Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

Zhou, Juefei; Liu, Liyuan; Chen, Chunpeng James; Zhang, Menghua; Lü, Xin; Zhang, Zhiwu; Huang, Xixia; Shi, Yiting

doi:10.1186/s12864-019-6224-x

Cited by 37 publications

(21 citation statements)

References 61 publications

(65 reference statements)

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“…However, the heritability results were similar to those of ssGBLUP calculated using the REML and Bayesian methods in this study. The estimated heritability of MFY and MPY was 0.30 (0.013) and 0.20 (0.011), respectively, which were significantly lower than the results estimated using the REML and Bayesian methods for different genetic relationship matrices of the multitrait model in this study [ 35 ]. In addition, the heritability of somatic scoring was lower than that of the American and Italian brown cattle populations (0.12 [ 36 ] and 0.14 [ 37 ], respectively).…”

Section: Discussioncontrasting

confidence: 76%

Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

Zhang

Luo

Liu

et al. 2022

Animals

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One-step genomic selection is a method for improving the reliability of the breeding value estimation. This study aimed to compare the reliability of pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP), single-trait and multitrait models, and the restricted maximum likelihood (REML) and Bayesian methods. Data were collected from the production performance records of 2207 Xinjiang Brown cattle in Xinjiang from 1983 to 2018. A cross test was designed to calculate the genetic parameters and reliability of the breeding value of 305 daily milk yield (305 dMY), milk fat yield (MFY), milk protein yield (MPY), and somatic cell score (SCS) of Xinjiang Brown cattle. The heritability of 305 dMY, MFY, MPY, and SCS estimated using the REML and Bayesian multitrait models was approximately 0.39 (0.02), 0.40 (0.03), 0.49 (0.02), and 0.07 (0.02), respectively. The heritability and estimated breeding value (EBV) and the reliability of milk production traits of these cattle calculated based on PBLUP and ssGBLUP using the multitrait model REML and Bayesian methods were higher than those of the single-trait model REML method; the ssGBLUP method was significantly better than the PBLUP method. The reliability of the estimated breeding value can be improved from 0.9% to 3.6%, and the reliability of the genomic estimated breeding value (GEBV) for the genotyped population can reach 83%. Therefore, the genetic evaluation of the multitrait model is better than that of the single-trait model. Thus, genomic selection can be applied to small population varieties such as Xinjiang Brown cattle, in improving the reliability of the genomic estimated breeding value.

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Section: Discussioncontrasting

confidence: 76%

Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

Zhang

Luo

Liu

et al. 2022

Animals

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“…Interestingly, the four genes were previously linked to FAT [62,78,79] or other milk components [80], confirming its close relationship with milk production traits. For instance, γ-aminobutyric acid type A genes (GABRG1 and GABRA2), which contributes to γ-aminobutyric acid (GABA) chloride ion channel activity and participates in GABA-A receptor activity, were previously associated with milk production traits in Holstein and Xinjiang Brown cattle [81,82].…”

Section: Candidate Genes For Milk Yieldmentioning

confidence: 99%

Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Pedrosa

Schenkel

Chen

et al. 2021

Genes

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Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

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“…Multiple algorithms have been developed to boost both the computational efficiency and the statistical power of MLM methods ( Kang et al, 2008 ; Zhou and Stephens, 2012 ). A recently developed GWAS model, named fixed and random model Circulating Probability Unification (FarmCPU) ( Liu et al, 2016 ), has been widely used for detecting QTLs for economically important traits ( Zhou J. et al, 2019 ; Tang et al, 2019 ; Wang et al, 2019 ). FarmCPU splits the MLM into separated fixed-effect and random-effect models and iteratively uses the two models to remove confounding, prevents model overfitting, and controls false positives simultaneously for an efficient computation ( Liu et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

et al. 2021

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The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.

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Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle

Cited by 37 publications

References 61 publications

Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

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