ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2014
Next generation genetic mapping of the Ligon-lintless-2 (Li₂) locus in upland cotton (Gossypium hirsutum L.).
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 41 citations in OpenAlex.
- Day-neutral flowering candidate genes identified by selection mapping in an upland cotton (Gossypium hirsutum L.) RIL population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- The brown fiber phenotype in cotton line SA-40 is linked to a missing Ty3-like retrotransposon upstream of theFrontiers in plant science · 2025Article
- A deletion/duplication in the Ligon lintless-2 locus induces siRNAs that inhibit cotton fiber cell elongation.Plant physiology · 2022Article
- Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton.Molecular genetics and genomics : MGG · 2021Article
- Elucidation of sequence polymorphism in fuzzless-seed cotton lines.Molecular genetics and genomics : MGG · 2021Article
- The loss of function of HEL, which encodes a cellulose synthase interactive protein, causes helical and vine-like growth of tomato.Horticulture research · 2020Article
- ThePlant physiology · 2020Article
- Investigation of thePlants (Basel, Switzerland) · 2020Article
- An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development.BMC plant biology · 2019Article
- Fine mapping and molecular characterization of the virescent gene vsp in Upland cotton (Gossypium hirsutum).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development.Molecular genetics and genomics : MGG · 2019Article
- The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.).BMC plant biology · 2018Article
- Genetic dissection of the fuzzless seed trait in Gossypium barbadense.Journal of experimental botany · 2018Article
- A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.BMC genomics · 2016Article
- Bulked sample analysis in genetics, genomics and crop improvement.Plant biotechnology journal · 2016Review
- The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton (Gossypium hirsutum L.) fibres.Journal of experimental botany · 2016Article
- Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum.BMC genetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageMapping-by-sequencing and novel subgenome-specific SNP markers were used to fine map the Ligon-lintless 2 ( Li 2 ) short-fiber gene in tetraploid cotton. These methodologies will accelerate gene identification in polyploid species. Next generation sequencing offers new ways to identify the genetic mechanisms that underlie mutant phenotypes. The release of a reference diploid Gossypium raimondii (D5) genome and bioinformatics tools to sort tetraploid reads into subgenomes has brought cotton genetic mapping into the genomics era. We used multiple high-throughput sequencing approaches to identify the relevant region of reference sequence and identify single nucleotide polymorphisms (SNPs) near the short-fiber mutant Ligon-lintless 2 (Li 2) gene locus. First, we performed RNAseq on 8-day post-anthesis (DPA) fiber cells from the Li 2 mutant and its wild type near isogenic line (NIL) Gossypium hirsutum cv. DP5690. We aligned sequence reads to the D5 genome, sorted the reads into A and D subgenomes with PolyCat and called SNPs with InterSNP. We then identified SNPs that would result in non-synonymous substitutions to amino acid sequences of annotated genes. This step allowed us to identify a 1-Mb region with 24 non-synonymous SNPs, representing the introgressed region that differentiates Li 2 from its NIL. Next, we sequenced total DNA from pools of F2 plants, using a super bulked segregant analysis sequencing (sBSAseq) approach. The sBSAseq predicted 82 non-synonymous SNPs among 3,494 SNPs in a 3-Mb region that includes the region identified by RNAseq. We designed subgenome-specific SNP markers and tested them in an F2 population of 1,733 individuals to construct a genetic map. Our resulting genetic interval contains only one gene, an aquaporin, which is highly expressed in wild-type fibers and is significantly under-expressed in elongating Li 2 fiber cells.
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.