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A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness

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Abstract

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Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR.

Abstract

The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from ‘Zisai Pearl’ × ‘Red Fuji’. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein–protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.

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Data availability

The apple genome used was a version of the Malus × domestica genome GDDH13_v1.1 (GDDH13, https://iris.angers.inra.fr/gddh13/).

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Acknowledgements

We would like to thank the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology) of the Ministry of Agriculture, People’s Republic of China, for providing the experimental platform.

Funding

This work was funded by the Modern Agricultural Industry Technology System (CARS-27), and the Key Research and Development Program of Hebei (21326353D; 21326308D). The funding bodies had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Authors and Affiliations

  1. College of Horticulture, China Agricultural University, Beijing, 100193, China

    Xianglong Yang, Bei Wu, Zhongyan Zhang, Xi Zhang, Yi Wang, Ting Wu, Xuefeng Xu, Zhenhai Han & Xinzhong Zhang

  2. College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China

    Jing Liu, Xuan Wang & Haie Zhang

  3. Testing and Analysis Center, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China

    Xuejun Ren

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  1. Xianglong Yang
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299_2022_2929_MOESM1_ESM.tif

Fig. S1 SNPs at the coding sequence did not alter the MdbHLH25 subcellular localization. The indicated eGFP constructs were transiently expressed in mcherry-N. benthamiana leaves and fluorescent images were obtained using confocal microscopy. Bars = 100 μm (TIF 99124 KB)

Table S1 Primers used for experimental validation in this study (XLSX 14 KB)

299_2022_2929_MOESM3_ESM.xlsx

Table S2 SNPs and InDels between the parental cultivar ‘Zisai Pearl’ and ‘Red Fuji’ within the overlapped QTL region (38426419–39485064 bp) on chromosome 16 of apple genome (XLSX 11 KB)

299_2022_2929_MOESM4_ESM.xlsx

Table S3 Phenotypic data of flesh firmness at harvest, flesh firmness retainability, flesh crispness at harvest, flesh crispness retainability, and KASP markers using 478 hybrids of three families derived from ‘Golden Delicious’, ‘Jonathan’, ‘Red Fuji’ and ‘Zisai Pearl’ (XLSX 90 KB)

299_2022_2929_MOESM5_ESM.xlsx

Table S4 The genotype effects of all markers using 478 hybrids from three families derived from ‘Golden Delicious’, ‘Jonathan’, ‘Red Fuji’ and ‘Zisai Pearl’ (XLSX 11 KB)

299_2022_2929_MOESM6_ESM.xlsx

Table S5 Joint genotype effects of markers on flesh firmness at harvest (FF), flesh crispness at harvest (FC), flesh firmness retainability (FFR), and flesh crispness retainability (FCR) phenotype values in hybrid plants from ‘Zisai Pearl’ (Z) × ‘Red Fuji’ (F), Z × ‘Golden Delicious’ (G), and ‘Jonathan’ (J) × G (XLSX 13 KB)

299_2022_2929_MOESM7_ESM.xlsx

Table S6 Phenotype values of flesh firmness/crispness at harvest and their retainability during cold storage of the parental cultivars (XLSX 11 KB)

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Yang, X., Wu, B., Liu, J. et al. A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness. Plant Cell Rep 41, 2379–2391 (2022). https://doi.org/10.1007/s00299-022-02929-z

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