Unraveling the diversity and cultural heritage of fruit crops through paleogenomics

Abstract

Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.

Keywords: ancient DNA; archaeobotany; cultivar; cultural history; genetic diversity; landrace.

Figure 1

The main methological steps for ancient DNA work: Laboratory work: FTIR is carried out to screen the samples. The best preserved samples are splitted into two; one half of a sample going for ¹⁴C analysis and the other for DNA extraction in a clean lab, and to the preparation of single-stranded (ss)DNA and/or double-stranded (ds)DNA libraries, which are then sequenced through shotgun or using targeted enrichment methods. (B) Analyses include alignment against reference genomes and assessment of authenticity and postmortem damage, and then various genetic analyses. From the lab to the field: collecting shoots from the closest-living cultivars and planting them to revive bygone heritage crops. Abbreviations: FTIR, Fourier transform infrared; NGS, next-generation sequencing.

Figure 2

Domestication centers and routes of dispersal for the three case studies as described in the main text. Abbreviations: kya, thousand years ago; P. dactylifera, Phoenix dactylifera; P. theophrasti, Phoenix theophrasti.

Figure 3

(A) Archaeobotanical grape pips. (B) Collecting samples of feral grapevines for DNA fingerprinting. (C) Cultivating grapevines from rotted cuttings sourced from the Western Negev in a heritage tree nursery. (D) Establishing an inaugural heritage vineyard in the Negev Highlands.