A good place for the would-be apple breeder to start is the series of videos and articles at Steven Edholm’s website describing his breeding project in Northern California, plus a wealth of background information. Commercial scale breeding methodology is clearly explained in a series of videos made by Markus Kobelt, founder of the Swiss company Lubera. We've also made a series of short practical guidance videos for beginners on You Tube at yvapplebreeders.
The News Letters of the Midwest Apple Improvement Association are another good source of practical information, as are the websites of university-based breeding programmes, like Purdue. An authorative entry point to the research literature is the review article by Janick et al. (1996)
My own starting point was a passage in the 1939 edition of N B Bagenal’s ‘Fruit Growing: Modern Cultural Methods’:
‘A very popular cross is that between Cox’s Orange Pippin and Gladstone. Assuming Gladstone to be the male parent and Cox’s the female parent, when the flower buds are about to unfold, cover over a few blossom buds of the two varieties with little bags made of specially prepared paper or muslin to keep out insects. When the petals begin to open, take off the bags from the Cox tree, and remove the stamens with a pair of forceps, leaving only three or four buds to a truss, and then put the bags on again. When the flowers of both parents are fully open, remove the bags and examine the styles of the Cox flowers. If the styles look sticky, they are in the right condition to receive pollen from the Gladstone flowers. These may be cut off and the stamens rubbed gently against the styles of the Cox flowers. Now put the bags on again and keep them on until the fruits are completely ripe.’
The treatment of seeds resulting from crosses is also dealt with:
‘The apple pips should be sown in shallow wooden boxes or earthenware pans containing one-third leaf mould, two-thirds good loam and a little sharp sand. The boxes or pans must be well drained with plenty of broken crocks at the bottom. They are placed in cold frames and need not be pampered in any way until after the seeds have germinated the following spring, when they will need protection from frost. The seedlings are potted up when a few inches high and gradually hardened off ready for planting out when the late frosts are over. The seedlings can either be left to grow on their own roots or, after two or three seasons’ growth their shoots may be cut off and grafted in the spring.’
For information on apple varieties, Nigel Deacon’s website is invaluable, providing a huge repository of knowledge about old English varieties, their history and cultivation, together with guidance on how to perform hand crosses. I’d also recommend the Orange Pippin website, particularly useful for checking the characteristics and parentage of varieties, together with the UK’s National Fruit Collection data base.
For printed information, one of the best sources is ‘The Book of Apples’ by Joan Morgan and Alison Richards (Ebury Press, London. 1993. ISBN 0091777593), detailing over 2000 varieties from around the world.
For anyone thinking of grafting seedling scion wood onto commercial rootstocks in order to accelerate flowering, there are plenty of ‘how to graft’ videos around. I've found those made by Stephen Hayes in the UK both clear and easy to learn from. Amongst written accounts the stand out is probably ‘The Grafter’s Handbook’ by R J Garner, who worked for many years at the East Malling Research Station in the UK.
On a more general level, Dan Neuteboom's comprehensive website is a great source of expert guidance on fruit tree growing and management. Up to date information on all aspects of commercial apple growing from a UK perspective, together with the underlying science, can be found online in the ‘Apple Best Practice Guide’ produced by the UK’s Agriculture and Horticulture Development Board.