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Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits
Sunday, 2019/11/10 | 06:22:50

Shaogui GuoShengjie Zhao[…]Yong Xu

Nature Genetics volume 51, pages 1616–1623 (2019) - Published: 01 November 2019

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.

 

https://www.nature.com/articles/s41588-019-0518-4

 

Fig. 2: GWAS of watermelon fruit quality traits.

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). 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. Known QTL regions are highlighted in light green. Significant GWAS signals are indicated by vertical black arrows. Candidate genes are indicated by diagonal arrows. Gray horizontal dashed lines indicate the Bonferroni-corrected significance thresholds of GWAS (α = 0.05 and α = 0.01, respectively). CHLH, magnesium-chelatase subunit H; ClFS1FRUIT SHAPE 1 (encoding an IQ domain protein); ClTST2, tonoplast sugar transporter; LCYB, lycopene β-cyclase; MENG, chloroplastic 2-phytyl-1,4-beta-naphthoquinone methyltransferase; PPO, polyphenol oxidase; RFS, raffinose synthase; SUS, sucrose synthase; WDR, WD40-repeat protein.

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