Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.)

Preethi, P.; Rahman, Shafeeq; Naganeeswaran, S.; Sabana, A A; Gangaraj, K.P.; Jerard, B. A.; Niral, V.; Rajesh, M. K.

doi:10.1007/s11033-020-05981-8

Cited by 26 publications

(12 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To the best of our knowledge, this is the first study that has sought to assess the genetic diversity of this important medicinal plant species. The frequency of EST-SSRs in M. savatieri is comparable to that of found in Rhododendron fortunei [31] and Cocos nucifera [32], although somewhat lower than that previously reported for Pongamia pinnata [33] and Stephanandra incisa [34], but notably higher than that in Paeonia suffruticosa [35] and Cephalotaxus oliveri [36]. These findings accordingly reveal the relatively broad range of SSR densities among plants at the species level.…”

Section: Discussionsupporting

confidence: 78%

Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers

et al. 2022

View full text Add to dashboard Cite

Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R2 = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis. Conclusions As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri.

show abstract

Section: Discussionsupporting

confidence: 78%

Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Minimum SSR motif repeats were identified by 10 mononucleotides, six dinucleotides, five trinucleotides, tetranucleotide, pentanucleotide, and hexanucleotide motif repeats. Primer 3 version 4.1.0 ( https://bioinfo.ut.ee/primer3/ ) (Preethi et al, 2020 ) was used to design the primers. Primer length ranged from 18 to 24 bp, GC contents ranged from 40 to 60%, annealing temperatures ranged from 55 to 60°C, and the size of PCR products ranged from 100 to 350 bp.…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers

Zhang

Zhang²,

Yang³

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.

show abstract

“…Most core germplasm collections represent only 5–20% of the total germplasm collected ( Hintum et al, 2000 ; Lv et al, 2020 ), thereby reducing conservation and management costs and improving the efficiency of germplasm utilization. However, woody plant germplasm is predominantly derived from natural populations with brief history of domestication and long generation time, therefore the accessions have a high intrinsic genetic diversity and core germplasm collections typically represent 10–45% of the complete germplasm collections within these species ( Belaj et al, 2012 ; Duan et al, 2017 ; Min et al, 2017 ; Preethi et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…EST-SSR (expressed sequence tags microsatellite markers) markers not only have the beneficial characteristics of high intraspecific polymorphism, co-dominant nature, and high reproducibility, but also originate from genomic coding regions and thus directly reflect the diversity of the underlying genes ( Adams et al, 1991 ; Wang et al, 2017 ; Parthiban et al, 2018 ). EST-SSRs have been commonly used to evaluate genetic diversity of Dendrobium officinale ( Xie et al, 2020 ), Paeonia rockii ( Guo et al, 2020 ), coconut ( Preethi et al, 2020 ), and Stevia rebaudiana ( Cosson et al, 2019 ) and to construct core germplasm collections of Rosa roxburghii ( Min et al, 2017 ), crape myrtle ( Ye et al, 2017 ), and olive ( Dervishi et al, 2021 ). Previous studies have applied ISSR (inter-simple sequence repeat) and RAPD (random amplified polymorphic DNA) molecular markers to evaluate the genetic diversity of the S. mukorossi population ( Mahar et al, 2011b ; Diao et al, 2016 ), however, there have been no studies or reports on the construction of Sapindus core germplasm collection.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Analysis of Sapindus in China and Extraction of a Core Germplasm Collection Using EST-SSR Markers

Liu

Gao

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Sapindus is an important forest tree genus with utilization in biodiesel, biomedicine, and it harbors great potential for biochemical engineering applications. For advanced breeding of Sapindus, it is necessary to evaluate the genetic diversity and construct a rationally designed core germplasm collection. In this study, the genetic diversity and population structure of Sapindus were conducted with 18 expressed sequence tag-simple sequence repeat (EST-SSR) markers in order to establish a core germplasm collection from 161 Sapindus accessions. The population of Sapindus showed high genetic diversity and significant population structure. Interspecific genetic variation was significantly higher than intraspecific variation in the Sapindus mukorossi, Sapindus delavayi, and combined Sapindus rarak plus Sapindus rarak var. velutinus populations. S. mukorossi had abundant genetic variation and showed a specific pattern of geographical variation, whereas S. delavayi, S. rarak, and S. rarak var. velutinus showed less intraspecific variation. A core germplasm collection was created that contained 40% of genetic variation in the initial population, comprising 53 S. mukorossi and nine S. delavayi lineages, as well as single representatives of S. rarak and S. rarak var. velutinus. These results provide a germplasm basis and theoretical rationale for the efficient management, conservation, and utilization of Sapindus, as well as genetic resources for joint genomics research in the future.

show abstract

Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.)

Cited by 26 publications

References 32 publications

Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers

Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers

Genetic Diversity Analysis of Sapindus in China and Extraction of a Core Germplasm Collection Using EST-SSR Markers

Contact Info

Product

Resources

About