Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms

Cao, Yuhao; Song, Xuemei; Shan, Huili; Jiang, Jingwei; Xiong, Pei; Wu, Jianliang; Shi, Fangxiong; Jiang, Yongqing

doi:10.3389/fgene.2020.00588

Cited by 21 publications

(9 citation statements)

References 28 publications

(26 reference statements)

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“…Here, we examined the relationship between the same population and body sizes traits. The result of data quality control can be found in the study by Cao et al (2020) .…”

Section: Resultsmentioning

confidence: 99%

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

et al. 2021

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Body size is an important indicator of growth and health in sheep. In the present study, we performed Genome-Wide Association Studies (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) associated with Hu sheep’s body size. After genotyping parental (G1) and offspring (G2) generation of the nucleus herd for meat production of Hu sheep and conducting GWAS on the body height, chest circumference, body length, tail length, and tail width of the two groups, 5 SNPs associated with body height and 4 SNPs correlated with chest circumference were identified at the chromosomal significance level. No SNPs were significantly correlated to body length, tail length, and width. Four out of the 9 SNPs were found to be located within the 4 genes. KITLG and CADM2 are considered as candidate functional genes related to body height; MCTP1 and COL4A6 are candidate functional genes related to chest circumference. The 9 SNPs found in GWAS were verified using the G3 generation of the nucleus herd for meat production. Nine products were amplified around the 9 sites, and 29 SNPs were found; 3 mutation sites, G > C mutation at 134 bp downstream of s554331, T > G mutation at 19 bp upstream of s26859.1, and A > G mutation at 81 bp downstream of s26859.1, were significantly correlated to the body height. Dual-luciferase reporter gene experiments showed that the 3 SNPs could significantly impact dual-luciferase and gene transcription activity.

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“…Here, we examined the relationship between the same population and body sizes traits. The result of data quality control can be found in the study by Cao et al (2020) .…”

Section: Resultsmentioning

confidence: 99%

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

et al. 2021

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“…Integrins are a family of heterodimeric cell-surface adhesion receptors that affect cell-matrix interaction. Some integrins encoding genes, including integrin alpha-2 ( ITGA2 ) and integrin alpha-11 ( ITGA11 ), have been proven to regulate the BW trait of swine and sheep, respectively [ 51 , 52 ]. In this study, integrin alpha-5 ( ITGA5 ) was speculated to be associated with bovine BW trait.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Based on Random Regression Model Reveals Candidate Genes Associated with Longitudinal Data in Chinese Simmental Beef Cattle

Duan

et al. 2021

Animals

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Body weight (BW) is an important longitudinal trait that directly described the growth gain of bovine in production. However, previous genome-wide association study (GWAS) mainly focused on the single-record traits, with less attention paid to longitudinal traits. Compared with traditional GWAS models, the association studies based on the random regression model (GWAS-RRM) have better performance in the control of the false positive rate through considering time-stage effects. In this study, the BW trait data were collected from 808 Chinese Simmental beef cattle aged 0, 6, 12, and 18 months, then we performed a GWAS-RRM to fit the time-varied SNP effect. The results showed a total of 37 significant SNPs were associated with BW. Gene functional annotation and enrichment analysis indicated FGF4, ANGPT4, PLA2G4A, and ITGA5 were promising candidate genes for BW. Moreover, these genes were significantly enriched in the signaling transduction pathway and lipid metabolism. These findings will provide prior molecular information for bovine gene-based selection, as well as facilitate the extensive application of GWAS-RRM in domestic animals.

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“…In meat production, the body weight (BW) of sheep is a key economic trail [ 35 ]. As pointed out by Cao et al [ 36 ], BWs measured at birth and other life stages are major indicators for productivity, health, and preventive management. In genetics, some SNPs are associated with BW, and the identification of these SNPs can improve the efficiency of sheep breeding programs.…”

Section: Methodsmentioning

confidence: 99%

“…Here, to investigate the effectiveness of the proposed method, we conduct experiments on the dataset of three measures of body weights of 240 Hu sheep, including birth weight, six-month weight, and weaning weight. The dataset is available in the GEO accession number GSE152717 [ 36 ]. We exclude some genes containing missing values.…”

Section: Methodsmentioning

confidence: 99%

A Modified Memetic Algorithm with an Application to Gene Selection in a Sheep Body Weight Study

Miao

Cai

et al. 2022

Animals

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Selecting the minimal best subset out of a huge number of factors for influencing the response is a fundamental and very challenging NP-hard problem because the presence of many redundant genes results in over-fitting easily while missing an important gene can more detrimental impact on predictions, and computation is prohibitive for exhaust search. We propose a modified memetic algorithm (MA) based on an improved splicing method to overcome the problems in the traditional genetic algorithm exploitation capability and dimension reduction in the predictor variables. The new algorithm accelerates the search in identifying the minimal best subset of genes by incorporating it into the new local search operator and hence improving the splicing method. The improvement is also due to another two novel aspects: (a) updating subsets of genes iteratively until the no more reduction in the loss function by splicing and increasing the probability of selecting the true subsets of genes; and (b) introducing add and del operators based on backward sacrifice into the splicing method to limit the size of gene subsets. Additionally, according to the experimental results, our proposed optimizer can obtain a better minimal subset of genes with a few iterations, compared with all considered algorithms. Moreover, the mutation operator is replaced by it to enhance exploitation capability and initial individuals are improved by it to enhance efficiency of search. A dataset of the body weight of Hu sheep was used to evaluate the superiority of the modified MA against the genetic algorithm. According to our experimental results, our proposed optimizer can obtain a better minimal subset of genes with a few iterations, compared with all considered algorithms including the most advanced adaptive best-subset selection algorithm.

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Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms

Cited by 21 publications

References 28 publications

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

Genome-Wide Association Study Based on Random Regression Model Reveals Candidate Genes Associated with Longitudinal Data in Chinese Simmental Beef Cattle

A Modified Memetic Algorithm with an Application to Gene Selection in a Sheep Body Weight Study

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