Gene-specific sex-linked genetic markers in date palm (Phoenix dactylifera L.)

Ali, Hoda Badry Mohammed; Abubakari, Adam; Wiehle, Martin; Krutovsky, Konstantin V.

doi:10.1007/s10722-017-0564-7

Cited by 8 publications

(13 citation statements)

References 17 publications

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“…This problem has recently been solved by the availability of date palm genomes (Al-Dous et al, 2011), verification of sex determination loci (Cherif et al, 2013) and construction of genetic map (Mathew et al, 2014), validating that date palm has a homomorphic XY chromosome system. This sex chromosome is currently being used to develop precise sex-specific markers for specific varieties and populations of date palm (Mohei et al, 2017; Ali et al, 2018; Intha & Chaiprasart, 2018). Thus, it is potential that genome sequencing of Asian Palmyra palm could help us verify the sex determination region and, perhaps, the sex determination system in Asian Palmyra palm.…”

Section: Discussionmentioning

confidence: 99%

“…Further attempts on developing sex identification markers in Asian Palmyra palm should be directed towards genomic-based approaches, particularly at the MSY. Genome analysis using SNPs have been successful in accessing sex determination loci in date palm (Al-Mahmoud et al, 2012; Ali et al, 2018) and other dioecious plant species (Zhou et al, 2018; Jia et al, 2019). Whole genome sequencing, genetic mapping, SNPs and genome-wide association study (GWAS) between male and female populations would be essential tools for further identification of sex-linked loci in Asian Palmyra palm.…”

Section: Discussionmentioning

confidence: 99%

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Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

Pipatchartlearnwong

Juntawong

Wonnapinij

et al. 2019

PeerJ

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BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries andde novotranscriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Althoughde novotranscriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

Pipatchartlearnwong

Juntawong

Wonnapinij

et al. 2019

PeerJ

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“…These plants include Carica papaya L. (Abreu et al 2015), Pistacia vera L. (Kafkas et al 2015), and Actinidia chinensis Planch. (Zhang et al 2015), Cucumis sativus L. (Pawełkowicz et al 2019), Phoenix dactylifera L. (Al-Ameri et al 2016;Ali et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Sex-linked Single Nucleotide Polymorphism (SNP) identification and molecular marker development of salacca (Salacca zalacca (Gaertn.) Voss)

PRIHATINI

DINARTI²,

SUTANTO³

et al. 2023

Biodiversitas

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Abstract. Prihatini R, Dinarti D, Sutanto A, Sudarsono. 2023. Sex-linked Single Nucleotide Polymorphism (SNP) identification and molecular marker development of salacca (Salacca zalacca (Gaertn.) Voss). Biodiversitas 24: 704-712. Salacca zalacca (Gaertn.) Voss is a native tropical fruit species of Indonesia with three different sex types, i.e., female, male, and hermaphrodite. Early sex identification plays a vital role in the dioecious plant development, cultivation, and breeding program. The morphological and histological markers cannot differentiate salacca sex types during vegetative stages, during which molecular approaches are offered. Isolation of salacca's partial Transducin Beta Like-3 (TBL3) gene was done using Phoenix dactylifera L. TBL3-specific primers. After DNA sequencing and multiple sequence alignment, the putative TBL3 aligned data was used to construct a phylogenetic tree, find SNAP primers, and use the generated markers as predictors for sex-type phenotypes of salacca. Phylogenetic analysis showed that the dendrogram of aligned TBL3 partial sequences of salacca and other taxa showed that the salacca TBL3 is closely related to P. dactylifera and Elaeis guineensis Jacq. since the three palms belong to the same Arecaceae family. The partial sequence of the TBL3 gene of hermaphrodite salacca revealed ten single nucleotide polymorphisms (SNPs) compared to those of female and male plants. Protein alignment of the sequence also showed several differences, which may lead to different flower morphogenesis. The salacca SNAP sex-types markers were developed from one of the SNP sites and validated using samples from farmer plantations. The SNAP primer pairs of STBL1F-Ref - STBL1-Rev amplified a 300 bp fragment from hermaphrodite samples, whereas no band was amplified from the female and male samples. On the contrary, primers STBL1F-Alt - STBL1-Rev amplified a 300 bp fragment from female and male plants but not from the hermaphrodite plants. The salacca's TBL3 sequences and the SNAP markers are valuable tools for further salacca genomic exploration.

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“…In the family Arecaceae, date palm (P. dactylifera) is a common example of plant sex polymorphism. The molecular studies of sex types in P. dactylifera have been conducted using several genes including transducin beta-like 3 [8], Glycerol-3-phosphate acyltransferase 3-like [9], MYB transcriptional factor [10], and Sex determining Region Y [11].…”

Section: Introductionmentioning

confidence: 99%

Development of Hermaphrodite Salacca (Salacca zalacca) SNAP Marker: A Novel Conservation Tool

Prihatini

Dinarti

Sutanto³

et al. 2022

IOP Conf. Ser.: Earth Environ. Sci.

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Salacca (Salacca zalacca) or snake fruit is a tropical fruit, which is considered to be originated from Indonesia. One of the challenges in salacca conservation is the wide genetic diversity of the plants due to their natural cross-breeding. Most S. zalacca are dioecious plants by having fertile female and male flowers on different individuals, except for Salak Bali which is regarded to be monoecious. Morphological and cytogenetic markers have failed to differentiate the salacca plants’ sex types during the vegetative phase, thus the molecular marker is an alternative. We explored the specific salacca gene sequence on various sex types of salacca plants to identify sex-related single nucleotide polymorphism. The SNAP markers were then developed using the chosen SNP and validated on a total of 30 salacca samples. Nine samples of salacca’s female, male, and hermaphrodites were amplified using designed primers. The produced bands were sequenced and analyzed using Geneious Prime software. The analysis implied 9 SNPs on the 446 bp of salacca’s specific partial sequences. The SNAP markers were designed based on SNP validation showed that the marker potentially used a hermaphrodite-specific marker. The development of molecular markers as an early salacca sex type detection tool may be helpful in fruit cultivation, accelerating the plant breeding program, as well as on conservation management.

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Gene-specific sex-linked genetic markers in date palm (Phoenix dactylifera L.)

Cited by 8 publications

References 17 publications

Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

Sex-linked Single Nucleotide Polymorphism (SNP) identification and molecular marker development of salacca (Salacca zalacca (Gaertn.) Voss)

Development of Hermaphrodite Salacca (Salacca zalacca) SNAP Marker: A Novel Conservation Tool

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