A bitter mystery: Sequencing the world's oldest plant genome Guo, S. G. et al. for 15min. The most highly associated SNP (Chr04:15442987) was located in LCYB, and leads to an amino acid change from a conserved phenylalanine to valine (F226V)34. Memorial Day weekend is the unofficial beginning of the summer picnic and cookout season in the U.S., which means it's also Genet. Ren, Y. et al. After the best K was analyzed, the population structure of the watermelon accessions was inferred using fastStructure64 (v1.0) with all SNPs at fourfold degenerated sites for each K (K=24). Shang, Y. et al. Raw BioNano data were cleaned by removing molecules matching any of the following rules: length less than 150kb, molecule signal-to-noise ratio less than 2.75 and label signal-to-noise ratio less than 2.75, or label intensity greater 0.8. Environ. Lippert, C. et al. USA 106, 1227312278 (2009). 3d), suggesting their importance in controlling fruit size and parallel evolution of these loci in different Citrullus species. 18, 188196 (2008). With the help of DNA and Egyptian tomb paintings, a long debate has been settled. Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.). The linkage disequilibrium (LD) decay rates were highest in C. colocynthis and C. amarus, followed by C. mucosospermus and C. lanatus landraces, and lowest in C. lanatus cultivars (Extended Data Fig. Chomicki, G. & Renner, S. S. Watermelon origin solved with molecular phylogenetics including Linnaean material: another example of museomics. 2 Hi-C interaction heatmap for each of the 11 chromosomes of the 97103 genome (v2). Among the selective sweeps detected between C. colocynthis and C. amarus, three regions overlapped with Qfwt2-1 and Qfwt3 (Fig. 131, 747756 (2012). Cloning and functional expression of alkaline alpha-galactosidase from melon fruit: similarity to plant SIP proteins uncovers a novel family of plant glycosyl hydrolases. Plant Physiol. Citrullus ecirrhosus and Citrullus rehmii are adapted to a desert environment and are endemic to southern Africa. 2c). New Phytol. Grasses like wheat, barley, rice and millets were one of the first ones to be domesticated, while fruits, due to their lengthy juvenile phases, were domesticated much later. 3a, Supplementary Fig. New Phytol. How natural and human selections leading to marked phenotypic changes have shaped the watermelon genome remains largely unknown. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. To obtain 8 Fruits And Vegetables Before & After Domestication | Bored Panda Mol. How to Pick, Cut, and Freeze Watermelon - Simply Recipes Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Breeding 20, 6372 (2007). Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. Bioinformatics 27, 21562158 (2011). A, Pharr, D. M. & Madore, M. A. in Photoassimilate Distribution in Plants and Crops 1st edn (eds Zamski, E. & Schaffer, A. Our study identifies a number of candidate loci associated with fruit quality traits and provides insights into the speciation and domestication of the modern sweet watermelon. The hidden, ancient history of summer's favorite fruit. Google Scholar. However, C. ecirrhosus was sister to C. amarus, C. mucosospermus and C. lanatus, instead of being most closely related to C. amarus, as proposed previously4. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits, https://doi.org/10.1038/s41588-019-0518-4. The XP-CLR scores per 100bp were averaged in each non-overlapping 10-kb window across each chromosome. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Li, B. Three peaks highly associated with rind color and rind stripe were found on chromosomes 4, 6 and 8, corresponding to the rind trait loci, Dgo, S and D, respectively18 (Fig. Why Prehistoric Herders Didn't Spit Out Their Watermelon Seeds Qfwt2-1 and Qfwt3 overlapped with both speciation and domestication sweeps (Fig. volume51,pages 16161623 (2019)Cite this article. Prediction of protein-coding genes was performed on the repeat-masked 97103 genome using Maker (v3.01.02)54. Guo, S., Zhao, S., Sun, H. et al. and S.H. Theor. Five watermelon fruit weight QTLs, Qfwt2-1, Qfwt2-2, Qfwt3, Qfwt5-1 and Qfwt5-2, have been identified using segregating populations9,24. Appl. To functionally characterize the role of ClAGA2 in fruit flesh sugar accumulation, we generated ClAGA2-mutated C. lanatus lines using CRISPRCas9 (Supplementary Fig. These two regions contained the sucrose synthase gene Cla97C10G194010 and the raffinose synthase gene Cla97C10G196740, which contribute to the synthesis of sucrose and raffinose, respectively, the dominant metabolites transported in watermelon fascicular phloem tissues15. Sci. Lambel, S. et al. Zhang, B. C., Tolstikov, V., Turnbull, C., Hicks, L. M. & Fiehn, O. Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits. 9). 205, 526532 (2015). 