Genome-wide association mapping of date palm fruit traits

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species

Orphan crops of archaeology-based crop history research

So-called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long-term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology-based crop history research. A meta-analysis and synthesis of archaeo- botanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and histor- ical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda-based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginal- ized and ‘forgotten’

Orphan crops of archaeology-based crop history research

Agrobiodiversity is central to sustainable farming worldwide. Cultivation, conservation and reintroduction of diverse plant species, including ‘forgotten’ and ‘underutilized’ crops, contribute to global agrobiodiversity, living ecosystems and sustainable food production. Such efforts benefit from traditional and historical knowledge of crop plants' evolutionary and cultural trajectories. This review is a first attempt at systematically gauging species representativeness in studies of archaeological plant remains. Results indicate that, in addition to discipline-specific methodological sources of bias, modern agricultural biases may replicate themselves in crop history research and influence understandings of ‘forgotten crops’. Recognizing these biases is an initial stride towards rectifying them and promoting agrobiodiversity in both research and practical applications. Summary: So-called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long-term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology-based crop history research. A meta-analysis and synthesis of archaeobotanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and historical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda-based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginalized and ‘forgotten’