Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

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Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

10.21203/rs.3.rs-40696/v1 ◽

2020 ◽

Author(s):

Lei Zhu ◽

Hua yu Zhu ◽

Yan man Li ◽

Xiang bin Wu ◽

Jin tao Li ◽

...

Keyword(s):

Genetic Diversity ◽

Comparative Genomics ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Motif Length ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Ssr Loci ◽

Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

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Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.3.309 ◽

2001 ◽

Vol 126 (3) ◽

pp. 309-317 ◽

Cited By ~ 59

Author(s):

O. Gulsen ◽

M.L. Roose

Keyword(s):

Simple Sequence Repeats ◽

Phylogenetic Trees ◽

Nuclear Genome ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Inter Simple Sequence Repeats ◽

Ssr Loci ◽

High Level ◽

Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

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Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

Canadian Journal of Plant Science ◽

10.4141/cjps2013-062 ◽

2013 ◽

Vol 93 (6) ◽

pp. 1089-1096 ◽

Cited By ~ 13

Author(s):

Shiyong Chen ◽

Xinquan Zhang ◽

Xiao Ma ◽

Linkai Huang

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Tibet Plateau ◽

Group Method ◽

Similarity Coefficients ◽

Arithmetic Average ◽

Pair Group ◽

Elymus Nutans ◽

Qinghai Tibet Plateau ◽

Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

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Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.3.357 ◽

2007 ◽

Vol 132 (3) ◽

pp. 357-367 ◽

Cited By ~ 12

Author(s):

P. Escribano ◽

M.A. Viruel ◽

J.I. Hormaza

Keyword(s):

Genetic Diversity ◽

Geographic Origin ◽

Germplasm Collection ◽

Ex Situ ◽

Group Method ◽

Pair Group ◽

Ssr Primers ◽

Upgma Cluster Analysis ◽

Ssr Loci ◽

Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

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Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species

The Journal of Agricultural Science ◽

10.1017/s0021859615001252 ◽

2016 ◽

Vol 154 (7) ◽

pp. 1254-1269 ◽

Cited By ~ 1

Author(s):

A. SINGH ◽

H. K. DIKSHIT ◽

D. SINGH ◽

N. JAIN ◽

M. ASKI ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Wild Species ◽

Expressed Sequence Tag ◽

Group Method ◽

Comparative Genomic ◽

Pair Group ◽

Ssr Loci ◽

Related Wild Species ◽

Expressed Sequence

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to analyse genetic diversity among three Lens species. The SSR loci amplified successfully in wild species, with 94·82% transferability in Lens culinaris subsp. orientalis, 95·4% in Lens nigricans, 98·81% in L. culinaris subsp. odemensis, 94·82% in L. culinaris subsp. tomentosus and 96·55% in Lens ervoides. Ninety-nine alleles (average 3·41 alleles/locus) were detected by 29 SSR markers. Based on the unweighted pair group method with arithmetic mean cluster analysis, all the genotypes were grouped into three clusters at a similarity level of 0·30. The diversity analysis indicated no species-specific clustering of the wild and cultivated species. Wild species L. nigricans and L. culinaris subsp. odemensis, L. culinaris subsp. orientalis and L. ervoides were grouped in Cluster I, whereas the Mediterranean land races of L. culinaris subsp. culinaris and L. culinaris subsp. tomentosus formed a separate group in Cluster II A. Cluster II B comprised L. ervoides, L. culinaris subsp. orientalis and L. culinaris subsp. culinaris. Clusters II C, II D and II F included cultivated Indian lentil genotypes. Cluster II E comprised Indian and Mediterranean germplasm lines. Cluster II F included three early maturing germplasm lines, whereas Cluster III included only two germplasm lines. The functional annotation of SSR-containing unigenes revealed that a majority of genes were involved in an important transport-related function or were a component of metabolic pathways. A high level of polymorphism of EST-SSRs and their transferability to related wild species indicated that these markers could be used for molecular screening, map construction, comparative genomic studies and marker-assisted selection.

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Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽

10.1139/g05-022 ◽

2005 ◽

Vol 48 (4) ◽

pp. 731-737 ◽

Cited By ~ 28

Author(s):

N A Barkley ◽

M L Newman ◽

M L Wang ◽

M W Hotchkiss ◽

G A Pederson

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Phylogenetic Relationships ◽

Expressed Sequence Tag ◽

Genetic Distances ◽

Group Method ◽

Arithmetic Means ◽

Pair Group ◽

Expressed Sequence ◽

Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

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Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers

HortScience ◽

10.21273/hortsci.50.6.797 ◽

2015 ◽

Vol 50 (6) ◽

pp. 797-800

Author(s):

Xiaoli Wang ◽

Zhiyong Wang ◽

Li Liao ◽

Xinyi Zhang ◽

Changjun Bai

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Warm Season ◽

Group Method ◽

Sequence Repeat ◽

Marker Assisted Breeding ◽

Arithmetic Means ◽

Pair Group ◽

Simple Sequence

Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

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Efficiency of different marker systems for molecular characterization of subtropical carrot germplasm

The Journal of Agricultural Science ◽

10.1017/s0021859609990591 ◽

2010 ◽

Vol 148 (2) ◽

pp. 171-181 ◽

Cited By ~ 3

Author(s):

T. JHANG ◽

M. KAUR ◽

P. KALIA ◽

T. R. SHARMA

Keyword(s):

Genetic Variability ◽

Ssr Markers ◽

Dna Markers ◽

Principal Component ◽

Group Method ◽

Data Set ◽

Breeding Lines ◽

Pair Group ◽

Ssr Loci ◽

Simple Sequence

SUMMARYGenetic variability in carrots is a consequence of allogamy, which leads to a high level of inbreeding depression, affecting the development of new varieties. To understand the extent of genetic variability in 40 elite indigenous breeding lines of subtropical carrots, 48 DNA markers consisting of 16 inter simple sequence repeats (ISSRs), 10 universal rice primers (URPs), 16 random amplification of polymorphic DNA (RAPD) and six simple sequence repeat (SSR) markers were used. These 48 markers amplified a total of 591 bands, of which 569 were polymorphic (0·96). Amplicon size ranged from 200 to 3500 base pairs (bp) in ISSR, RAPD and URPs markers and from 100 to 300 bp in SSR markers. The ISSR marker system was found to be most efficient with (GT)n motifs as the most abundant SSR loci in the carrot genome. The unweighted pair group method with arithmetic mean (UPGMA) analysis of the combined data set of all the DNA markers obtained by four marker systems classified 40 genotypes in two groups with 0·45 genetic similarity with high Mantel matrix correlation (r=0·92). The principal component analysis (PCA) of marker data also explained 0·55 of the variation by first three components. Molecular diversity was very high and non-structured in these open-pollinated genotypes. The study demonstrated for the first time that URPs can be used successfully in genetic diversity analysis of tropical carrots. In addition, an entirely a new set of microsatellite markers, derived from the expressed sequence tags (ESTs) sequences of carrots, has been developed and utilized successfully.

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Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽

10.3390/plants8110471 ◽

2019 ◽

Vol 8 (11) ◽

pp. 471

Author(s):

Jae-Ryoung Park ◽

Won-Tae Yang ◽

Yong-Sham Kwon ◽

Hyeon-Nam Kim ◽

Kyung-Min Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Group Method ◽

Sequence Repeat ◽

Rice Varieties ◽

Red Pericarp ◽

Simple Sequence ◽

Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

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