Evidence map›Paper›PMID 39294563›Full record

ArticleBMC genomics2024

Development and validation of a 5K low-density SNP chip for Hainan cattle.

Huan Wang, Hui Wu, Wencan Zhang, Junming Jiang, Hejie Qian, Churiga Man, Hongyan Gao, Qiaoling Chen, Li Du, Si Chen and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. 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.

  1. Development and validation of a high density SNP array for indigenous Indian pigs.Mammalian genome : official journal of the International Mammalian Genome Society · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Development and Application of a 40 K Liquid Capture Chip for Beef Cattle.Animals : an open access journal from MDPI · 2025
    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

11 authors.

Huan Wang *Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Hui Wu *Xinjiang Barkol Kazakh Autonomous County Animal Husbandry Veterinary Station, Barkol Kazakh Autonomous County, Xinjiang, PR China.
Wencan ZhangHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Junming JiangHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Hejie QianHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Churiga ManHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Hongyan GaoHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Qiaoling ChenHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Li DuHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
Si ChenHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China. chensi.ruth@hotmail.com.
Fengyang WangHainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China. fywang68@163.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThis study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included.

resultsA total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65-99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways.

conclusionThe development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.

Indexed as

Oligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideAnimalsCattleFemaleGenotypeMaleReproducibility of ResultsGenotypingHainan cattleSNP chipTargeted sequencing

Identifiers

PMID39294563
PMCPMC11409743

What OpenQuestion holds

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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.