Background

Apple, Malus x domestica Borkh., is the most important deciduous tree fruit crop grown in the United States and around the world. Apple production figures in the United States have surpassed 5.1 million short tons at an estimated value of over $17 billion. The apple is consumed fresh, and in multiple processed and cooked forms including juice, sauce, and canned fruit cocktails, among various other uses. The importance of apple in a balanced human diet is well known, and pertains to its fiber, vitamins, and antioxidant content.

The genus Malus belongs to the Rosaceae family. This family includes several important genera that account for most of our important deciduous fruit crops including apple (Malus), pear (Pyrus), and stone fruits (Prunus) such as peach, cherry, plum, apricot, almond, as well as other valuable ornamental plants including roses (Rosa), Mespilus (medlar), and Crataegus (hawthorn), among others. Among these various genera, Malus serves as the most valuable in terms of commercial value. It is composed of over 25 species and hybrids. Over 2,500 clones of species, hybrids, cultivated apples, and selections are maintained at the National Germplasm Repository (Geneva, NY). Of these, a core collection of 200 accessions has also been maintained at five different sites around the United States, including Illinois (Urbana) and New York (Geneva). The two leading apple breeding programs in the United States include the collaborative PRI program of the Universities of Illinois, Purdue, and Rutgers, and that of Cornell University. The PRI program has focused on development, naming, and release of over a dozen apple cultivars, carrying resistance to the fungal disease apple scab as well as resistance to other important diseases, including 'GoldRush', 'Enterprise', and 'Juliet'. The New York apple breeding program has named and released several cultivars that are now grown commercially, including 'Empire', and 'Jonagold', and scab-resistant cultivars such as 'Liberty' and 'Freedom' as well as five fire blight resistant apple rootstocks. In addition, the University of Illinois has made significant strides in investigating the molecular genetics of scab resistance; while, Cornell University has led the effort to investigate fire blight and develop transgenic lines with enhanced resistance to fire blight.

Most cultivated apples are diploids (2n=34), self-incompatible, and display a juvenile period of 6 to 10 years or more. The apple has a relatively small genome, 1.54 pg DNA/2C or 750 Mb per haploid genome which is similar to that of the sorghum genome and about the same size of the tomato genome. Molecular mapping studies of the apple have also been underway with over 370 isozymes, RAPDs, RFLPs, SSRs, and AFLPs mapped to linkage groups. Several apple cultivars have been transformed via Agrobacterium-mediated transformation, and promising transgenic lines with enhanced resistance to important diseases such as apple scab and fire blight have been developed in the PI's (Korban) and Co-PI's (Aldwinckle) laboratories. In the PI's (Dr. Korban) laboratory, two bacterial artificial chromosome (BAC) libraries have been constructed, one from a wild Malus species (M. floribunda 821 that carries a major gene for scab resistance as well as other important horticultural traits) and a second from a newly-bred apple cultivar ('GoldRush') developed from the PRI breeding program. This effort has recently led to the discovery and cloning of a cluster of receptor-like genes within the Vf locus. Thus, the apple serves as an ideal model system for all members of the Rosaceae family, and is primed to benefit from a program in functional genomics.

This project focuses on developing genomic research tools and genome expression studies addressing flowering, fruiting, and pathogen response on a genome-wide scale for one of the most important economic woody perennial plants, the apple.