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Attention Score in Context
| Title |
Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses
|
|---|---|
| Published in |
BMC Genomics, April 2015
|
| DOI | 10.1186/s12864-015-1534-0 |
| Pubmed ID | |
| Authors |
Xiaoming Song, Tingting Ge, Ying Li, Xilin Hou |
| Abstract |
Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC. A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future. This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 50% |
| Scientists | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 32 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 6 | 19% |
| Student > Ph. D. Student | 4 | 13% |
| Student > Master | 4 | 13% |
| Professor > Associate Professor | 2 | 6% |
| Other | 2 | 6% |
| Other | 4 | 13% |
| Unknown | 10 | 31% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 17 | 53% |
| Biochemistry, Genetics and Molecular Biology | 2 | 6% |
| Unspecified | 1 | 3% |
| Computer Science | 1 | 3% |
| Earth and Planetary Sciences | 1 | 3% |
| Other | 0 | 0% |
| Unknown | 10 | 31% |
Attention Score in Context
This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 April 2015.
All research outputs
#14,807,732
of 22,800,560 outputs
Outputs from BMC Genomics
#6,135
of 10,649 outputs
Outputs of similar age
#148,474
of 264,968 outputs
Outputs of similar age from BMC Genomics
#166
of 267 outputs
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So far Altmetric has tracked 10,649 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 37th percentile – i.e., 37% of its peers scored the same or lower than it.
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We're also able to compare this research output to 267 others from the same source and published within six weeks on either side of this one. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.