Evidence map›Paper›PMID 37621321›Full record

Article3 Biotech2023

Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India.

Thiruvothur Venkatesan Raja, Rani Alex, Umesh Singh, Sushil Kumar, Achintya Kumar Das, Gyanendra Sengar, Amit Kumar Singh, Abhirupa Ghosh, Sudipto Saha, Abhijit Mitra

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PubMed Full text at PMC Publisher
In one paragraph

Article in 3 Biotech, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 29% of its field
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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Article
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

10 authors at 4 institutions in 1 country.

Thiruvothur Venkatesan Raja *Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.
Rani Alex *National Dairy Research Institute, Karnal, Haryana India.
Umesh SinghMolecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.
Sushil KumarMolecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.
Achintya Kumar DasMolecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.
Gyanendra SengarNational Research Centre on Pigs, Rani (Near Airport), Guwahati, Assam 781 131 India.
Amit Kumar SinghMolecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.
Abhirupa GhoshDivision of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India.
Sudipto SahaDivision of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India.
Abhijit MitraMolecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India.ORCID 0000-0003-4011-2579
Central Institute for Research on Cattle · INBose Institute · INICAR-National Research Centre on Pig · INNational Dairy Research Institute · IN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Frieswal™ is a crossbred cattle evolved by ICAR-Central Institute for Research on Cattle utilizing more than 15,000 cattle maintained at more than 37 military farms spread all over the agro-climatic regions of the country. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs. The results of variant calling revealed 1,487,851 SNPs and 128,175 INDELs at a read depth of 10. A total of 3,775,079 effects were identified, and majority (66.41%) of the effects were in the intron region of the genome followed by intergenic (21.87%). Majority (99.18%) of the variants had the modifier effect. The results revealed a higher magnitude of transitions as compared to the transversion. The classification of SNPs by functional class revealed a majority of missense (43%) and silent (56%) effects. Out of 26,278 genes identified, 1841 SNPs were annotated in 207 candidate genes responsible for various milk production and reproduction traits. The observed heterozygosity was 0.2804 against the expected heterozygosity value of 0.2978. The overall average inbreeding coefficient ( Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03701-0.

Indexed as

ddRADFrieswal cattleGenetic diversityPathway analysisSNP annotationSNP identification

Identifiers

PMID37621321
PMCPMC10444711
OpenAlexW4386073800

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.