8, 43214325 (1980). Levi, A. et al. 127, 21052115 (2014). The strongest associated SNP on chromosome 3 overlapped with the seed coat color QTL qrc-c8-1 (ref. 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. ad, Selective sweeps in C. mucosospermus compared with C. colocynthis (speciation sweeps) (a), in C. lanatus landrace compared with C. mucosospermus (domestication sweeps) (b), in C. lanatus cultivar compared with C. lanatus landrace (improvement sweeps) (c) and in C. amarus compared with C. colocynthis (speciation sweeps) (d). Genetics 164, 15671587 (2003). Phylogenetic relationships between the Citrullus accessions were inferred using 89,914 SNPs at fourfold degenerate sites. BMC Genomics 15, 767 (2014). Bot. Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae. 4). H.Z., J.S., G.G., N.H., M.L., Y.D., Y.W., S.T and Y.Z. Plants with wild-type ClAGA2 in the same segregation population were used as negative controls. Collectively, our findings shed important light on the evolution and domestication history of watermelons and reveal genome bases underlying the formation of fruit quality traits in sweet watermelon. A chromosome-level genome of a Kordofan melon illuminates the - PNAS 11, 5874 (2018). Breeding Sci. Chaisson, M. J. and W.L. 97, 177185 (2006). The genomic region near ClBt was highly differentiated between C. lanatus landraces and C. mucosospermus (Supplementary Fig. For each group, the D value (sum(ABBA)-sum(BABA))/(sum(ABBA)+sum(BABA)) was weighted using the genotype frequency of the outgroup. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Grabherr, M. G. et al. By Dr Oscar Alejandro Prez Escobar and Chelsea Snell Squeezed and sliced into fresh cocktails and salads, the bright pink juicy flesh of a watermelon is an iconic summer delight. Watermelon plants carrying mutations in the ClAGA2 gene were generated using CRISPRCas9 gene editing technology following our previously established protocol74. The decays of LD (r2) with physical distance (kilobases) for SNPs in five different Citrullus groups are shown. The sugar transporter ClTST2 has been selected for during both domestication and improvement, facilitating sugar accumulation in the vacuoles of fruit flesh cells. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Genome Biol. When one has tasted it, he knows what the angels eat." - Mark Twain Qfwt2-2 and Qfwt5-2 were not found in domestication or improvement sweeps, indicating their potential in the future improvement of sweet watermelon fruit size. Adjacent 10-kb windows with an average XP-CLR score no less than 80% of the genome-wide average were joined, and were further merged if two regions were separated by only one low-score 10-kb window. A kinship (K) matrix generated with the FaST-LMM program (v2.07)71 was used to correct the population structure. 2 and Supplementary Tables 10,11). The bars represent standard errors. The authors declare no competing interests. The large size of harvestable plant organs is one of the most important characteristics that farmers choose when keeping and propagating seeds. The geographic region of watermelon domestication has longremained unclear with competing hypotheses favoring southernAfrica, West Africa, and Northeast Africa, especially the Kordofanregion (9, 11-19), a former province of Sudan bordering North andSouth Darfur, and part of the western Sahel savannas. 19, 3268 (2018). A PSY1 gene, Cla97C01G008760, within the flesh color QTL qFC.1 (ref. Zhang, S. P. et al. Vol. Together, these results indicate that ClAGA2 contributes to sugar accumulation in watermelon fruit flesh through facilitating the metabolism of raffinose into glucose, fructose and sucrose, and could have already been selected for early on in the progenitor of sweet watermelon, as indicated by the already reduced genetic diversity in C. mucosospermus. The selected loci and candidate genes involved in each process are shown above and below the arrows, respectively. Mol. At the SNP site leading to a premature stop codon of ClBt associated with non-bitterness25 (Chr01:3,216,322C to T), all C. colocynthis, C. amarus and C. mucosospermus accessions carrying bitter fruits had the homozygous bitter allele (C), whereas the homozygous non-bitterness allele (T) was found in all 12 non-bitter C. mucosospermus and all C. lanatus accessions, suggesting that this non-bitterness allele arose in the progenitor of C. lanatus and is fixed in sweet watermelons. PLoS One 9, e112963 (2014). 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. Genet. lanatus) Citrullus colocynthis. Shan Wu The green-striped, red-fleshed watermelon might not look inherently mysterious, but botanists have long puzzled over which wild plant the modern domesticated crop originated from. designed the project and collected the samples. 