Pall., were compared using simple sequence repeat (SSR) marker analysis to determine the relationship of germplasm collected from Turkey to those collected from Russia and northern and eastern regions of Europe. SSR fragments were produced with all five primer pair - cherry selection combinations. Cherry selections exhibited high levels of polymorphism with 5 to 20 different putative alleles amplified per primer pair. The primer pair PMS 49, isolated from sweet cherry, showed a high level of polymorphism with 20 putative alleles identified. However, SSR analysis was not able to differentiate among some selections. Overall, Turkish selections tended to group together and separated from other cherry selections. The Turkish germplasm did not exhibit many of the putative SSR alleles identified in the broader germplasm pool; however, it exhibited many novel alleles. This study demonstrated the importance of including germplasm from Turkey, an important ancestral region for sour cherry, when building a germplasm collection. It also demonstrated the utility of SSR markers in identifying genetic variation "gaps" within a germplasm collection

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

Fruit size QTL analysis of an F1 population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry

Maximizing fruit size is critical for profitable sweet cherry (Prunus avium L.) production. Yet, despite its importance, little is known about the genetic control of fruit size. The objective of this study was to identify quantitative trait loci (QTLs) for fruit size and two essential components of fruit size, mesocarp cell number and size. This study utilized a double pseudo-testcross population derived from reciprocal crosses between a sweet cherry cultivar with ~8 g fruit, ¿Emperor Francis¿ (EF), and a wild forest sweet cherry selection with ~2 g fruit, ¿New York 54¿ (NY). A total of 190 F1 progeny previously utilized for the construction of the linkage maps were evaluated in 2006 and 2007 for fruit weight, length, and diameter; mesocarp cell number and length; and pit length and diameter. In 2008, a subset of this population was again evaluated for fruit weight. Correlation analysis revealed that the three fruit size traits were highly correlated with each other, and mesocarp cell number, not cell length, was correlated with fruit size. Three QTLs were identified for each fruit size trait, and one QTL was identified for mesocarp cell number. Fruit size QTLs were found on linkage group 2 on the EF map (EF 2) and linkage groups 2 and 6 on the NY map (NY 2 and NY 6). On EF 2, the cell number QTL clustered with the fruit size QTL, suggesting that the underlying basis of the fruit size increase associated with this QTL was an increase in mesocarp cell number. On NY 6, pit length and diameter QTLs clustered with those for fruit size, suggesting that the underlying morphological basis of this fruit size QTL is the difference in pit siz

Large-Scale Standardized Phenotyping of apple in RosBREED

The USDA - Specialty Crop Research Initiative-funded RosBREED project is focused on enabling marker-assisted breeding in the Rosaceae. New molecular tools for selection need to be developed before this technology will be widely accepted and applied to apple breeding programs. As well as detailed genotypic data of inter-related progenies, parents and ancestor cultivars, fully descriptive phenotypic data also need to be collected. For apple, fruit phenotyping begins at harvest, followed by 10 and 20 weeks regular storage, each followed by 7 days shelf life at room temperature. The standardized phenotyping protocols agreed by breeding teams in Washington, Minnesota and New York states will be presented in this paper

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