Several fruit quality-related genes were found in these and other sweeps, indicating their potential contribution to the aromatic flavor, texture and nutritional profiles of cultivated watermelon fruit (Supplementary Note). Sci. Watermelon domestication was shaped by stepwise selection and - PubMed Furthermore, the fixation index (FST) between C. mucosospermus and C. lanatus was only 0.299, whereas the pairwise FST between C. amarus and the other species ranged from 0.509 to 0.686 (Extended Data Fig. 7 (Suppl. 30), was found in a genomic region with greatly reduced nucleotide diversity in C. mucosospermus and C. lanatus compared with C. colocynthis (Supplementary Fig. 75) to be expressed under the Arabidopsis U6 promoter, alongside the Zea mays codon-optimized Cas9 driven by the double CaMV 35S promoter. Plant J. Stanke, M., Tzvetkova, A. Red arrows represent gene flow between lineages. LD decay was calculated for all pairs of SNPs within 500kb using PopLDdecay66 (v3.27) with parameters -MaxDist 500 -Het 0.1 -Miss 0.1. b, c, Alignments of 20-kb insert size mate-pair reads at the potential inversion breakpoint regions. Watermelon (Citrullus lanatus, 2n=2=22) is one of the most popular fruit crops worldwide. Domesticated watermelon ( Citrullus lanatus subsp. ), Ministry of Science and Technology of China (2016YFD0101007 and 2015BAD02B02 to S.G.), National Natural Science Foundation of China (31801886 to H.S. The cleaned reads were aligned to the 97103 genome using BWA-MEM46 (v0.7.12) with default parameters. The variant call format and VCFtools. Red fruit flesh color was later selected for in sweet watermelons by maintaining an amino acid substitution in the lycopene metabolism enzyme LCYB. A.) 281, 4046140472 (2006). In this study, we first assembled an improved genome sequence of the watermelon cultivar 97103 using PacBio long reads combined with BioNano optical and Hi-C chromatin interaction maps. The Birthplace of the First Domesticated Watermelon Has Been Found Therefore, C. mucosospermus was used as a representative of the progenitor of C. lanatus. PCR amplicons were used to genotype the ClAGA2 mutant plants by Sanger sequencing. The fruits of C. amarus are larger than those of C. colocynthis, suggesting that fruit enlargement has also been selected for in C. amarus after its split from the ancestor of C. mucosospermus and C. lanatus. Colors of branches in the tree indicate different species (matching the colors shown in a). 1b,c and Extended Data Fig. ), Innovation Program of Beijing Academy of Agricultural and Forestry Sciences (KJCX20170102 to Y.X. Sci. 2 teaspoons honey. Were Ancient Egyptians the First to Domesticate Wild Watermelons? Hortic. X.Z. Sci. GWAS analyses were performed using the linear mixed model algorithm implemented in the FaST-LMM program. Bioinformatics 30, 21142120 (2014). The enriched biological processes for these improvement-specific genes included glucose import and cell wall modification (Supplementary Table 14). Grilled Watermelon with Jalapeos, Feta and Honey Rind stripes were categorized into no-stripe, netted, narrow, middle and wide stripe. Zhong, S. et al. Evol. 4, fruit size enlargement occurred in C. lanatus and C. mucosospermus and in C. amarus lineages, involving different but overlapping sets of QTLs. Significant GWAS signals are indicated by vertical black arrows. The hidden, ancient history of summer's favorite fruit. In a 1949 study on watermelon breeding published in the scintillating-sounding journal Economic Botany, G.K. Parris wrote that "Most of the varieties 40 to 50 years ago have disappeared, . Extended Data Fig. Environ. Watermelon genome decoded: Scientists find clues to - ScienceDaily PCA plots of the first three components of Citrullus accessions excluding C. naudinianusand (PC1PC3, PC2PC3) (a) and C. mucosospermus and C. lanatus accessions (PC1PC3, PC2PC3) (b), and all accessions in the seven Citrullus species (PC1PC2, PC1PC3, PC2PC3) (c). The fruit of C. colocynthis had low levels of disaccharides and monosaccharides, but abundant raffinose and stachyose, whereas the fruit of C. lanatus showed an opposite pattern (Supplementary Fig. Watermelon has been domesticated for more than 4,000 years, and has been improved by domestication and modern breeding from wild watermelons with small fruits harboring hard, pale-colored and bitter- or bland-tasting flesh, into modern sweet watermelons carrying large fruits with crisp sweet and red flesh and a thin rind2. Finally, 31 scaffolds with a total size of 362.7Mb (99.3% of the assembly) were clustered into 11 chromosomes ranging from 27.1 to 37.9Mb in length (Extended Data Figs. Rind colors were categorized into yellow, white, light green, middle green, green and dark green. Cytomolecular characterization of rDNA distribution in various Citrullus species using fluorescent in situ hybridization. Stachyose and raffinose, arriving at the fruit sink, are rapidly metabolized into disaccharides and monosaccharides by -galactosidases29. Korf, I. Gene finding in novel genomes. Two C. lanatus accessions from Sudan located in the deepest branch of the C. lanatus clade are indicated by the arrow. To improve the accuracy, only candidate selective sweeps with the top 50% of ratios between the two compared populations were kept. Extended Data Fig. 1b) was largely consistent with the previously reported phylogeny4,5, with the most morphologically distinct Citrullus species, C. naudinianus, sister to the other six species, followed by C. colocynthis and C. rehmii. A watermelon fruit captured in a seventeenth-century painting by Italian artist Giovanni Stanchi displayed unevenly colored pinkish flesh, a thick rind and many dark-colored seeds, which may represent a sweet watermelon in the midst of its domestication. In total, 172 sweeps in C. mucosospermus were identified, covering 14.0Mb and 416 genes (Fig. Duplicated read pairs were marked with Picard (v2.0.1) with the parameter OPTICAL_DUPLICATE_PIXEL_DISTANCE=250. 1d). Raw Illumina reads were processed to remove adapter sequences using Picard v2.0.1 (https://broadinstitute.github.io/picard/). Sweet dessert watermelons spread across the Mediterranean world during Roman times. The average ratio of shared variation sites of the two groups was calculated in each of the 200-kb windows with a step size of 20kb. Researchers Uncover the Watermelon's Origins - Smithsonian Magazine One fruit per plant was harvested 30 d after self-pollination. Briefly, a small piece of flesh from the mature fruit was tasted by three people trained to detect bitterness, and the fruit samples were categorized into bitter and non-bitter groups. Based on the identified improvement sweeps, QBRX2-1 was also under selection during the breeding of modern cultivars, whereas QBrix6 was probably only selected for during domestication (Fig. Wild banana. We identified an introgression from C. amarus to C. lanatus on chromosome 6 at around 28.329.3Mb (Supplementary Fig. 19, 3268 (2018). High-level expression of a novel chromoplast phosphate transporter ClPHT4;2 is required for flesh color development in watermelon. Cantarel, B. L. et al. The Kordofan melon, which is about six inches wide, white on the inside and a pale, gently striated green on the outside, has long been grown by farmers in what is now Sudan. Approximately 55.55% of the assembly was annotated as repeat sequences, a substantially higher percentage than in the previous assembly (46.60%) (Supplementary Table 4), and 22,596 high-confidence genes were predicted in the assembly (Supplementary Note). ), Leading Talents of Guangdong Province Program (00201515 to S.H. PubMedGoogle Scholar. A genetic linkage map for watermelon derived from a testcross population: (Citrullus lanatus var. Selection for flesh sweetness started in the progenitor of C. lanatus and continues through modern breeding on loci controlling raffinose catabolism and sugar transport. Exploring the public RNA-seq datasets in the Cucurbit Genomics Database27 revealed that the expression of ClBt was detected in the leaf but not in the flower, fruit, seed or root tissues, suggesting that the mechanisms by which ClBt regulates watermelon fruit bitterness may be complicated. Flesh sweetness QTLs: FCE10.1, QBrix6, QBRX2-1 and Qfru2-3. Vol. National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China, Shaogui Guo,Honghe Sun,Yi Ren,Jie Zhang,Haiying Zhang,Guoyi Gong,Changlong Wen,Shouwei Tian,Maoying Li,Yanping Wang,Xingping Zhang&Yong Xu, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China, Shengjie Zhao,Yun Deng,Xuqiang Lu,Jianli Shang,Nan He,Junpu Liu,Yingchun Zhu&Wenge Liu, Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA, Honghe Sun,Xin Wang,Shan Wu,Lei Gao&Zhangjun Fei, Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China, U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA, U.S. Department of Agriculture-Agricultural Research Service, U.S. There has been a long standing debate about when and where watermelons were historically domesticated, to become the sweet, red, fleshy summer treat we've come to know and love. CRISPRCas9-positive lines selected on the basis of Basta herbicide resistance were further genotyped using primers flanking the gRNA targeting sequence (Supplementary Table 20). 36, 26302638 (2008). 104, 134139 (2013). Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. CA, C. amarus; CC, C. colocynthis; CE, C. ecirrhosus; CL_CUL, C. lanatus cultivar; CL_LR, C. lanatus landrace; CM, C. mucosospermus; CN, C. naudinianus; CR, C. rehmii. Cucurbit genomics database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. 14), might be interconnected through shared genetic components. 2e,f). Illumina RNA-seq reads were assembled using Trinity (v2.5.1)55 with the de novo mode and the genome-guided mode, respectively. The images or other third party material in this article are included in the articles Creative Commons license, unless indicated otherwise in a credit line to the material.