2019, 113 (2019). For PacBio Iso-Seq, full-length complementary DNA was synthesized from a mixture of total RNA from the six tissues using the SMARTer PCR cDNA Synthesis Kit (Takara Bio). [4] Considerable breeding effort has developed disease-resistant varieties. 5 Scatterplot of GC content on read depth. This much improved 97103 genome provides a robust reference for watermelon research and genetic improvement. USA 107, 1353213537 (2010). The only diecious and most morphologically unique species, Citrullus naudinianus, is commonly found in sub-Saharan Africa3,5. These accessions were sequenced to an average depth of 14.5 and coverage of 92.2% of the 97103 genome. 20, 393402 (2010). c, Principal component analysis of Citrullus accessions excluding C. naudinianus (left), and of C. mucosospermus and C. lanatus accessions (right). BMC Plant Biol. CAS The libraries were sequenced using the P6-C4 chemistry on a PacBio Sequel sequencing platform (PacBio) at Nextomics Biosciences (Wuhan, China). 9, 586596 (1981). Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. The variant call format and VCFtools. Nat. in Genetics and Genomics of Cucurbitacae (eds Grumet, R., Katzir, N. & Garcia-Mas, J.) You are using a browser version with limited support for CSS. Duplicated read pairs were marked with Picard (v2.0.1) with the parameter OPTICAL_DUPLICATE_PIXEL_DISTANCE=250. To improve its quality, we assembled the 97103 genome de novo using PacBio long reads, combined with BioNano optical and Hi-C chromatin interaction maps. CAS ALS, acetolactate synthase; BEBT, benzyl alcohol O-benzoyltransferase; BGAL, -galactosidase; ClAGA2, alkaline -galactosidase; ClBt, bitter fruit bHLH transcription factor; ClTST2, tonoplast sugar transporter; CML, calmodulin; CRTISO, carotenoid isomerase; GLOX, glyoxal oxidase; HSF, heat stress transcription factor; LAX, auxin transporter; LCYB, lycopene -cyclase; PAP, purple acid phosphatase; PE, pectinesterase; PG, polygalacturonase; PMT, polyol/monosaccharide transporter; PSY1, phytoene synthase 1; RLK, receptor-like protein kinase; SLO1, SLOW GROWTH 1 (encoding an E motif-containing pentatricopeptide repeat protein); STP, sugar transporter; XTH, xyloglucan endotransglucosylase/hydrolase. 16) and harboring a lycopene -cyclase gene (LCYB, Cla97C04G070940). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. For sugar content, phenotypic data of the population grown in Xinxiang and the population grown in Yanqing were analyzed separately for GWAS, whereas for other traits, phenotypic data from the two populations were combined for the analyses. 213, 12081221 (2017). 66, 244259 (2016). Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. By contrast, C. amarus, C. mucosospermus and C. lanatus landraces and cultivars produced larger fruits with average weights of approximately 3.3, 1.7, 3.7 and 3.4kg, respectively (Supplementary Fig. Modern corn was first domesticated 8,000 years ago in Mexico. Danecek, P. 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. Finally, genetic maps7,8,9 were used to generate pseudochromosomes. Accompanying the disappearance of flesh bitterness, fruits of watermelon landraces became sweet. Signatures of selection in the watermelon genome were revealed for speciation, domestication and improvement of the watermelon, the fruit characteristics of which changed during speciation and more significantly after domestication (Fig. Gao, Z. We identified an introgression from C. amarus to C. lanatus on chromosome 6 at around 28.329.3Mb (Supplementary Fig. Regions with ratios of 0.7 or less and five or more SNPs were defined as introgressions. Using GWAS, genomic regions associated with key fruit quality traits were identified, providing useful information for watermelon breeding and further identification of causal variations. 29, 644652 (2011). ), Innovation Program of Beijing Academy of Agricultural and Forestry Sciences (KJCX20170102 to Y.X. Each sample had three biological replicates. Genome Res. 75) to be expressed under the Arabidopsis U6 promoter, alongside the Zea mays codon-optimized Cas9 driven by the double CaMV 35S promoter. 7). In the late 1800s, a . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. ISSN 1061-4036 (print). 