A major QTL identification and candidate gene analysis of watermelon fruit cracking using QTL-seq and RNA-seq

Yuanfeng Zhan; Wei Hu; Huang He; Xuanmin Dang; Songbi Chen; Zhilong Bie

doi:10.3389/fpls.2023.1166008

A major QTL identification and candidate gene analysis of watermelon fruit cracking using QTL-seq and RNA-seq

Front Plant Sci. 2023 May 15:14:1166008. doi: 10.3389/fpls.2023.1166008. eCollection 2023.

Authors

Yuanfeng Zhan^{1

2}, Wei Hu², Huang He², Xuanmin Dang², Songbi Chen², Zhilong Bie¹

Affiliations

¹ College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
² Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Abstract

Fruit cracking decreases the total production and the commercial value of watermelon. The molecular mechanisms of fruit cracking are unknown. In this study, 164 recombinant inbred lines (RILs) of watermelon, derived from the crossing of the WQ1 (cracking-sensitive) and WQ2 (cracking-tolerant) lines, were sequenced using specific length amplified fragment sequencing (SLAF-seq). A high-density genetic linkage map was constructed with 3,335 markers spanning 1,322.74 cM, at an average 0.40 cM across whole-genome flanking markers. The cracking tolerance capacity (CTC), depth of fruit cracking (DFC), rind thickness (RT), and rind hardness (RH) were measured for quantitative trait locus (QTL) analysis. Of the four traits analyzed, one major QTL with high phenotypic variation (41.04%-61.37%) was detected at 76.613-76.919 cM on chromosome 2, which contained 104 annotated genes. Differential gene expression analysis with RNA sequencing (RNA-seq) data between the two parents identified 4,508 differentially expressed genes (DEGs). Comparison of the genes between the QTL region and the DEGs obtained eight coexisting genes. Quantitative real-time PCR (qRT-PCR) analysis revealed that these genes were significant differentially expressed between the two parents. These results provide new insights into the identification of QTLs or genes and marker-assisted breeding in watermelon.

Keywords: DEGs; QTL-seq; RNA-seq; SLAF-seq; fruit cracking.

Grants and funding

This work was supported by Hainan Provincial Natural Science Foundation of China (no.321RC647), Hainan Province Science and Technology Special Fund (no. ZDYF2021XDNY290), the Social Public-Interest Scientific Institution Reform Fund (no. PZS2022019), and Hainan Province Science and Technology Special Fund (no. ZDYF2022XDNY332).