scholarly journals Assessment of genetic diversity and variety identification based on developed retrotransposon-based insertion polymorphism (RBIP) markers in sweet potato (Ipomoea batatas (L.) Lam.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yusha Meng ◽  
Wenjin Su ◽  
Yanping Ma ◽  
Lei Liu ◽  
Xingguo Gu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sweet Potato ◽  
Variety Identification ◽  
Group Method ◽  
Insertion Polymorphism ◽  
Ltr Retrotransposon ◽  
Germplasm Resources ◽  
Ltr Retrotransposons ◽  
Diversity Assessment

AbstractSweet potato, a dicotyledonous and perennial plant, is the third tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. Here, we reported a structure-based analysis of the sweet potato genome, a total of 21555 LTR retrotransposons, which belonged to the main LTR-retrotransposon subfamilies Ty3-gypsy and Ty1-copia were identified. After searching and selecting using Hidden Markov Models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were screened. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. Fifty-six amplicons with an average polymorphism of 91.07% were generated in 105 sweet potato germplasm resources based on RBIP markers. A Unweighted Pair Group Method with Arithmatic Mean (UPGMA) dendrogram, a model-based genetic structure and principal component analysis divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All the three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato and have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction. The results could provide a good theoretical reference and guidance for germplasm research and breeding.

scholarly journals Assessment of Genetic Diversity and Variety Identification Based on Developed Retrotransposon-Based Insertion Polymorphism (RBIP) Markers in Sweet Potato (Ipomoea Batatas (L.) Lam)

2021 ◽  
Author(s):  
Yusha Meng ◽  
Wenjin Su ◽  
Yanping Ma ◽  
Lei Liu ◽  
Xingguo Gu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Variety Identification ◽  
Insertion Polymorphism ◽  
Ltr Retrotransposon ◽  
Germplasm Resources ◽  
Ltr Retrotransposons ◽  
Crop Species

Abstract Sweet potato, a dicotyledonous and perennial plant, is the third most crucial tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. These LTR retrotransposons play a significant role in sweet potato genotypes. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. We report a structure-based analysis of the sweet potato genome for the main LTR-retrotransposon subfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 21555 LTR retrotransposons. By searching using hidden Markov models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were found. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. RBIP markers of the genetic diversity and population structure of 105 sweet potato germplasm resources revealed 56 amplicons with an average polymorphism of 91.07%. Sweet potato accessions were collected from 6 provinces of China, Japan and America. A UPGMA dendrogram, a model-based genetic structure and principal component analysis (PCA) divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato.

scholarly journals Protein-Based Genetic Diversity Assessment of Tilapia guineensis and Sarotherodon melanotheron Populations from South-West Nigerian Coastal Waters

2020 ◽  
pp. 9-15
Author(s):  
E. A. Ukenye ◽  
I. Megbowon ◽  
M. M. A. Akinwale ◽  
M. A. Fowora ◽  
I. Chidume ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Group Method ◽  
Cichlid Species ◽  
Diversity Assessment ◽  
Sds Page ◽  
Sarotherodon Melanotheron

The present study was carried out to investigate the genetic differences in the Protein banding pattern of Tilapia guineensis and Sarotherodon melanotheron populations in Southwest Nigeria using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). Four populations of Tilapia guineensis and three populations of Sarotherodon melanotheron from Ondo and Lagos states were considered for the study. The sarcoplasmic protein of the studied Cichlid species resolved on 12% SDS-PAGE revealed variations in their genetic diversity indices (number of alleles, shanon information index, heterozygosity and percentage polymorphism). T. guineensis had more proteins and higher genetic diversity as was revealed by the genetic diversity parameters and was found to be more polymorphic with a percentage polymorphism of 78.57% than S. melanotheron (57.14%). The two species had similarity coefficient of 0.82 indicating high genetic similarity between them. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram also revealed some level of genetic similarity between the studied populations and among the two species. Analysis of molecular variance (AMOVA) confirmed the low genetic variation among the populations of the cichlid species and demonstrated that genetic variation was mostly within populations in both species. It is established from the study that Tilapia guineensis had higher genetic diversity than Sarotherodon melanotheron and the two species are closely related. Further study involving molecular markers is encouraged to complement this finding.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

