Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS
Natural populations of <i>Rhanterium eppaposum</i> Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity an...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-05-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/11/11/1435 |
| _version_ | 1797492072379318272 |
|---|---|
| author | Fadila Al Salameen Nazima Habibi Sami Al Amad Bashayer Al Doaij |
| author_facet | Fadila Al Salameen Nazima Habibi Sami Al Amad Bashayer Al Doaij |
| author_sort | Fadila Al Salameen |
| collection | DOAJ |
| description | Natural populations of <i>Rhanterium eppaposum</i> Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local <i>Rhanterium</i> plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of <i>Rhanterium</i>. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (F<sub>ST</sub> = 0.029; <i>p</i> = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel’s test returned a very weak correlation coefficient of r<sup>2</sup> = 0.101 (<i>p</i> = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation. |
| first_indexed | 2024-03-10T00:58:21Z |
| format | Article |
| id | doaj.art-18b0e4046f874af299713f78e732c761 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T00:58:21Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-18b0e4046f874af299713f78e732c7612023-11-23T14:38:37ZengMDPI AGPlants2223-77472022-05-011111143510.3390/plants11111435Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBSFadila Al Salameen0Nazima Habibi1Sami Al Amad2Bashayer Al Doaij3Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitNatural populations of <i>Rhanterium eppaposum</i> Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local <i>Rhanterium</i> plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of <i>Rhanterium</i>. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (F<sub>ST</sub> = 0.029; <i>p</i> = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel’s test returned a very weak correlation coefficient of r<sup>2</sup> = 0.101 (<i>p</i> = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation.https://www.mdpi.com/2223-7747/11/11/1435next-generation sequencingsingle nucleotide polymorphismsnative plantpopulation structuremolecular diversitydesert species |
| spellingShingle | Fadila Al Salameen Nazima Habibi Sami Al Amad Bashayer Al Doaij Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS Plants next-generation sequencing single nucleotide polymorphisms native plant population structure molecular diversity desert species |
| title | Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS |
| title_full | Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS |
| title_fullStr | Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS |
| title_full_unstemmed | Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS |
| title_short | Genetic Diversity of <i>Rhanterium eppaposum</i> Oliv. Populations in Kuwait as Revealed by GBS |
| title_sort | genetic diversity of i rhanterium eppaposum i oliv populations in kuwait as revealed by gbs |
| topic | next-generation sequencing single nucleotide polymorphisms native plant population structure molecular diversity desert species |
| url | https://www.mdpi.com/2223-7747/11/11/1435 |
| work_keys_str_mv | AT fadilaalsalameen geneticdiversityofirhanteriumeppaposumiolivpopulationsinkuwaitasrevealedbygbs AT nazimahabibi geneticdiversityofirhanteriumeppaposumiolivpopulationsinkuwaitasrevealedbygbs AT samialamad geneticdiversityofirhanteriumeppaposumiolivpopulationsinkuwaitasrevealedbygbs AT bashayeraldoaij geneticdiversityofirhanteriumeppaposumiolivpopulationsinkuwaitasrevealedbygbs |