SSR-based population structure, molecular diversity and identity cards of Ziziphus species from Pakistan and China

Uddin, Nisar; Ali, Niaz; Nisar, Mohammad; Liu, Mengjun; Liu, Zhiguo; Noor, Muhammad; Rahman, Inayat Ur

doi:10.1007/s10722-021-01138-z

Cited by 12 publications

(11 citation statements)

References 42 publications

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“…Although Z. mauritiana accessions clustered with Z. jujuba in population structure analysis, phylogenetic and PCA analysis were more sensitive, revealing that these accessions were distinct in comparison with either the Z. jujuba or the Z. oxyphylla, with some admixture with Z. nummularia. These results agree with the findings of Uddin et al (2021) for a larger collection of 200 genotypes (including the 141 accessions studied here) characterized using three highly polymorphic SSRs. The country of origin of the Z. jujuba did not influence the population structure and, although the limited number of Chinese Z. jujuba cultivars in this collection clustered together, this clade was within the wider Z. jujuba clade, suggesting that the molecular diversity in the wild Z. jujuba from Pakistan could be a useful source of diverse alleles for the cultivated varieties.…”

Section: Discussionsupporting

confidence: 91%

“…spinosa) and domesticated, cultivated Z. jujuba (Guo et al, 2020; was found in these studies. Our finding that relatively high genetic diversity has been retained in the Z. jujuba accessions from Pakistan in comparison with those from China is, therefore, surprising, but is consistent with previous findings for this collection (Uddin et al, 2021). This result might have reflected the smaller number of Z. jujuba from China in the panel, but polymorphic information content was also higher in the small number of Z. mauritiana than in the Chinese Z. jujuba.…”

Section: Discussionsupporting

confidence: 91%

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Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

Uddin

Shinde

Tesfamicael

et al. 2021

Preprint

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Ziziphus are economically and nutritionally important fruiting plants that were domesticated in China around 7000 years ago. We identified genetic diversity in 141 accessions of four, different species collected in Pakistan and in China, including wild species of Ziziphus mauritiana, Z. nummularia and Z. oxyphllya, and both wild and domesticated Z. jujuba Mill. Population structure, phylogenetic analysis and principal coordinates analysis based on 10,889 high-quality SNPs derived from genotyping-by-sequencing indicated that the accessions clustered into two major groups. The wild Pakistani Z. jujuba and Z. nummularia exhibited higher genetic diversity and polymorphic information content (0.37 and 0.23 respectively) than other species. We further conducted a genome-wide association study and discovered six highly significant marker-trait associations for fruit weight and plant height in this population. Our study provides important information for future breeding of Ziziphus species.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 91%

Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

Uddin

Shinde

Tesfamicael

et al. 2021

Preprint

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“…Total genomic DNA was extracted from the young leaves of selected genotypes using a modified CTAB (Cetyl trimethyl ammonium bromide) method [21]. Fresh leaves of Ziziphus species were ground to powder and placed into an Eppendorf tube where 800 µL of extraction buffer (3% CTAB, 5 M NaCl, 0.5 M EDTA, 1 M Tris-HCl pH 8.0) with 2 µL β-mercaptoethanol were added and incubated at 65 • C for 30 min.…”

Section: Genomic Dna Extractionmentioning

confidence: 99%

“…Moreover, wild plants like Z. nummularia have received little attention to date [20], so the primary goal of this study was to measure intraspecies genetic variation within a population of Z. nummularia adapted to different geographical regions. Various tools like morphological and SDS-PAGE seed storage protein have already been used to identify the diversity among different genotypes of Z. nummularia collected from Pakistan [21]. However, due to environmental fluctuations, morphological characterization was found unstable in the majority of cases [18,19].…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Genetic Variability within Ziziphus nummularia Genotypes by Phenotypic Traits and SSR Markers with Special Reference to Geographic Distribution

