Evidence map›Paper›PMID 28128280›Full record

ArticleScientific reports2017

Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs.

Umesh K Reddy, Padma Nimmakayala, Venkata Lakshmi Abburi, C V C M Reddy, Thangasamy Saminathan, Richard G Percy, John Z Yu, James Frelichowski, Joshua A Udall, Justin T Page and 3 more

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In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Umesh K ReddyGus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
Padma NimmakayalaGus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
Venkata Lakshmi AbburiGus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
C V C M ReddyGus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
Thangasamy SaminathanGus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
Richard G PercyUSDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
John Z YuUSDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
James FrelichowskiUSDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
Joshua A UdallWIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA.
Justin T PageWIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA.
Dong ZhangPlant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.
Tariq ShehzadPlant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.
Andrew H PatersonPlant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.

Indexed as

DomesticationGenetics, PopulationAllelesChromosome MappingGenetic VariationGenome, PlantGossypiumHaplotypesPhylogenyPolymorphism, Single NucleotideTetraploidy

Identifiers

PMID28128280
PMCPMC5269598

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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.