Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

G. A. Oliveira Júnior; B. C. Perez; J. B. Cole; M. H.A. Santana; J. Silveira; G. Mazzoni; R. V. Ventura; M. L. Santana; H. N. Kadarmideen; D. J. Garrick; J. B.S. Ferraz

doi:10.2527/jas2017.1752

Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

G. A. Oliveira Júnior^*, B. C. Perez, J. B. Cole, M. H.A. Santana, J. Silveira, G. Mazzoni, R. V. Ventura, M. L. Santana, H. N. Kadarmideen, D. J. Garrick, J. B.S. Ferraz

^*Corresponding author for this work

16 Citations (Scopus)

Abstract

Zebu animals (Bos indicus) are known to take longer to reach puberty compared with taurine animals (Bos taurus), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being −0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant (P < 0.05) terms associated with HP—“Munc18 Proteins,” “Fucose,” and “Hemoglobins”—and with NF—“Cathepsin B,” “Receptors, Neuropeptide,” and “Palmitic Acid.” This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

Original language	English
Journal	Journal of Animal Science
Volume	95
Issue number	11
Pages (from-to)	4796-4812
Number of pages	17
ISSN	0021-8812
DOIs	https://doi.org/10.2527/jas2017.1752
Publication status	Published - Nov 2017

Keywords

Beef cattle
Enrichment analysis
Genomewide association study
Genomics
Linkage disequilibrium
Medical subject headings terms

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Oliveira Júnior, G. A., Perez, B. C., Cole, J. B., Santana, M. H. A., Silveira, J., Mazzoni, G., Ventura, R. V., Santana, M. L., Kadarmideen, H. N., Garrick, D. J., & Ferraz, J. B. S. (2017). Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. Journal of Animal Science, 95(11), 4796-4812. https://doi.org/10.2527/jas2017.1752

Oliveira Júnior, GA, Perez, BC, Cole, JB, Santana, MHA, Silveira, J, Mazzoni, G, Ventura, RV, Santana, ML, Kadarmideen, HN, Garrick, DJ & Ferraz, JBS 2017, 'Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers', Journal of Animal Science, vol. 95, no. 11, pp. 4796-4812. https://doi.org/10.2527/jas2017.1752

@article{6e375a98ecf442c6a7d671fbf2700ac8,

title = "Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers",

abstract = "Zebu animals (Bos indicus) are known to take longer to reach puberty compared with taurine animals (Bos taurus), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being −0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant (P < 0.05) terms associated with HP—“Munc18 Proteins,” “Fucose,” and “Hemoglobins”—and with NF—“Cathepsin B,” “Receptors, Neuropeptide,” and “Palmitic Acid.” This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.",

keywords = "Beef cattle, Enrichment analysis, Genomewide association study, Genomics, Linkage disequilibrium, Medical subject headings terms",

author = "{Oliveira J{\'u}nior}, {G. A.} and Perez, {B. C.} and Cole, {J. B.} and Santana, {M. H.A.} and J. Silveira and G. Mazzoni and Ventura, {R. V.} and Santana, {M. L.} and Kadarmideen, {H. N.} and Garrick, {D. J.} and Ferraz, {J. B.S.}",

year = "2017",

month = nov,

doi = "10.2527/jas2017.1752",

language = "English",

volume = "95",

pages = "4796--4812",

journal = "Journal of Animal Science",

issn = "0021-8812",

publisher = "American Society of Animal Science",

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T1 - Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

AU - Oliveira Júnior, G. A.

AU - Perez, B. C.

AU - Cole, J. B.

AU - Santana, M. H.A.

AU - Silveira, J.

AU - Mazzoni, G.

AU - Ventura, R. V.

AU - Santana, M. L.

AU - Kadarmideen, H. N.

AU - Garrick, D. J.

AU - Ferraz, J. B.S.

PY - 2017/11

Y1 - 2017/11

N2 - Zebu animals (Bos indicus) are known to take longer to reach puberty compared with taurine animals (Bos taurus), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being −0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant (P < 0.05) terms associated with HP—“Munc18 Proteins,” “Fucose,” and “Hemoglobins”—and with NF—“Cathepsin B,” “Receptors, Neuropeptide,” and “Palmitic Acid.” This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

AB - Zebu animals (Bos indicus) are known to take longer to reach puberty compared with taurine animals (Bos taurus), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being −0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant (P < 0.05) terms associated with HP—“Munc18 Proteins,” “Fucose,” and “Hemoglobins”—and with NF—“Cathepsin B,” “Receptors, Neuropeptide,” and “Palmitic Acid.” This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

KW - Beef cattle

KW - Enrichment analysis

KW - Genomewide association study

KW - Genomics

KW - Linkage disequilibrium

KW - Medical subject headings terms

U2 - 10.2527/jas2017.1752

DO - 10.2527/jas2017.1752

M3 - Journal article

C2 - 29293733

AN - SCOPUS:85033803263

SN - 0021-8812

VL - 95

SP - 4796

EP - 4812

JO - Journal of Animal Science

JF - Journal of Animal Science

IS - 11

ER -

Genomic study and medical subject headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

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Keywords

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