125, 16031618 (2012). Nimmakayala, P. et al. In total, 10,195,082 SNPs with a minor allele frequency of 0.01 or greater and a missing data rate of 50% or less in the entire population were used for GWAS. Notably, after long-term domestication and variety improvement, the phenotype traits and metabolites of modern sweet watermelon have changed significantly, and a better flavor of watermelon has . B. et al. However, whether these loci have contributed to watermelon fruit size enlargement during speciation, domestication or improvement remains unknown. Twelve accessions were clustered into unexpected species groups and were therefore excluded from downstream analyses (Supplementary Table 5). Cucurbit genomics database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Rind stripes were categorized into no-stripe, netted, narrow, middle and wide stripe. Alignments of fully sequenced BACs, JN402338 (a), JN402339 (b), JX027061 (c) and JX027062 (d), to the 97103 v1 (top) and v2 (bottom) genome assemblies. Breeding 37, 146 (2017). Nucleic Acids Res. Am. Chin, C. S. et al. 78, 1014 (2014). November 3, 2022 The 6,000-year-old watermelon seeds from Uan Muhuggiag (left) border a child eating a modern watermelon. The optimal K, which indicates the most likely number of clusters in the population, was calculated. The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation, whereas sugar and carotenoid contents were positively selected during domestication. Nat. Phytoene synthase (PSY) is the first rate-limiting enzyme in the carotenogenesis pathway and defines the size of the carotenoid pool32. 81, 559575 (2007). The mutants showed substantially reduced soluble sugars, glucose, fructose and sucrose contents in fruit flesh, but had increased raffinose content (Supplementary Fig. Theor. To freeze: Cut your watermelon into chunks and spread them out on a baking sheet. PubMed Internet Explorer). Xing, H. L. et al. as evidenced in ancient hieroglyphics. 7,13b). 4, fruit size enlargement occurred in C. lanatus and C. mucosospermus and in C. amarus lineages, involving different but overlapping sets of QTLs. 20, 12971303 (2010). The final repeats were classified using the RepeatClassifier program of RepeatModeler and then used to identify repeat sequences in the 97103 genome using RepeatMasker. Fruit flesh SSC was measured using a sample of juice collected from the center of each watermelon with a hand-held digital PAL-1 refractometer (Atago). MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Nucleic Acids Res. Vegetable Lab, Charleston, SC, USA, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China, U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA, You can also search for this author in 16a), containing 136 genes, including genes encoding acetolactate synthase, purple acid phosphatase, calcium-binding protein, glyoxal oxidase and receptor-like protein kinases that may function in powdery mildew resistance or tolerance to hypoxia or low phosphate conditions (Supplementary Table 19). 8) and the Fusarium oxysporum race 2 resistance locus qFon2-2 (ref. 21) and was located in Cla97C03G057100, which encodes a polyphenol oxidase that polymerizes o-quinones to produce black, brown or red pigments22. Introgression of genomic regions containing beneficial alleles from wild relatives has contributed to the improvement of cultivated crops37,38. Google Scholar. Total RNA was extracted from these samples using the QIAGEN RNeasy Plant Mini Kit (QIAGEN). In total, 13 regions were found to be associated with seed coat color (Fig. Genet. Illustration courtesy nps.gov Pharaonic Fruit People have been eating watermelons for millennia. Biosynthesis, regulation, and domestication of bitterness in cucumber. The genome sequence of 97013 has been deposited at DDBJ/ENA/GenBank under the accession AGCB00000000. Sun, T. H. et al. Genetic mapping of a major codominant QTL associated with beta-carotene accumulation in watermelon. Seeds photo by Susanne Renner / Illustration by Emily Lankiewicz About. PubMed Central Those are produced by crossing diploid and tetraploid lines of watermelon, with the resulting seeds producing sterile triploid plants. ISSN 1546-1718 (online) BEBT, benzyl alcohol O-benzyltransferase; BGAL, -galactosidase; Chr, chromosome; ClTST2, tonoplast sugar transporter; CRTISO, carotenoid isomerase; HSF, heat stress transcription factor; LAX, auxin transporter; PE, pectinesterase; PG, polygalacturonase; PMT, polyol/monosaccharide transporter; RLK, receptor-like protein kinase; SLO1, SLOW GROWTH 1 (encoding an E motif-containing pentatricopeptide repeat protein); STP, sugar transporter; XTH, xyloglucan endotransglucosylase/hydrolase. CC, C. colocynthis; CA, C. amarus; CM, C. mucosospermus; CL_LR, C. lanatus landrace; CL_CUL, C. lanatus cultivar. Using DNA from greenhouse-grown plants representing all species and hundreds of varieties of watermelon, scientists discovered that watermelons most likely came from wild crop progenitors in northeast Africa. Extended Data Fig. PubMed 19), and Cla97C04G068530, which encodes a magnesium-chelatase subunit H involved in chlorophyll synthesis20. BMC Bioinformatics 13, 238 (2012). Langmead, B. Gene flow analysis further suggested admixture between C. mucosospermus and C. lanatus (Fig. Another fruit weight QTL, Qfwt5-1, was found to be under selection only during watermelon improvement (Fig. Localization of a new gene for bitterness in cucumber. Korf, I. Gene finding in novel genomes. 