ArticleBMC genomics2012
Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb.Database : the journal of biological databases and curation · 2024Article
- The art of tartness: the genetics of organic acid content in fresh fruits.Horticulture research · 2024Article
- Genetic Structure and Biodiversity in WildLife (Basel, Switzerland) · 2023Article
- Allelic variation of MdMYB123 controls malic acid content by regulating MdMa1 and MdMa11 expression in apple.Plant physiology · 2023Article
- Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (3 Biotech · 2023Article
- Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB.Frontiers in plant science · 2023Article
- Article
- Construction of a high-density bin-map and identification of fruit quality-related quantitative trait loci and functional genes in pear.Horticulture research · 2022Article
- Construction of a high-density genetic linkage map and QTL analysis of morphological traits in an F1Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.).Scientific reports · 2021Article
- A candidate PpRPH gene of the D locus controlling fruit acidity in peach.Plant molecular biology · 2021Article
- Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gramineae/non-Gramineae species.Journal of applied genetics · 2020Article
- Identification of two QTLs associated with high fruit acidity in apple using pooled genome sequencing analysis.Horticulture research · 2020Article
- A Ma10 gene encoding P-type ATPase is involved in fruit organic acid accumulation in apple.Plant biotechnology journal · 2019Article
- Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Frontiers in plant science · 2019Article
- Apple whole genome sequences: recent advances and new prospects.Horticulture research · 2019Review
- Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection.Breeding science · 2018Article
- Article
- Identification of massive molecular markers inPlant diversity · 2017Article
- First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi.PloS one · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundApple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome.
resultsA total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation.
conclusionsThis study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.