A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials and DNA Extraction
2.2. Resequencing and Polymorphic InDel Detection
2.3. Detection of Candidate InDels Discriminating Sex
2.4. Development of a Sex-Discriminating InDel Marker
3. Results
3.1. Resequencing and InDel Detection
3.2. Selection of Polymorphic InDels Occurring in Sex-Related Genes
3.3. Development of a Sex-Discriminating InDel Marker
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sex | Species | Accession | |||
---|---|---|---|---|---|
Female | Actinidia arguta | K5-1-8 | K5-1-12 | K5-2-3 | K5-2-13 |
K5-2-18 | K5-4-7 | K5-7-3 | K5-7-5 | ||
K5-10-1 | K5-10-5 | K5-12-6 | Chiak | ||
Hardy Red | Ilse | Autumn Sense | |||
(A. arguta × A. deliciosa) × A. arguta | Skinny Green | ||||
Male | A. arguta | K5-2-22 | K5-3-3 | K5-3-6 | K5-3-7 |
K5-3-8 | K5-3-12 | K5-3-13 | K5-3-18 | ||
K5-4-8 | K5-5-1 | K5-5-12 | K5-5-14 | ||
K5-6-10 | K5-9-1 | K5-9-8 | K5-11-1 | ||
K5-11-2 | K5-11-3 | K5-11-8 | K5-13-6 | ||
K5-14-1 |
Sex-Related Gene | Gene ID 1 | Description | Identity (%) | E-Value |
---|---|---|---|---|
GbMADS1 | Acc28871 | Agamous-like MADS-box protein | 68.33 | 1.08 × 10−41 |
GbMADS2 | ||||
GbMADS4 | ||||
GbMADS18 | ||||
CYP703 | Acc28333 | Cytochrome P450 CYP736A12 like | 58.84 | 1.85 × 10−75 |
TDF1 | Acc28900 | Hypothetical protein | 78.63 | 7.05 × 10−57 |
Acc28821 | Transcription factor like | 73.85 | 1.77 × 10−49 | |
Acc28639 | Transcription factor like | 68.64 | 2.73 × 10−39 | |
Acc28638 | Transcription factor like | 68.64 | 2.73 × 10−39 | |
Acc28429 | Myb-related protein | 73.26 | 1.98 × 10−30 | |
GDSL esterase/lipase | Acc28776 | GDSL esterase/lipase, partial | 74.78 | 9.52 × 10−145 |
AP3Y | Acc28719 | Agamous-like MADS-box protein | 69.49 | 5.06 × 10−12 |
Acc28717 | Agamous-like MADS-box protein | 62.22 | 2.03 × 10−22 |
Variation | Position (bp) | InDel (Reference/Alternative) | Gene ID 1 | Region | Description | |
---|---|---|---|---|---|---|
Female | Male | |||||
Insertion | 12,919,896 | -/AT | -/- | Acc28719 | Exon | Agamous-like MADS-box protein |
14,557,224 | -/AG | -/- | Acc28871 | Intron | Agamous-like MADS-box protein | |
14,559,075 | -/- | -/T | Acc28871 | Intron | Agamous-like MADS-box protein | |
14,570,161 | -/- | -/ATTCGGTGAATCTGACACTT | Acc28871 | Intron | Agamous-like MADS-box protein | |
Deletion | 12,896,671 | TGAT/- | TGAT/TGAT | Acc28717 | Exon | Agamous-like MADS-box protein |
14,814,902 | A/A | A/- | Acc28900 | Intron | Hypothetical protein | |
14,815,837 | -/- | -/T | Acc28900 | Intron | Hypothetical protein |
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Oh, S.; Kim, J.; Kim, Y.; Lee, M.; Kim, D. A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta. Horticulturae 2023, 9, 1310. https://doi.org/10.3390/horticulturae9121310
Oh S, Kim J, Kim Y, Lee M, Kim D. A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta. Horticulturae. 2023; 9(12):1310. https://doi.org/10.3390/horticulturae9121310
Chicago/Turabian StyleOh, Sewon, Jung Kim, Yumi Kim, Mockhee Lee, and Daeil Kim. 2023. "A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta" Horticulturae 9, no. 12: 1310. https://doi.org/10.3390/horticulturae9121310
APA StyleOh, S., Kim, J., Kim, Y., Lee, M., & Kim, D. (2023). A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta. Horticulturae, 9(12), 1310. https://doi.org/10.3390/horticulturae9121310