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. 13). A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. 105, 555563 (2002). ), China Agriculture Research System (CARS-25 to Y.X. Grilled Watermelon with Jalapeos, Feta and Honey Hybrid scaffolds were assembled from PacBio assembly and BioNano genome maps using the script hybridScaffold.pl in the Solve package with parameters -c hybridScaffold_config_aggressive.xml -u CACGAG -B 2 -N 2 -f. Natl Acad. Zhong, S. et al. Harvesting genes to improve watermelons -- ScienceDaily PacBio reads were aligned to the raw assembly using BLASR (v5.1)45 with parameters -bam -bestn 5 -minMatch 18 -nproc 6 -minSubreadLength 1000 -minAlnLength 500 -minPctSimilarity 70 -minPctAccuracy 70 -hitPolicy randombest -randomSeed 1, followed by correction of errors in the assembled contigs with Arrow (v2.2.2; PacBio). 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. Fruit weight QTLs: Qfwt2-1, Qfwt3 and Qfwt5-1. 130, 319330 (2017). 104, 134139 (2013). Thank you for visiting nature.com. Each fruit was cut lengthwise, photographed and sampled to evaluate flesh sweetness, bitterness, fruit shape, rind color, rind stripe, seed color and flesh color. Combined with previous findings on genome organization differences between C. amarus and C. lanatus shown by ribosomal DNA chromosome landmarks6,11 and indicated by non-Mendelian segregation in genetic populations derived from crosses between C. amarus and C. lanatus12, these results suggest that C. amarus and the lineage including C. mucosospermus and C. lanatus might have been derived from different ancestral populations or evolved independently after divergence. This $30 Cooling Eye Balm Is Saving My Tired, Puffy Eyes This Summer and Beyond. Gray horizontal dashed lines indicate the Bonferroni-corrected significance thresholds of GWAS (=0.05 and =0.01, respectively). Watermelon origin solved with molecular phylogenetics including Nucleic Acids Res. Raw Illumina reads were processed to remove adapter sequences using Picard v2.0.1 (https://broadinstitute.github.io/picard/). CAS 8). 14, 327 (2014). McKenna, A. et al. d, Schematic representation of Pattersons D test of gene flow between Citrullus species. Renner, S. S., Sousa, A. designed and managed the project. Surprisingly, the watermelon, called C. lanatus since the 1930s (Bailey, 1930; Mansfeld, 1959; c. 650 scientific papers in Web of Science, accessed 25 May 2014), and its supposed relatives in the genus Citrullus have never been analyzed with modern molecular-phylogenetic methods using verifiably identified material (meaning material in permanent. 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). Putative introgressions between two groups were identified using a likelihood ratio test approach67 with all SNPs. In total, 620 genes in selective sweeps were unique to the improvement process of sweet watermelon (Supplementary Fig. Purple dots represent forward alignments, while blue dots represent reverse alignments. Proteins from SwissProt and from Arabidopsis, watermelon, cucumber and melon were aligned to the 97103 genome using Spaln (v2.1.4)59, and the resulting alignments were used as protein homology evidence. 3c). & Wessler, S. R. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. The Mystery of the Watermelon's Origins May Have Been Solved - Gizmodo 12d). 30), was found in a genomic region with greatly reduced nucleotide diversity in C. mucosospermus and C. lanatus compared with C. colocynthis (Supplementary Fig. Nucleic Acids Res. Plants 2, 16183 (2016). 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, . Article Illumina RNA-seq reads were assembled using Trinity (v2.5.1)55 with the de novo mode and the genome-guided mode, respectively. To investigate how environment and human selection have shaped the genomes of Citrullus species, we searched for signatures of selection in the watermelon genome. J. Hum. Plant. Wang, Y. Q., Hu, L. P., Liu, G. M., Zhang, D. S. & He, H. J. Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. 45, 5158 (2013). af, Manhattan plots of GWAS of sugar content using the watermelon population grown in Xinxiang (a) and Yanqing (b), and Manhattan plots of GWAS of flesh color (c), fruit shape (d), rind stripe (e), rind color (f) and seed color (g). 729757 (Marcel Dekker, 1996). Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Samples were then loaded into IrysChips (BioNano Genomics) and imaged on an Irys imaging instrument (BioNano Genomics) at Nextomics Biosciences. One fruit per plant was harvested 30 d after self-pollination. Transfer them to a bag, remove as much air as possible, seal it up, and toss it in the freezer.

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