Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

Area of Science:

• Plant genetics
• Horticultural science
• Population genetics

Background:

• Apple (Malus x domestica Borkh.) is a vital temperate fruit crop with significant economic and cultural value.
• Ancient apple cultivars are maintained through grafting, with some potentially dating back to Roman times.
• Molecular markers are crucial for reconstructing pedigrees and understanding the historical movement of plant materials.

Purpose of the Study:

• To identify relationships within a large set of apple cultivars using whole-genome SNP data.
• To reconstruct apple pedigrees and elucidate the history of apple cultivar development and trade.
• To analyze genetic relationships among over 1400 apple genotypes.

Main Methods:

• Utilized whole-genome SNP data (approx. 253K SNPs) for pedigree reconstruction.
• Employed simple exclusion tests based on Mendelian errors to identify parent-offspring relationships.
• Integrated historical data and family structures to orient parent-offspring pairings.

Main Results:

• Identified over 1000 parent-offspring relations and 295 complete families.
• Uncovered the significant impact of Renaissance cultivars ('Reinette Franche', 'Margil') and an 18th-century cultivar ('Alexander') on modern apple varieties.
• Observed frequent inter-regional crosses, particularly from the 19th century onwards, and noted that many ancient cultivars had limited identifiable offspring.

Conclusions:

• The study leveraged a large dataset of unique European apple genotypes for successful pedigree reconstruction.
• Findings illuminate the history of selection and breeding in European apple cultivars.
• The reconstructed pedigrees provide valuable insights for accelerating future apple breeding and selection efforts.