Dataset Information

Discovery of the Genomic Region and Candidate Genes of the Scarlet Red Flesh Color (Yscr ) Locus in Watermelon (Citrullus Lanatus L.).

ABSTRACT: The flesh color of watermelon (Citrullus lanatus) is an important fruit quality trait that helps to determine fruit attractiveness and is potentially beneficial to human health. Previous inheritance analyses determined that a single dominant gene, Yscr , produces the scarlet red flesh color rather than the coral red flesh color in watermelon. However, no genomic region or gene-based molecular markers for the locus Yscr have been reported thus far. In the present study, two high-density genetic maps and whole-genome variation detection aided by genome resequencing were first map the flesh color locus Yscr to a small region on chromosome 6 based on two independent populations derived from two scarlet red-fleshed lines and two coral red-fleshed lines. Two major quantitative trait loci located in the same genomic regions were identified in the F2 and BC1P2 populations and explained 90.36% and 75.1% of the phenotypic variation in flesh color, respectively. Based on the genetic variation in the two parental lines, newly developed PCR-based markers narrowed the Yscr region to 40 Kb. Of the five putative genes in this region, four encoded glycine-rich cell wall structural proteins, which implied that a new regulatory mechanism might occur between scarlet red- and coral red-fleshed in watermelon. Moreover, the genotypes of two newly developed InDel markers (InDel27_fc6 and InDel28_fc6) were completely consistent with the phenotypes in the F2 and BC1P2 populations and all 56 scarlet red-fleshed watermelon accessions. The results presented here provide valuable information for marker-assisted selection of flesh color breeding and the functional validation of candidate genes in watermelon.

SUBMITTER: Li N

PROVIDER: S-EPMC7043143 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Discovery of the Genomic Region and Candidate Genes of the Scarlet Red Flesh Color (Yscr ) Locus in Watermelon (Citrullus Lanatus L.).

Li Na N Shang Jianli J Wang Jiming J Zhou Dan D Li Nannan N Ma Shuangwu S

Frontiers in plant science 20200219

The flesh color of watermelon (Citrullus lanatus) is an important fruit quality trait that helps to determine fruit attractiveness and is potentially beneficial to human health. Previous inheritance analyses determined that a single dominant gene, Yscr , produces the scarlet red flesh color rather than the coral red flesh color in watermelon. However, no genomic region or gene-based molecular markers for the locus Yscr have been reported thus far. In th ...[more]

PMID: 32140168

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Project description:BackgroundFruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluating the appearance quality and a key contributor influencing consumers' preferences. But the molecular mechanism of this intricate trait remains largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed.ResultsA total of 13 carotenoids and 16,781 differentially expressed genes (DEGs), including 1295 transcription factors (TFs), were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted the hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be the hub genes and may play an essential role in yellow flesh formation.ConclusionsThe composition and contents of carotenoids in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting candidate genes and molecular basis governing flesh color formation in watermelon fruit.

Project description:Watermelon fruit texture and quality are determined by flesh firmness. As a quality trait, flesh firmness is controlled by multigenes. Defining the key regulatory factors of watermelon flesh firmness is of great significance for watermelon genetic breeding. In this study, the hard-flesh egusi seed watermelon PI186490 was used as the male parent, the soft-flesh cultivated watermelon W1-1 was used as the female parent, and 175 F2 generations were obtained from selfing F1. Primary mapping of the major genes controlling center flesh firmness was achieved by bulked-segregant analysis (BSA)-Seq analysis and molecular marker technology. Finally, major genes were delimited in the physical interval between 6,210,787 and 7,742,559 bp on chromosome 2 and between 207,553 and 403,137 bp on chromosome 8. The content of each cell wall component and hormone was measured, and comparative transcriptome analysis was performed during fruit development in watermelon. The protopectin, cellulose, hemicellulose, indole-3-acetic acid (IAA) and abscisic acid (ABA) contents were measured, and paraffin sections were made during the three fruit developmental stages. The results revealed that protopectin, celluloses, and hemicelluloses exhibited similar trends for flesh firmness, while the IAA and ABA concentrations continued to decrease with fruit ripening. Paraffin sections showed that PI186490 cells were more numerous, were more tightly packed, had clearer cell wall edges and had thicker cell walls than W1-1 cells at every developmental stage. Comparative transcriptome analysis was conducted on RNA samples of flesh during fruit development and ripening in W1-1 and PI186490. The results from the localization interval transcriptome analysis showed that Cla016033 (DUF579 family member), which may influence the cell wall component contents to adjust the flesh firmness in watermelon fruit, was different in W1-1 and PI186490 and that Cla012507 (MADS-box transcription factor) may be involved in the regulation of fruit ripening and affect the hardness of watermelon fruit.

Dataset Information

Discovery of the Genomic Region and Candidate Genes of the Scarlet Red Flesh Color (Yscr ) Locus in Watermelon (Citrullus Lanatus L.).

Publications

Discovery of the Genomic Region and Candidate Genes of the <i>Scarlet Red Flesh Color</i> (<i>Y<sup>scr</sup></i> ) Locus in Watermelon (<i>Citrullus Lanatus</i> L.).

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