Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: an endangered medicinal plant

Tilwari, Anita; Sharma, Rajesh

doi:10.1007/s11033-021-06278-0

Cited by 9 publications

(5 citation statements)

References 46 publications

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“…The PIC corresponds to its ability to detect polymorphisms among the individuals in a population [23]. The maximum PIC value for dominant markers is 0.5 [24][25][26][27][28][29]. Our results from the dominant SCoT markers showed a mean PIC = 0.3.…”

Section: Efficiency Of Scot and Indel Markers For Genetic Diversity A...mentioning

confidence: 57%

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Kulyan

Самарина

Shkhalakhova

et al. 2023

IJMS

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Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus Citrus. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency.

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Section: Efficiency Of Scot and Indel Markers For Genetic Diversity A...mentioning

confidence: 57%

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Kulyan

Самарина

Shkhalakhova

et al. 2023

IJMS

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“…Polymorphism information content (PIC) corresponds to its ability to detect the polymorphism among individuals of a population [ 26 , 27 ]. The PIC maximal value for dominant markers is 0.5 [ 26 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ]; that is what we obtain as output from the online tool [ 35 ]. On the other hand, some studies reported a PIC value for dominant markers higher than 0.5 [ 36 , 37 , 38 , 39 ].…”

Section: Discussionmentioning

confidence: 99%

Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars

Самарина

Malyarovskaya

Reim

et al. 2021

Plants

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Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20–50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.

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“…Evaluation of genetic diversity is critical for the breeding processes and effective conservation strategies of genetic resources because genetic diversity provides the basis for evolutionary change, including acclimation and adaptive responses to changes in local environmental conditions [9]. Based on the assessment of genetic diversity, conservation strategies for medicinal plants like Salvia o cinalis [10], Vitex rotundifolia [11] and Gloriosa superba [12] have been made. Nevertheless, the genetic diversity of many medicinal plants has not been studied, resulting in our ignorance of their gene pool and the extent of genetic structure changes.…”

Section: Backgroudmentioning

confidence: 99%

Genetic Diversity and Phylogeography of cultivated and wild Ophipogon japonicus based on chloroplast DNA exploration for origin and sustainable cultivation

Zhao

Shen

Zhang

et al. 2023

Preprint

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Background Ophipogon japonicus, planted in Sichuan (CMD) and Zhejiang (ZMD) Province in China, has a long cultivation history that can trace back to Ming dynasty (500 years ago) and Song dynasty (600 years ago) respectively. During the long period of domestication, the genetic diversity of cultivated O. japonicus has decreased a lot so that this species is facing with plant degradation. Therefore, it is urgent to clarify the genetic diversity and origin of cultivated O. japonicus to establish a theoretical basis for the utilization and conservation of the genetic resources of O. japonicus. Result We analyzed the genetic diversity and population structure of 266 O. japonicus individuals from 23 sampling sites based on 4 chloroplast DNA sequences (atpB-rbcL、rpl16、psbA-trnH and rpl20-5’rps12), identified the effects of domestication on genetic diversity of cultivars and determined the geographic origins of cultivars. The results showed that cultivated O. japonicus and wild O. japonicus had 4 haplotypes and 15 haplotypes respectively. The genetic diversity of two cultivars (Hd = 0.35700, π = 0.06667) was much lower than the wild populations (Hd = 0.76200, π = 0.20378), and the level of genetic diversity in CMD (Hd = 0.01900, π = 0.00125) was lower than that in ZMD (Hd = 0.06900, π = 0.01096). Genetic differentiation between the cultivated and the wild (FST= 0.82044) was significant, especially between the two cultivars (FST= 0.98254). This species showed a more pronounced phylogeographical structure (NST > GST, P < 0.05). The result of phylogenetic tree showed that demonstrated with the outgroup O. amblyphyllus Wang et Dai, the genetic difference between CMD and ZMD is not enough to distinguish the cultivars from two producing area. Besides, both CMD and ZMD have a closer relationship with wild populations in Sichuan than that in Zhejiang. In addition, according to the TCS network and MaxEnt suggested that the wild population TQ located in Sichuan Province should be served as the ancestor of cultivated O. japonicus, which is supported by RASP analysis. Conclusion These results suggest that cultivated O. japonicus has experienced dramatic loss of genetic diversity under anthropogenic influence. The genetic differentiation between CMD and ZMD was likely to be influenced by founder effect and strong artificial selection for plant traits. It appears that wild populations in Sichuan area were involved in the origin of not only CMD but also ZMD. Furthermore, some scientific strategies are suggested for resource conservation of O. japonicus based on its genetic diversity and population structure in this study.

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Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: an endangered medicinal plant

Cited by 9 publications

References 46 publications

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars

Genetic Diversity and Phylogeography of cultivated and wild Ophipogon japonicus based on chloroplast DNA exploration for origin and sustainable cultivation

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