Genetic Variation in Invasive Populations of Yellow Toadflax (Linaria vulgaris) in the Western United States

Weed Science ◽  
2008 ◽  
Vol 56 (3) ◽  
pp. 394-399 ◽  
Author(s):  
Sarah M. Ward ◽  
Scott D. Reid ◽  
Judy Harrington ◽  
Jason Sutton ◽  
K George Beck
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Diversity Index ◽  
Gene Diversity ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Invasive Weed ◽  
Yellow Toadflax

Intraspecific genetic variation may contribute significantly to invasiveness and control problems, but has been characterized to date in relatively few invasive weed species. We examined 56 intersimple sequence repeat (ISSR) loci in 220 individuals from 11 invading populations of yellow toadflax sampled across five western states. All populations showed high levels of genetic diversity. Estimated values for Shannon's diversity measure ranged from 0.217 to 0.388, and for expected heterozygosity from 0.178 to 0.260. Nei's total gene diversity index (HT), on the basis of all individuals across all populations, was 0.267. Partitioning of genetic variance using analysis of molecular variance revealed 1.7% of genetic variation among regional population groups, 29.1% among populations within groups, and 69.2% within populations, consistent with expectations for an outcrossing species but suggesting little geographic differentiation. Pairs of adjacent individuals identical at all ISSR loci that appeared to be ramets of a single clone were detected in only one population. This indicates that patch expansion in yellow toadflax is driven more by sexual reproduction via seed than by rhizomatous clonal spread, at least at the spatial scale of sampling for this study. Eight populations had significant values for Mantel's R at P = 0.05, suggesting some fine-scale positive genetic structuring, possibly from restricted gene flow. Population clustering on the basis of Nei's genetic distance between populations and unweighted pair group method with arithmetic mean did not reflect geographic location. It is likely that multiple introductions of this species have occurred across the Intermountain West, followed by extensive genetic recombination. High levels of genetic diversity within yellow toadflax populations pose management challenges, as already seen in reports of variable response to herbicide application and limited impacts of biocontrol agent releases.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Genetic Diversity of Seven Deciduous Azalea Species (Rhododendron spp. section Pentanthera) Native to the Eastern United States

2008 ◽  
Vol 133 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Matthew Chappell ◽  
Carol Robacker ◽  
Tracie M. Jenkins
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Diversity ◽  
Interspecific Variation ◽  
Genetic Distances ◽  
Anthropogenic Activity ◽  
Group Method ◽  
Aflp Analysis ◽  
Eastern United States

Despite the ecologic and economic importance of native deciduous azaleas (Rhododendron L. section Pentanthera G. Don), our understanding of interspecific variation of North American deciduous azalea species comes principally from morphologic studies. Furthermore, little is known concerning intraspecific or interpopulation genetic variation. With ever-increasing loss and fragmentation of native azalea habitat in the eastern United States due to anthropogenic activity, it is imperative that an understanding of natural genetic variation among and within species and populations is acquired. The present study addresses questions of genetic diversity through the use of amplified fragment length polymorphism (AFLP) analysis. Twenty-five populations of seven species of native azalea were analyzed using three primer pairs that amplified a total of 417 bands. Based on analysis of molecular variance (AMOVA) and estimates of Nei's coefficients of gene diversity (H S, H T, and G ST), the majority of variation found in deciduous azalea occurs within populations. Variation both among species and among population was low, likely the effect of common ancestry as well as frequent introgression among members (and populations) of section Pentanthera. The latter was evident in four populations of R. prunifolium (Small) Millais and R. canescens (Michaux) Sweet that were highly related to R. austrinum (Small) Rehder and R. viscosum (L.) Torrey, respectively. Despite these outliers, most populations were grouped into species based on Nei's unbiased genetic distances viewed as an unweighted pair group method with arithmetic mean (UPGMA) phenogram. The significance of these results is discussed in relation to breeding in section Pentanthera.

