# Natural variations in MdBPM2/MdRGLG3‐MdNAC83 network controlling the quantitative segregation of apple fruit storability

## TL;DR

This study identifies a genetic network involving MdNAC83 and related genes that control apple fruit storability, improving breeding and genetic prediction models.

## Contribution

The study reveals a novel genetic network with Mendelian variations in six genes that regulate apple fruit storability.

## Key findings

- Variants in MdNAC83 promoter and coding regions affect gene expression and activity of target genes.
- MdBPM2 and MdRGLG3 regulate MdNAC83 through ubiquitination, with SNPs reducing their activity.
- Adding functional markers to SNP arrays improved prediction accuracy of fruit storability traits.

## Abstract

Dissecting quantitative traits into Mendelian factors is a great challenge in genetics. Apple fruit storability is a complex trait controlled by multi‐genes with unequal effects. We previously identified 62 quantitative trait loci (QTLs) associated with apple fruit storability and genomics‐assisted prediction (GAP) models were trained using 56 QTL‐based markers. Here, three candidate genes, MdNAC83, MdBPM2, and MdRGLG3, were screened from the regions of QTLs with large G’ value and large genetic effects. Both a 216‐bp deletion and an SNP934 T/C at the promoter of MdNAC83 were associated with higher MdNAC83 expression but an SNP388 G/A at the coding region significantly reduced the activity to activate the expression of the target genes MdACO1, MdMANA3, and MdXTH28. MdBPM2 and MdRGLG3 participated in the ubiquitination of MdNAC83. SNP657 T/A of MdBPM2 and SNP167 C/G of MdRGLG3 caused a reduction in the activity to ubiquitinate MdNAC83. By the addition of functional markers to the GenoBaits SNP array, the prediction accuracy of the updated GAP models increased to 0.7723/0.6231 and 0.5639/0.5345 for flesh firmness/crispness at harvest and flesh firmness/crispness retainability, respectively. The variation network involving eight simple Mendelian variations in six genes helps to gain insight into the molecular quantitative genetics, to improve breeding strategy, and to provide targets for future genome editing.

During postharvest cold storage of apples, the NAC transcription factor MdNAC83 binds to the promoters and activates the expression of downstream genes and is regulated by E3 ligases, which promote its ubiquitination and degradation. Genetic variants in MdNAC83 and its downstream genes form a network to regulate apple fruit storability.