Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

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.

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Background:Painful vertebral osteoporotic compression fractures (OCFs) are often treated with cement augmentation, although controversies exist as to whether or not this increases the secondary fracture risk. Prevention of secondary fracture includes treatment of underlying osteoporosis. The purposes of this study were to determine (1) whether cement augmentation increases the rate of secondary fracture compared with nonoperative management, (2) whether anti-osteoporotic medications reduce the rate of secondary fracture, and (3) the rate of osteoporosis treatment with medications following vertebral OCF.Methods:The PearlDiver database was queried for all patients with a diagnosis of OCF from 2015 to 2019. Patients were excluded if they were <50 years old, had a diagnosis of spinal neoplasm or infection, or underwent lumbar fusion in the perioperative period. Secondary fracture risk was assessed using univariate and multivariate logistic regression analysis, with kyphoplasty, vertebroplasty, anti-osteoporotic medications, age, gender, and Elixhauser Comorbidity Index as variables.Results:A total of 36,145 patients were diagnosed with an OCF during the study period. Of those, 25,904 (71.7%) underwent nonoperative management and 10,241 (28.3%) underwent cement augmentation, including 1,556 who underwent vertebroplasty and 8,833 who underwent kyphoplasty. Patients who underwent nonoperative management had a secondary fracture rate of 21.8% following the initial OCF, compared with 14.5% in the vertebroplasty cohort and 18.5% in the kyphoplasty cohort, which was not a significant difference on multivariate analysis. In the entire cohort, 2,833 (7.8%) received anti-osteoporotic medications and 33,312 (92.2%) did not. The rate of secondary fracture was 10.1% in patients who received medications and 21.9% in those who did not, which was a significant difference on multivariate analysis (odds ratio = 1.23, p < 0.001).Conclusions:Cement augmentation did not alter the rate of secondary fracture, whereas anti-osteoporotic medications significantly decreased the risk of subsequent OCF by 19%. Only 7.8% of patients received a prescription for an anti-osteoporotic medication following the initial OCF.Level of Evidence:Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

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Rice was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns had predictive value and allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

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