Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage ‘TO1000.’ Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14–0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

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

Horticulturae ◽

10.3390/horticulturae7060143 ◽

2021 ◽

Vol 7 (6) ◽

pp. 143

Author(s):

Lei Zhu ◽

Huayu Zhu ◽

Yanman Li ◽

Yong Wang ◽

Xiangbin Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Group Method ◽

Motif Length ◽

Pair Group ◽

Ssr Loci ◽

Ssr Frequency ◽

Basic And Applied Research ◽

Simple Sequence

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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Comparative genomic analysis of simple sequence repeats in three Plasmodium species

Parasitology Research ◽

10.1007/s00436-010-2086-5 ◽

2010 ◽

Vol 108 (2) ◽

pp. 451-458 ◽

Cited By ~ 5

Author(s):

Suchi Tyagi ◽

Meenu Sharma ◽

Aparup Das

Keyword(s):

Simple Sequence Repeats ◽

Plasmodium Species ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Simple Sequence

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Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

Molecules ◽

10.3390/molecules23082014 ◽

2018 ◽

Vol 23 (8) ◽

pp. 2014 ◽

Cited By ~ 7

Author(s):

Puyue Ouyang ◽

Dali Kang ◽

Xiaolu Mo ◽

Enwei Tian ◽

Yanyu Hu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genomic Analysis ◽

Comparative Genomic ◽

Polymorphism Analysis ◽

Large Set ◽

Pogostemon Cablin ◽

Geographical Regions ◽

Molecular Assisted Selection ◽

Diversity Studies

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10–40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.

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Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.138.4.290 ◽

2013 ◽

Vol 138 (4) ◽

pp. 290-296 ◽

Cited By ~ 19

Author(s):

Raúl De la Rosa ◽

Angjelina Belaj ◽

Antonio Muñoz-Mérida ◽

Oswaldo Trelles ◽

Inmaculada Ortíz-Martín ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeats ◽

Expressed Sequence Tag ◽

Paternity Testing ◽

High Level ◽

Repeated Motifs ◽

Expressed Sequence ◽

Simple Sequence ◽

Olive Breeding ◽

Genomic Project

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

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