Validation of PDE9A Gene Identified in GWAS Showing Strong Association with Milk Production Traits in Chinese Holstein

Yang, Shaohua; Bi, X. J.; Xie, Yi; Li, Cong; Zhang, Shengli; Zhang, Qin; Sun, Dan

doi:10.3390/ijms161125976

Cited by 19 publications

(12 citation statements)

References 36 publications

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“…Previously, SLC37A1 was associated with MY, FP, and PP (Kemper et al, 2016;Raven et al, 2016;Pausch et al, 2017), supporting our results for MY, and with other milk components such as α S1 -CN and α-LA (Sanchez et al, 2017), phosphorus concentration , and FA composition (Olsen et al, 2017). The PDE9A gene is a cGMP-specific phosphodiesterase also highly expressed in mammary gland and previously associated with milk production traits (Yang et al, 2015).…”

Section: Resultssupporting

confidence: 88%

Genome-wide association study for milk production traits in a Brazilian Holstein population

Iung

Petrini

Ramírez-Díaz

et al. 2019

Journal of Dairy Science

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Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.

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Section: Resultssupporting

confidence: 88%

Genome-wide association study for milk production traits in a Brazilian Holstein population

Iung

Petrini

Ramírez-Díaz

et al. 2019

Journal of Dairy Science

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“…This top cluster is directly involved in mammary gland development, regulation of response to a stimulus, gland development, epithelium development, tissue development, animal organ development, system development and multicellular organism development. This was partly in agreement to works reported by Yang et al [ 43 ] on QTL associated with follicle stimulating hormone production in Chinese Holstein cattle.…”

Section: Discussionsupporting

confidence: 93%

A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds

et al. 2018

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Using GWAS to identify candidate genes associated with cattle morphology traits at a functional level is challenging. The main difficulty of identifying candidate genes and gene interactions associated with such complex traits is the long-range linkage disequilibrium (LD) phenomenon reported widely in dairy cattle. Systems biology approaches, such as combining the Association Weight Matrix (AWM) with a Partial Correlation in an Information Theory (PCIT) algorithm, can assist in overcoming this LD. Used in a multi-breed and multi-phenotype context, the AWM-PCIT could aid in identifying udder traits candidate genes and gene networks with regulatory and functional significance. This study aims to use the AWM-PCIT algorithm as a post-GWAS analysis tool with the goal of identifying candidate genes underlying udder morphology. We used data from 78,440 dairy cows from three breeds and with own phenotypes for five udder morphology traits, five production traits, somatic cell score and clinical mastitis. Cows were genotyped with medium (50k) or low-density (7 to 10k) chips and imputed to 50k. We performed a within breed and trait GWAS. The GWAS showed 9,830 significant SNP across the genome (p < 0.05). Five thousand and ten SNP did not map a gene, and 4,820 SNP were within 10-kb of a gene. After accounting for 1SNP:1gene, 3,651 SNP were within 10-kb of a gene (set1), and 2,673 significant SNP were further than 10-kb of a gene (set2). The two SNP sets formed 6,324 SNP matrix, which was fitted in an AWM-PCIT considering udder depth/ development as the key trait resulting in 1,013 genes associated with udder morphology, mastitis and production phenotypes. The AWM-PCIT detected ten potential candidate genes for udder related traits: ESR1, FGF2, FGFR2, GLI2, IQGAP3, PGR, PRLR, RREB1, BTRC, and TGFBR2.

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“…A QTL for percentage protein was found at the orthologous bovine position of our QTL on the CHI 1 in Chinese Holstein cows 49 . Later, 11 more SNPs were identified on the phosphodiesterase 9A ( PDE9A ) gene, located in the QTL confidence interval, associated with the different milk production traits 50 . This gene is involved in the activation of the cGMP dependent pathway and is therefore a strong candidate for our QTL for PC on CHI1.…”

Section: Discussionmentioning

confidence: 99%

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

Martin

Palhière

Maroteau

et al. 2017

Sci Rep

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The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.

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Validation of PDE9A Gene Identified in GWAS Showing Strong Association with Milk Production Traits in Chinese Holstein

Cited by 19 publications

References 36 publications

Genome-wide association study for milk production traits in a Brazilian Holstein population

Genome-wide association study for milk production traits in a Brazilian Holstein population

A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

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