The increasing availability of genomic tools improves our ability to investigate the patterns of genetic diversity and relatedness among individuals. The pedigrees of many apple cultivars are completely unknown, often reducing the efficiency of breeding programs. Using a multilocus simple sequence repeat dataset, we applied a novel multi-generation pedigree-network reconstruction procedure based on the software FRANz in a Malus × domestica collection (101 cultivated and 22 wild apples) with partially known pedigree relationships. The procedure produced 78 parent–offspring relationships organized into three networks and showed high power for detecting real pedigree links (98.5 %) and a low false-positive rate (9.0 %). The largest reconstructed pedigree network spanned four generations and involved 65 cultivars. The availability of detailed pedigree connections confirmed that recent genealogical relationships affect population genetic structure in apple. Finally, our analysis enabled us to confirm or discard several pedigrees known only anecdotically, among which the cultivar Grimes Golden was validated as a parent of the widely grown cultivar Golden Delicious. The pedigree reconstruction protocol here described will be of broad applicability to other collections and crop species

Salvi, S.; Micheletti, D.; Magnago, P.; Fontanari, M.; Viola, R.; Pindo, M.; Velasco, R. (2014). One-step reconstruction of multi-generation pedigree networks in apple (Malus x domestica Borkh.) and the parentage of Golden Delicious. MOLECULAR BREEDING, 34 (2): 511-524. doi: 10.1007/s11032-014-0054-y handle: http://hdl.handle.net/10449/25019

One-step reconstruction of multi-generation pedigree networks in apple (Malus x domestica Borkh.) and the parentage of Golden Delicious

Salvi, Silvio;Micheletti, Diego;Magnago, Pierluigi;Fontanari, Marco;Viola, Roberto;Pindo, Massimo;Velasco, Riccardo
2014-01-01

Abstract

The increasing availability of genomic tools improves our ability to investigate the patterns of genetic diversity and relatedness among individuals. The pedigrees of many apple cultivars are completely unknown, often reducing the efficiency of breeding programs. Using a multilocus simple sequence repeat dataset, we applied a novel multi-generation pedigree-network reconstruction procedure based on the software FRANz in a Malus × domestica collection (101 cultivated and 22 wild apples) with partially known pedigree relationships. The procedure produced 78 parent–offspring relationships organized into three networks and showed high power for detecting real pedigree links (98.5 %) and a low false-positive rate (9.0 %). The largest reconstructed pedigree network spanned four generations and involved 65 cultivars. The availability of detailed pedigree connections confirmed that recent genealogical relationships affect population genetic structure in apple. Finally, our analysis enabled us to confirm or discard several pedigrees known only anecdotically, among which the cultivar Grimes Golden was validated as a parent of the widely grown cultivar Golden Delicious. The pedigree reconstruction protocol here described will be of broad applicability to other collections and crop species
Apple parentage
Coancestry
Pedigree reconstruction
Population structure
Settore AGR/07 - GENETICA AGRARIA
2014
Salvi, S.; Micheletti, D.; Magnago, P.; Fontanari, M.; Viola, R.; Pindo, M.; Velasco, R. (2014). One-step reconstruction of multi-generation pedigree networks in apple (Malus x domestica Borkh.) and the parentage of Golden Delicious. MOLECULAR BREEDING, 34 (2): 511-524. doi: 10.1007/s11032-014-0054-y handle: http://hdl.handle.net/10449/25019
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