Identification of genetic regions associated with sex determination in date palm: A computational approach
DOI:
https://doi.org/10.36253/caryologia-1780Keywords:
DNA based markers, DAPC, LFMM, MCA, Phoenix dactylifera, Sex determinationAbstract
Sex determination of date palm seedlings is the challengeable effort for breeders. Different studies based on molecular markers and genome sequencing have provided some insight in to the genetic regions related to sex determination in date palms in general. But due to differences in cultivar population structure and also cost of whole genome sequencing, we may need a more suitable approach in developing countries for this task. Therefore, we suggest using a combination of different available molecular markers and a computational approach to identify the genetic regions involved in sex differentiation in date palm cultivars. In this study we used twenty-three cultivars including 7 male and 16 female cultivars that were examined by 30 different dominant and co-dominant molecular markers which deal with different genomic regions. Grouping of the tree samples based on 178 loci resulted in genetic differentiation of the studied male and female palm trees. Multiple correspondence analysis (MCA) bi-plot also showed genetic difference within male and female trees. Heatmap plot specified those markers which differentiate date palm trees. SSR (simple sequence repeats) and IRAP (inter retrotransposon amplified polymorphism) markers provided sex linked markers for male cultivars. In present study, we introduced sex specific alleles for Iranian male date palm cultivars as a fast track in seedlings. Different association studies performed identified the candidate genetic regions which are significantly associated with sex differentiation in date palm cultivars.
Downloads
References
Abdi H, Williams LJ (2010) Principal component analysis Wiley interdisciplinary reviews: Comput Stat 2: 433-459.?
Adawy SS, Jiang J, Atia MA (2014) Identification of novel sex-specific PCR-based markers to distinguish the genders in Egyptian date palm trees. Int J Agric Sci Res 4: 45-54.?
Al-Ameri AA, Al-Qurainy F, Gaafar ARZ, Khan S, Nadeem M (2016) Molecular identification of sex in Phoenix dactylifera using inter simple sequence repeat markers. BioMed Res Intl 2016: 1-5.
Al-Dous EK, George B, Al-Mahmoud M E, Al-Jaber MY, Wang H, Salameh YM, Malek J A (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnol 29: 521.?
Al-Mssallem I S, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu J (2013) Genome sequence of the date palm Phoenix dactylifera L. Nature Commun 4: 1-9.?
Biswas MK, Xu Q, Deng XX (2010) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hort 124: 254-26.?
Collins C, Jombbart T (2015) Genome-Wide association studies. Impeerial college London. MRC Center. For Outbreak Analysis and Modeling: 1-61.
Elmeer K, Mattat I (2012) Marker-assisted sex differentiation in date palm using simple sequence repeats. 3 Biotech. 2: 241-247.?
Frichot E, Schoville SD, Bouchard G, Francois O (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30:1687-1699.
Hassanzadeh Khankahdani H, Bagheri A (2016) Identification of genetic variation of male and female date palm (Phoenix dactylifera L.) cultivars using morphological and molecular markers. Intl J Hort Sci Technol 6: 63-76.?
Hazzouri KM, Gros-Balthazard M, Flowers JM, Copetti D, Lemansour A, Lebrun M, Purugganan MD (2019) Genome-wide association mapping of date palm fruit traits. Nature Commun 10: 1-14.? https://doi.org/10.1038/s41467-019-12604-9
Jaskani MJ, Awan FS, Ahmad S, Khan IA (2016) Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers. 3 Biotech 6:22.?
Maryam Jaskani MJ, Awan FS, Ahmad S, Khan IA (2016) Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers. 3 Biotech 6(22): 1-7.
Nouroz F, Mukaramin A (2019) Genomic and evolutionary diversity of LTR retrotransposons in date palm (Phoenix dactylifera) Pakistan J Bot 51: 1637-1644.?
Saboori S, Noormohammadi Z, Sheidai M, Marashi S (2020) SCoT molecular markers and genetic fingerprinting of date palm (Phoenix dactylifera L.) cultivars. Genet Resour Crop Evol 67: 73-82.?
Saboori S, Noormohammadi Z, Sheidai M, Marashi S (2021) Insight into date palm diversity: genetic and morphological investigations. Plant Mol Biol Rep 39: 137-145.?
Torres MF, Mathew LS, Ahmed I, Al-Azwani IK, Krueger R, Rivera-Nuñez D, Malek JA (2018) Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nature Commun 9: 1-9.? DOI: 10.1038/s41467-018-06375-y
Zhang F, Chen W, Zhu Z et al. (2019) OSCA: a tool for omic-data-based complex trait analysis. Genome Biol 20: 107 . https://doi.org/10.1186/s13059-019-1718-z
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2022 Zahra, Masoud Sheidai, Seyed Samih Marashi, Somayeh Saboori, Neda Moradi, Samaneh Naftchi, Faezeh Rostami
This work is licensed under a Creative Commons Attribution 4.0 International License.
- Copyright on any open access article in a journal published byCaryologia is retained by the author(s).
- Authors grant Caryologia a license to publish the article and identify itself as the original publisher.
- Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.
- The Creative Commons Attribution License 4.0 formalizes these and other terms and conditions of publishing articles.
- In accordance with our Open Data policy, the Creative Commons CC0 1.0 Public Domain Dedication waiver applies to all published data in Caryologia open access articles.
