Development of cpSSR markers for analysis of genetic diversity in Gladiolus cultivars

Singh, Niraj Kumar; Pal, Amita; Roy, R. K.; Tamta, Sushma; Rana, T. S.

doi:10.1016/j.plgene.2017.05.003

Cited by 13 publications

(11 citation statements)

References 41 publications

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“…The cpSSR markers are excellent tools for phylogenetic research due to several characteristics, including non-recombination, haploidy, uniparental inheritance, and the low substitution rate [ 39 ]. They are especially valuable for intraspecific population genetic variation research [ 40 , 41 ] and interspecific evolutionary and identification studies [ 42 , 43 , 44 , 45 , 46 ]. A previous study reported that 213 SSRs and 44 long repeats were identified in the cp genome of C. illinoinensis [ 47 ], while 252 SSRs and 55 long repeats were identified in our study.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis

Jia

Chen

Huang

et al. 2022

Genes

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Carya cathayensis, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of C. cathayensis was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (rps15, rpoA, rpoB, petD, ccsA, atpI, and ycf1-2) were possibly under positive selection compared with the other Juglandaceae species. Phylogenetic relationships of 46 species inferred that Juglandaceae is monophyletic, and that C. cathayensis is sister to Carya kweichowensis and Carya illinoinensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.

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Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis

Jia

Chen

Huang

et al. 2022

Genes

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“…In addition, the origin and genetic diversity of sweet potato germplasms have been explained using nuclear SSRs and cpSSRs [12,13]. These methods, non-recombinant and uniparentally inherited nature, are widely used for evolutionary and phylogenetic studies as they have been demonstrated to be effective indicators of the genetic structure of a population [26,27].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

Lee

et al. 2019

Agronomy

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Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the germplasm collection of the National Agrobiodiversity Center (NAC). Eight of the nine cpSSR showed polymorphisms, while Ibcp31 did not. The number of alleles per locus ranged from two to four. In general, the Shannon index for each cpSSR ranged from 0.280 to 1.123 and the diversity indices and unbiased diversity ranged from 0.148 to 0.626, and 0.210 to 0.627, respectively. Results of the median-joining network showed 33 chlorotypes in 558 sweet potato accessions. In factor analysis, 558 sweet potato accessions were divided into four clusters, with clusters I and II composed only of the sweet potato accessions from Korea, Japan, Taiwan, and the USA. The results of this study confirmed that the genetic diversity of the female parents of sweet potato accessions conserved at the NAC is low and therefore more sweet potato accessions need to be collected. These results will help to establish an efficient management plan for sweet potato genetic germplasms at the NAC.

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“…It is established that chloroplast genome is characterized by conserved genic sequences, non-recombination and maternal inheritance in plants [34]. Out of 12 chloroplast SSRs identi ed by Singh and coworkers [40], seven were polymorphic among gladiolus genotypes.…”

Section: Discussionmentioning

confidence: 99%

“…A total of 65 microsatellite markers identi ed for gladiolus and related genera/species available in public domain viz. cpSSRs [40], genomic SSRs [10,20,24,47], EST derived SSRs from Iris spp. [50] and intergenic spacer sequences [41] were screened for ampli cation and detection of polymorphism among gladiolus genotypes.…”

Section: Source Of Ssrs and Pcr Analysismentioning

confidence: 99%

“…In last few years, microsatellite markers have been developed for iridaceous owers like Crocus sativus [24], Herbertia zebrina [10], Sisyrinchium micranthum [47]. Few chloroplast SSRs have been developed from plastid sequences of gladiolus genus and are available in public domain [40]. Genomic SSRs with high discriminating power have also been reported recently in Gladiolus palustris, an endangered European tetraploid species [20].…”

Section: Introductionmentioning

confidence: 99%

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

Hiremath

Singh

Jain

et al. 2021

Preprint

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Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Development of cpSSR markers for analysis of genetic diversity in Gladiolus cultivars

Cited by 13 publications

References 41 publications

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis

The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

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