Whole genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Weihong Fu; Lin Zhao; Wanjun Qiu; Xu Xu; Meng Ding; Liming Lan; Shenchun Qu; Sanhong Wang

doi:10.1016/j.xplc.2024.100973

Whole genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Plant Commun. 2024 May 14:100973. doi: 10.1016/j.xplc.2024.100973. Online ahead of print.

Authors

Weihong Fu¹, Lin Zhao², Wanjun Qiu¹, Xu Xu¹, Meng Ding¹, Liming Lan¹, Shenchun Qu¹, Sanhong Wang³

Affiliations

¹ College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China.
² Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu,Xuzhou 221131,China.
³ College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China;. Electronic address: wsh3xg@njau.edu.cn.

PMID: 38751120
DOI: 10.1016/j.xplc.2024.100973

Abstract

Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We conducted whole genome sequencing (WGS) of the apple varieties 'Gala' and 'Xiahongrou', along with their F1 hybrid, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTL)s related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, on a stable QTL of linkage group (LG) 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences the binding of the transcription factor MdMYB2, impacting MdNADP-ME expression. In our study of various apple genotypes, this SNP was linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium of sugar and acid content in apple fruits.

Keywords: apple; malate degradation; promoter; quantitative trait locus; sugar content.