Application of ISSR in Genetic Relationship Analysis of Sorghum Species

2008 ◽  
Vol 34 (8) ◽  
pp. 1480-1483 ◽  
Author(s):  
Xue-En FANG
Keyword(s):  
Genetic Relationship ◽  
Relationship Analysis

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Liping Guan ◽  
Ke Cao ◽  
Yong Li ◽  
Jian Guo ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

scholarly journals Genetic Relationships among 11 Nonheading Chinese Cabbage Accessions and the SCAR Marker Specific for ‘Suzhouqing’

HortScience ◽  
2018 ◽  
Vol 53 (9) ◽  
pp. 1288-1293
Author(s):  
Xuelin Shen ◽  
Yanmei Zhang ◽  
Zhao Lei ◽  
Yibo Lin ◽  
Minxu Cao ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Genetic Relationship ◽  
Yangtze River ◽  
Scar Marker ◽  
Yangtze River Delta ◽  
River Delta ◽  
The Other ◽  
The Yangtze River ◽  
Relationship Analysis ◽  
The Yangtze River Delta

‘Suzhouqing’ is a unique landrace of nonheading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] with a long history of cultivation in Suzhou of Jiangsu Province, China. However, transitional and overlapped morphologic traits make it difficult to authenticate this accession from other nonheading Chinese cabbages. Genetic relationship between ‘Suzhouqing’ and the related 10 popular accessions in the Yangtze River Delta were analyzed using two well-studied single-copy nuclear genes—ARGONAUTES 7 (AGO7) and BcMF15; the molecular identification of ‘Suzhouqing’ was determined based on the intersimple sequence repeat–sequence-characterized amplified region (ISSR-SCAR) marker. The results indicated that ‘Suzhouqing’ could be identified specifically from the other 10 accessions based on 21 specific nucleotide variations of the AGO7 gene. Sequence variations show a strong correlation with leaf morphology, suggestive of partial causal links between the two. Genetic relationship analysis showed that five accessions with close geographic locations had a very close genetic relationship, whereas the genetic relationship of the other five accessions was related to their morphologic similarity. One exception, ‘AJH’, might undergo a special evolutionary process. Furthermore, ISSR-880 was screened as the specific primer to identify accession ‘Suzhouqing’, and a specific discrimination ISSR-SCAR marker was explored, which amplified no target band in any other accessions. The development of molecular markers for the specific identification of ‘Suzhouqing’ in 11 popular accessions in the Yangtze River Delta could provide a theoretical basis for the protective identification of other agricultural crops.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

2019 ◽  
Author(s):  
Liping Guan ◽  
ke Cao ◽  
yong Li ◽  
jian guo ◽  
qiang xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results: In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8,386~12,298 structure variants (SVs), 2,111~2,581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions: The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

2019 ◽  
Author(s):  
Liping Guan ◽  
ke Cao ◽  
yong Li ◽  
jian guo ◽  
qiang xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Abstract Background: Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results: In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8,386~12,298 structure variants (SVs), 2,111~2,581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions: The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Molecular characterization and genetic relationship of marigolds (Tagetes spp.) based on simple sequence repeat markers

2014 ◽  
Vol 12 (3) ◽  
pp. 317-322 ◽  
Author(s):  
Sukhuman Whankaew ◽  
Supaporn Hasthanasombut ◽  
Ratchadaporn Thaikert ◽  
Piengtawan Tappiban ◽  
Duncan R. Smith ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Polymorphic Information Content ◽  
Resolving Power ◽  
Individual Identification ◽  
Tagetes Patula ◽  
Species Classification ◽  
Dna Library ◽  
Relationship Analysis ◽  
Relationship Of ◽  
Simple Sequence

In this study, simple sequence repeats (SSRs) specific to marigold were developed using the inter-SSR technique and a SSR-enriched genomic DNA library. In addition, SSRs derived from sunflower (Helianthus annuus) were also tested for transferability to marigold. In total, 38 polymorphic markers with 112 observed alleles were identified in 20 African marigolds (Tagetes erecta L.) consisting of 14 commercial varieties and six Thai landraces, and six French marigolds (Tagetes patula L.). The number of alleles per locus ranged from 2 to 7. The averages of expected and observed heterozygosities were 0.48 and 0.32, respectively. Polymorphic information content values ranged from 0.10 to 0.71, and resolving power (Rp) values ranged from 0.23 to 2.77. The SSRs were successfully applied to the differentiation of the 26 marigold samples into clusters of African commercial varieties, Thai landraces and French marigold. The genetic relationship analysis revealed that the African commercial varieties were more closely related to the Thai landraces than to the French marigold. The results of the study indicate that the SSRs developed are effective for genetic diversity analysis, species classification and individual identification.

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