Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

Abstract

Fruit characteristics of sweet watermelon are largely the result of human selection. Here we report an improved watermelon reference genome and whole-genome resequencing of 414 accessions representing all extant species in the Citrullus genus. Population genomic analyses reveal the evolutionary history of Citrullus, suggesting independent evolutions in Citrullus amarus and the lineage containing Citrullus lanatus and Citrullus mucosospermus. Our findings indicate that different loci affecting watermelon fruit size have been under selection during speciation, domestication and improvement. A non-bitter allele, arising in the progenitor of sweet watermelon, is largely fixed in C. lanatus. Selection for flesh sweetness started in the progenitor of C. lanatus and continues through modern breeding on loci controlling raffinose catabolism and sugar transport. Fruit flesh coloration and sugar accumulation might have co-evolved through shared genetic components including a sugar transporter gene. This study provides valuable genomic resources and sheds light on watermelon speciation and breeding history.

Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon

“…And the unchanged nucleotide sequence of the cDNA, gDNA, and about 2,000bp bases before gene Cla97C04G068460 in WT4 according to the resequecing result further confirmed that gene Cla97C04G068460 would not be the gene for Clyr. With GWAS analysis, three candidate genes associated with rind color and rind stripe were found on chromosomes 4, 6, and 8, corresponding to the rind trait loci S (foreground stripe pattern), D (depth of rind color), and Dgo (background rind color) (Park et al, 2016;Guo et al, 2019). Since Dgo gene (Cla97C04G068530/Cla002769) encodes a magnesium-chelatase subunit H involved in chlorophyll synthesis, which was not mapped in the candidate region, so the relationship between Dgo and yellow-rind trait in WT4 should be further studied.…”

Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons

“…To evaluate the selection of ClVST1, we analyzed the haplotype of ClVST1 and identified that the SNP C99A is the nonsynonymous mutation most associated with sugar content in a collection of 326 wild and cultivated watermelon accessions (Guo et al, 2019), with all nonsweet watermelons harboring the allele CC ). Yellow and red fluorescence indicates plasma membrane and chloroplast in leaf protoplasts, respectively (g).…”

“…The SNPs from 326 representative watermelon accessions (Guo et al, 2019) were used for nucleotide diversity (p) calculation using a 50 kb sliding window. We calculated the ratio of diversity (p semi-wild /p cultivated ) for each window using VCFTOOLS (Danecek et al, 2011) to calculate the pairwise genomic differentiation for semi-wild and cultivated populations of watermelon.…”

“…All cultivars and landraces showed higher sugar content than all wild ancestor watermelons, while the semi-wild accessions contained both sweet and nonsweet watermelons. Furthermore, we performed an association study on 326 representative watermelon accessions collected on a worldwide basis (Table S3), using genomic resequencing data (Guo et al, 2019) covering a 0-10-Mb of Chr2 that contains the QTL Qsuc2-1. The most significant SNPs, out of 32 000 SNPs identified in this region, were located at C42T and C99A of the ClVST1 (ORF6) coding region in QTL Qsuc2-1 (Fig.…”

Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

“…Association mapping has identi ed candidate trait-associated genes in various crops such as Arabidopsis 49 , rice 50 , maize 51 , peach 23 , watermelon 52 and tomato 31 . In this study, we identi ed a total of 239 signi cant signals corresponding to 129 genome loci associated with the 27 assessed agronomic traits.…”