A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.info:eu-repo/semantics/acceptedVersio

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.This work was supported by funding from the Agricultural Science and Technology Innovation Program (to Yongyang Xu, S.H., Z.Z. and H.W.), the China Agriculture Research System (CARS-25 to Yongyang Xu and H.W.), the Leading Talents of Guangdong Province Program (00201515 to S.H.), the Shenzhen Municipal (The Peacock Plan KQTD2016113010482651 to S.H.), the Dapeng district government, National Natural Science Foundation of China (31772304 to Z.Z.), the Science and Technology Program of Guangdong (2018B020202007 to S.H.), the National Natural Science Foundation of China (31530066 to S.H.), the National Key R&D Program of China (2016YFD0101007 to S.H.), USDA National Institute of Food and Agriculture Specialty Crop Research Initiative (2015-51181-24285 to Z.F.), the European Research Council (ERC-SEXYPARTH to A.B.), the Spanish Ministry of Economy and Competitiveness (AGL2015–64625-C2-1-R to J.G.-M.), Severo Ochoa Programme for Centres of Excellence in R&D 2016–2010 (SEV-2015–0533 to J.G.-M.), the CERCA Programme/Generalitat de Catalunya to J.G.-M. and the German Science Foundation (SPP1991 Taxon-OMICS to H.S.)

Diagnostic accuracy of Ber-EP4 for metastatic adenocarcinoma in serous effusions: a meta-analysis.

Numerous studies have investigated the utility of Ber-EP4 in differentiating metastatic adenocarcinoma (MAC) from malignant epithelial mesothelioma (MM) and/or reactive mesothelial cells (RM) in serous effusions. However, the results remain controversial. The aim of this study is to determine the overall accuracy of Ber-EP4 in serous effusions for MAC through a meta-analysis of published studies. Publications addressing the accuracy of Ber-EP4 in the diagnosis of MAC were selected from the Pubmed, Embase and Cochrane Library. Data from selected studies were pooled to yield summary sensitivity, specificity, positive and negative likelihood ratio (LR), diagnostic odds ratio (DOR), and receiver operating characteristic (SROC) curve. Statistical analysis was performed by Meta-Disc 1.4 and STATA 12.0 softwares. 29 studies, based on 2646 patients, met the inclusion criteria and the summary estimating for Ber-EP4 in the diagnosis of MAC were: sensitivity 0.8 (95% CI: 0.78-0.82), specificity 0.94 (95% CI: 0.93-0.96), positive likelihood ratio (PLR) 12.72 (95% CI: 8.66-18.7), negative likelihood ratio (NLR) 0.18 (95% CI: 0.12-0.26) and diagnostic odds ratio 95.05 (95% CI: 57.26-157.77). The SROC curve indicated that the maximum joint sensitivity and specificity (Q-value) was 0.91; the area under the curve was 0.96. Our findings suggest that BER-EP4 may be a useful diagnostic adjunctive tool for confirming MAC in serous effusions

Funnel graph for the assessment of potential publication bias of the 29 included studies.

<p>The funnel graph plots the log of the diagnostic odds ratio (DOR) against the standard error of the log of the DOR (an indicator of sample size). Solid circles represent each study in the meta-analysis. The line indicates the regression line.</p

Forest plots of the sensitivity and speci­ficity for Ber-EP4 in the diagnosis of metastatic adenocarcinoma for all studies.

<p>The point estimates of sensitivity and specificity for each study are shown as solid circles and the size of each solid circle indicates the sample size of each study. Error bars are 95% confidence intervals.</p

Summary receiver operating characteristic curve for Ber-EP4 in the diagnosis of metastatic adenocarcinoma for all studies.

<p>Solid circles represent each study included in the meta-analysis. The size of each solid circle indicates the size of each study. The regression SROC curve summarizes the overall diagnostic accuracy.</p

Flow chart of selection process for eligible articles.

<p>Flow chart of selection process for eligible articles.</p

Summary of the studies included in the meta-analysis.

<p>TP, true positive; FP, false positive; FN, false negative; TN, true negative.</p><p>Summary of the studies included in the meta-analysis.</p

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Extended data and supplementary information are available at https://doi.org/10.1038/s41588-019-0522-8Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop