Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon

Hong Zhang; Xuejun Zhang; Meihua Li; Yong Yang; Zhiqiang Li; Yuhui Xu; Haojie Wang; Dengming Wang; Yongbing Zhang; Huaisong Wang; Qiushi Fu; Jing Zheng; Hongping Yi

doi:10.1016/j.ygeno.2022.110306

Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon

Genomics. 2022 Mar;114(2):110306. doi: 10.1016/j.ygeno.2022.110306. Epub 2022 Feb 4.

Authors

Hong Zhang¹, Xuejun Zhang², Meihua Li², Yong Yang², Zhiqiang Li³, Yuhui Xu³, Haojie Wang², Dengming Wang², Yongbing Zhang², Huaisong Wang⁴, Qiushi Fu⁵, Jing Zheng⁶, Hongping Yi⁷

Affiliations

¹ Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China. Electronic address: [email protected].
² Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China.
³ Adsen Biotechnology Co., Ltd., Urumchi 830022, China.
⁴ The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: [email protected].
⁵ The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: [email protected].
⁶ The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
⁷ Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China. Electronic address: [email protected].

PMID: 35131474
DOI: 10.1016/j.ygeno.2022.110306

Abstract

Melon is a popular fruit vegetable crop worldwide with diverse morphological variation. We report a high-density genetic map of melon and nine major QTLs with physical region ranging from 43.47 kb to 1.89 Mb. Importantly, two seed-related trait QTLs were repeatedly detected in two environments, and the mapping region was narrowed to 522 kb according to a regional linkage analysis. A total of 40 annotated genes were screened for nonsynonymous variations, of which EVM0009818, involved in cytokinin-activated signaling, was differentially expressed in the young fruits of parents based on RNA-seq. Selective sweep analysis identified 152 sweep signals for seed size, including the two seed-related QTLs and nine homologs that have been verified to regulate seed size in Arabidopsis or rice. This work illustrates the power of a joint analysis combining resequencing-based genetic map for QTL mapping and a combination of KASP genotyping and RNA-seq analysis to facilitate QTL fine mapping.

Keywords: Fruit- and seed-related traits; High-density genetic map; Melon; QTL; RNA-seq; Resequencing; Selective sweep.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping
Cucurbitaceae* / genetics
Fruit* / anatomy & histology
Fruit* / genetics
Phenotype
Quantitative Trait Loci
Seeds / genetics