scholarly journals Comparison of AFLPs, RAPD Markers, and Isozymes for Diversity Assessment of Garlic and Detection of Putative Duplicates in Germplasm Collections

2003 ◽  
Vol 128 (2) ◽  
pp. 246-252 ◽  
Author(s):  
Meryem Ipek ◽  
Ahmet Ipek ◽  
Philipp W. Simon
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Morphological Diversity ◽  
Mantel Test ◽  
Group Method ◽  
Aflp Analysis ◽  
Additional Tool ◽  
Germplasm Collections ◽  
Diversity Assessment

Garlic (Allium sativum L.) is an asexually propagated crop that displays much morphological diversity. Studies which have assessed garlic diversity with isozymes and randomly amplified polymorphic DNA (RAPD) markers generally agreed with the morphological observations but sometimes failed to discriminate clones. To discriminate among closely related garlic clones in more detail, we introduced amplified fragment-length polymorphism (AFLPs) to evaluate the genetic diversity and phenetic relatedness of 45 garlic clones and three A. longicuspis clones and we compared AFLP results with RAPD markers and isozymes. Three AFLP primer combinations generated a total of 183 polymorphic fragments. Although similarities between the clusters were low (≥0.30), some clones within the clusters were very similar (>0.95) with AFLP analysis. Sixteen clones represented only six different banding patterns, within which they shared 100% polymorphic AFLPs and RAPD markers, and likely are duplicates. In agreement with the results of other investigators, A. longicuspis and A. sativum clones were clustered together with no clear separation, suggesting these species are not genetically or specifically distinct. The topology of AFLP, RAPD, and isozyme dendrograms were similar, but RAPD and isozyme dendrograms reflected less and much less polymorphism, respectively. Comparison of unweighted pair group method with arithmetic averaging (UPGMA) dendrograms of AFLP, RAPD, and isozyme cluster analyses using the Mantel test indicated a correlation of 0.96, 0.55, and 0.57 between AFLP and RAPD, AFLP and isozyme, and RAPD and isozyme, respectively. Polymorphic AFLPs are abundant in garlic and demonstrated genetic diversity among closely related clones which could not be differentiated with RAPD markers and isozymes. Therefore, AFLP is an additional tool for fingerprinting and detailed assessment of genetic relationships in garlic.

Establishment of an effective set of simple sequence repeat markers for sunflower variety identification and diversity assessment

2005 ◽  
Vol 83 (1) ◽  
pp. 66-72 ◽  
Author(s):  
L S Zhang ◽  
V Le Clerc ◽  
S Li ◽  
D Zhang
Keyword(s):  
Genetic Diversity ◽  
Helianthus Annuus ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Inbred Lines ◽  
Variety Identification ◽  
Large Set ◽  
Sequence Repeat ◽  
Diversity Assessment ◽  
Simple Sequence

The objective of this study was to identify an efficient set of simple sequence repeat (SSR) markers for sunflower (Helianthus annuus L.) variety fingerprinting, relying on semi-automated analysis conditions. Based on criteria such as quality of amplification products, co-dominant and single locus, 78 SSR markers were selected and used to assess the genetic variability among a large set of 124 sunflower inbred lines, including 67 female maintainers (M lines) and 57 male restorers (R lines). They revealed a total of 276 alleles across the 124 elite inbred lines, with a mean of 3.5 alleles per SSR locus. The polymorphism index content per locus varied from 0.06 to 0.81, with an average of 0.51. Relationships among the inbred lines were studied using estimations of Rogers' distances. The great majority of the distance estimates ranged between 0.4 and 0.6, but distances between some pairs of lines were less than 0.1. The genetic diversity value was similar within each subset of R and M lines and low, but significant differentiation was found (GST = 0.049) between the two pools. The selected set of SSRs proved to be useful both for sunflower fingerprinting and genetic diversity assessment.Key words: genetic diversity, genotyping, Helianthus annuus, multiplex PCR, simple sequence repeats (SSR).

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