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

Yang, Xianglong; Wu, Bei; Liu, Jing; Zhang, Zhongyan; Wang, Xuan; Zhang, Haie; Ren, Xuejun; Zhang, Xi; Wang, Yi; Wu, Ting; Xu, Xuefeng; Han, Zhenhai; Zhang, Xinzhong

doi:10.1007/s00299-022-02929-z

Cited by 4 publications

(1 citation statement)

References 44 publications

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“…These data demonstrated that both SNP379 G/T and the functional variation(s) in the promoter of MdSAUR36 contributed to the small-fruit trait in Malus accessions. Multiple genetic variations in one gene like MdSAUR36 further broaden the phenotypic segregation spectrum of the target trait(Zheng et al, 2020;Yang et al, 2022).…”

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Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Tian,

Wu,

Liu

et al. 2024

Mol Breeding

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Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most the differences in fruit size between Malus species. In this study, by using an interspeci c hybrid population between M. asiatica 'Zisai Pearl' and M. domestica cultivar 'Red Fuji', we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in 'Zisai Pearl' led to a lower promoter activity than that of 'Red Fuji'. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in 'Zisai Pearl', exerted signi cant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 con rmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malusaccession and be potentially used in molecular assisted breeding via interspeci c hybridization.

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confidence: 99%

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Tian,

Wu,

Liu

et al. 2024

Mol Breeding

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Natural variations in MdNAC18 exert major genetic effect on apple fruit harvest date by regulating ethylene biosynthesis genes

Wen,

Wu,

Wang

et al. 2024

JIPB

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Dissecting the genetic control of apple fruit harvest date (AFHD) into multiple Mendelian factors poses a significant challenge in modern genetics. Here, a quantitative trait locus (QTL) for AFHD was fine‐mapped to the NAC transcription factor (TF) MdNAC18 within the interval defined by the overlap of QTLs Z03.5/Z03.6 and F03.2/F03.3. One direct target of MdNAC18 is the ethylene biosynthesis gene MdACO1. The single nucleotide polymorphisms (SNPs) SNP517 and SNP958 in the MdNAC18 coding sequence modulated activation of MdACO1 by MdNAC18. SNP1229 in the MdACO1 promoter destroyed the MdNAC18 binding site and thus abolished MdNAC18 binding. SNP517 and SNP958 also affected MdNAC18 activation of the TF gene MdARF5; MdARF5 activates the ethylene biosynthesis gene MdACS1. SNP517 and SNP958 in MdNAC18, SNP1229 and SNP769 (linked to InDel62) in MdACO1, and InDel162 in MdACS1 constituted a genetic variation network. The genetic effect of this network on AFHD was estimated as 60.3 d, accounting for 52.6% of the phenotype variation of the training population. The joint effects of these polymorphisms increased the accuracy of a genomics‐assisted prediction (GAP) model for AFHD (r = 0.7125). Together, our results suggest that genetic variation in MdNAC18 affects AFHD by modulating ethylene biosynthesis and provide an optimized GAP model for apple breeding.

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Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Tian,

Wu,

Liu

et al. 2023

Preprint

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Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between M. asiatica ‘Zisai Pearl’ and M. domestica cultivar ‘Red Fuji’, we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in ‘Zisai Pearl’ led to a lower promoter activity than that of ‘Red Fuji’. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in ‘Zisai Pearl’, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malusaccession and be potentially used in molecular assisted breeding via interspecific hybridization.

show abstract

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

Cited by 4 publications

References 44 publications

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Natural variations in MdNAC18 exert major genetic effect on apple fruit harvest date by regulating ethylene biosynthesis genes

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

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