Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq
Phosphorus is a macronutrient indispensable for plant growth and development. Plants utilize specialized transporters (PHT) to take up inorganic phosphorus and distribute it throughout the plant. The PHT transporters are divided into five families: PHT1 to PHT5. Each PHT family has a particular phys...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-06-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1529358/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850221353294102528 |
|---|---|
| author | David Chan-Rodriguez Brian Wakimwayi Koboyi Sirine Werghi Bradley J. Till Julia Maksymiuk Fatemeh Shoormij Abuya Hilderlith Anna Hawliczek Maksymilian Królik Hanna Bolibok-Brągoszewska |
| author_facet | David Chan-Rodriguez Brian Wakimwayi Koboyi Sirine Werghi Bradley J. Till Julia Maksymiuk Fatemeh Shoormij Abuya Hilderlith Anna Hawliczek Maksymilian Królik Hanna Bolibok-Brągoszewska |
| author_sort | David Chan-Rodriguez |
| collection | DOAJ |
| description | Phosphorus is a macronutrient indispensable for plant growth and development. Plants utilize specialized transporters (PHT) to take up inorganic phosphorus and distribute it throughout the plant. The PHT transporters are divided into five families: PHT1 to PHT5. Each PHT family has a particular physiological and cellular function. Rye (Secale cereale L.) is a member of Triticeae, and an important source of variation for wheat breeding. It is considered to have the highest tolerance of nutrient deficiency, among Triticeae. To date, there is no report about genes involved in response to phosphorus deficiency in rye. The aim of this study was to: (i) identify and characterize putative members of different phosphate transporter families in rye, (ii) assess their sequence diversity in a collection of 94 diverse rye accessions via low-coverage resequencing (DArTreseq), and (iii) evaluate the expression of putative rye Pht genes under phosphate-deficient conditions. We identified 29 and 35 putative Pht transporter genes in the rye Lo7 and Weining reference genomes, respectively, representing all known Pht families. Phylogenetic analysis revealed a close relationship of rye PHT with previously characterized PHT proteins from other species. Quantitative RT PCR carried out on leaf and root samples of Lo7 plants grown in Pi-deficient and control condition demonstrated that ScPht1;6, ScPht2 and ScPht3;3 are Pi-deficiency responsive. Based on DArTreseq genotyping of 94 diverse rye accessions we identified 820 polymorphic sites within rye ScPht, including 12 variants identified by the SIFT algorithm as having a potentially deleterious effect, of which three are scored as high confidence. SNP density varied markedly between ScPht genes. This report is the first step toward elucidating the mechanisms of rye’s response to Pi deficiency. Our findings point to multiple layers of adaptation to local environments, ranging from gene copy number variation to differences in level of polymorphism across Pht family members. DArTreseq genotyping permits for a quick and cost-effective assessment of polymorphism levels across genes/gene families and supports identification and prioritization of candidates for further studies. Collectively our findings provide the foundation for selecting most promising candidates for further functional characterization. |
| format | Article |
| id | doaj-art-a1bd6d2dd8554669a8a84fefc73ca3c7 |
| institution | OA Journals |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-a1bd6d2dd8554669a8a84fefc73ca3c72025-08-20T02:06:44ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-06-011610.3389/fpls.2025.15293581529358Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseqDavid Chan-Rodriguez0Brian Wakimwayi Koboyi1Sirine Werghi2Bradley J. Till3Julia Maksymiuk4Fatemeh Shoormij5Abuya Hilderlith6Anna Hawliczek7Maksymilian Królik8Hanna Bolibok-Brągoszewska9Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandVeterinary Genetics Laboratory, University of California, Davis, Davis, CA, United StatesDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, IranDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandDepartment of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, PolandPhosphorus is a macronutrient indispensable for plant growth and development. Plants utilize specialized transporters (PHT) to take up inorganic phosphorus and distribute it throughout the plant. The PHT transporters are divided into five families: PHT1 to PHT5. Each PHT family has a particular physiological and cellular function. Rye (Secale cereale L.) is a member of Triticeae, and an important source of variation for wheat breeding. It is considered to have the highest tolerance of nutrient deficiency, among Triticeae. To date, there is no report about genes involved in response to phosphorus deficiency in rye. The aim of this study was to: (i) identify and characterize putative members of different phosphate transporter families in rye, (ii) assess their sequence diversity in a collection of 94 diverse rye accessions via low-coverage resequencing (DArTreseq), and (iii) evaluate the expression of putative rye Pht genes under phosphate-deficient conditions. We identified 29 and 35 putative Pht transporter genes in the rye Lo7 and Weining reference genomes, respectively, representing all known Pht families. Phylogenetic analysis revealed a close relationship of rye PHT with previously characterized PHT proteins from other species. Quantitative RT PCR carried out on leaf and root samples of Lo7 plants grown in Pi-deficient and control condition demonstrated that ScPht1;6, ScPht2 and ScPht3;3 are Pi-deficiency responsive. Based on DArTreseq genotyping of 94 diverse rye accessions we identified 820 polymorphic sites within rye ScPht, including 12 variants identified by the SIFT algorithm as having a potentially deleterious effect, of which three are scored as high confidence. SNP density varied markedly between ScPht genes. This report is the first step toward elucidating the mechanisms of rye’s response to Pi deficiency. Our findings point to multiple layers of adaptation to local environments, ranging from gene copy number variation to differences in level of polymorphism across Pht family members. DArTreseq genotyping permits for a quick and cost-effective assessment of polymorphism levels across genes/gene families and supports identification and prioritization of candidates for further studies. Collectively our findings provide the foundation for selecting most promising candidates for further functional characterization.https://www.frontiersin.org/articles/10.3389/fpls.2025.1529358/fullryeSecale cereale L.Pht genesphosphate deficiencyphylogenetic relationshipsgene diversity |
| spellingShingle | David Chan-Rodriguez Brian Wakimwayi Koboyi Sirine Werghi Bradley J. Till Julia Maksymiuk Fatemeh Shoormij Abuya Hilderlith Anna Hawliczek Maksymilian Królik Hanna Bolibok-Brągoszewska Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq Frontiers in Plant Science rye Secale cereale L. Pht genes phosphate deficiency phylogenetic relationships gene diversity |
| title | Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq |
| title_full | Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq |
| title_fullStr | Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq |
| title_full_unstemmed | Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq |
| title_short | Phosphate transporter gene families in rye (Secale cereale L.) – genome-wide identification, characterization and sequence diversity assessment via DArTreseq |
| title_sort | phosphate transporter gene families in rye secale cereale l genome wide identification characterization and sequence diversity assessment via dartreseq |
| topic | rye Secale cereale L. Pht genes phosphate deficiency phylogenetic relationships gene diversity |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1529358/full |
| work_keys_str_mv | AT davidchanrodriguez phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT brianwakimwayikoboyi phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT sirinewerghi phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT bradleyjtill phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT juliamaksymiuk phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT fatemehshoormij phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT abuyahilderlith phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT annahawliczek phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT maksymiliankrolik phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq AT hannabolibokbragoszewska phosphatetransportergenefamiliesinryesecalecerealelgenomewideidentificationcharacterizationandsequencediversityassessmentviadartreseq |