Uddin

Noor

Ali

et al. 2023

Genes

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Understanding the impacts and constraints of climate change on Ziziphus nummularia′s geographical distribution is crucial for its future sustainability. In this study, we analyze information obtained from the field investigation, the distribution and response of climatic changes of Ziziphus nummularia by the use of ArcGIS analysis. The genetic diversity of 180 genotypes from three populations was studied by morphological attributes and simple sequence repeat (SSR). The results showed that the significant bioclimatic variable limiting the distribution of Z. nummularia was the mean temperature (bio 10_18.tif and bio19). Under the current climatic change, the suitable growth region of Z. nummularia is Swat (35.22° N, 72.42° E), while the future distribution would be Buner (34.39° N, 72.61° E), respectively. A total of 11 phenotypic traits were noted and had significant phenotypic variation among the traits. A total of 120 alleles were amplified. The alleles per locus ranged from 2 to 6, averaging 4.42, whereas PIC ranged from 0.33 to 0.79. Within a mean value of 0.67 per locus, expected heterozygosity was 0.57, observed heterozygosity was 0.661, and average gene diversity was 0.49. Flow estimates (6.41) indicated frequent gene flow within genotypes. The clustering, STRUCTURE, and PCoA analysis indicated Swat and Buner migration routes and evolution as well. The results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries had retained unique alleles. This may facilitate the development of agronomically desirable cultivars. However, climate change has impacted species distributions, requiring strategies to conserve genetic resources in different areas.

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“…Bidara (Ziziphus mauritiana L.) plant is found in various parts of the world, including Africa (Stadlmayr et al 2013), Australia and Fiji (Dhileepan 2017), India (Prakash et al 2010), Pakistan (Sharif et al 2019), China (Uddin et al 2021) and Malaysia (Jaelani et al 2020). In Indonesia, Z. mauritiana grows wild in areas up to 400 m above sea level, including in areas with extreme temperatures and dryness (Gunawan et al 2017;Zandalinas et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Variability of secondary metabolites from leaves of Ziziphus mauritiana obtained from different locations in Sumbawa, Indonesia

NAIRFANA¹,

Nikmatullah

Sarjan

et al. 2022

Biodiversitas

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Abstract. Nairfana I, Nikmatullah A, Sarjan M, Tandeang A. 2022. Variability of secondary metabolites from leaves of Ziziphus mauritiana obtained from different locations in Sumbawa, Indonesia. Biodiversitas 23: 4948-4958. Bidara (Ziziphus mauritiana L.) is an evergreen shrub that grows in many parts of the world, and is an important plant in arid and semi-arid regions for the environment, food, and health. The plant has been used traditionally as medicine, and more recently, growing scientific evidence demonstrated the active compounds of bidara leaves. However, little is known about the plant's secondary metabolite profiles in different environments. This research aimed to characterize the secondary metabolites profile of bidara leaf obtained from the different habitats of semi-arid Sumbawa Island, Indonesia, and to evaluate their relationship based on cluster analysis of the secondary metabolite diversity. The leaf samples were collected from bidara plants obtained in 3 districts on Sumbawa Island: West Sumbawa (SB), Sumbawa (KS), and Dompu (DP) Districts, each from different ecosystems: lowland coastal/savanna, lowland near residential areas, and mid-highland areas of residential or forest-edge. The leaf samples were extracted by maceration with multilevel extraction using solvents with decreased polarity (h-hexane, ethyl acetate, ethanol 70%, methanol, and distilled water, respectively), followed by phytochemical screening for the presence of alkaloid, flavonoid, saponin, and phenolic. The results showed variation in the phytochemical components of bidara leaves obtained from a different environment, with secondary metabolites of DP leaves being more diverse than KS and other SB. All samples contained polar alkaloids and flavonoids, while the DP1 samples also contained non-polar flavonoids. The SB1 and DP samples also contained saponin. Interestingly, phenolic was only detected in the polar extracts of DP1 leaves. Cluster analysis based on the secondary metabolites profile distinguished the SB1 and DP1 bidara from others. Further study is required to understand if the variation is resulted from bidara adaptation to a different environment or also due to genetic variation of the bidara in Sumbawa Island.

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SSR-based population structure, molecular diversity and identity cards of Ziziphus species from Pakistan and China

Cited by 12 publications

References 42 publications

Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

Characterization of the Genetic Variability within Ziziphus nummularia Genotypes by Phenotypic Traits and SSR Markers with Special Reference to Geographic Distribution

Variability of secondary metabolites from leaves of Ziziphus mauritiana obtained from different locations in Sumbawa, Indonesia

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