ELF3 and FOXA2 Loci, Probable Putative Trans-QTL for Abnormal Sperm Percentage in Cattle: An In-silico Analysis

1
ELF3 and FOXA2 Loci, Probable Putative Trans-QTL
for Abnormal Sperm Percentage in Cattle An
In-silico Analysis

• Suneel Kumar Onteru, Varij Nayan Dheer Singh
• Animal Biochemistry Division
• National Dairy Research Institute
• Karnal-132001

2
Outline

• A Goal for Animal Genomics
• Need for In-Silico Trans QTL Identification
• Methodology
• Results
• Conclusion Future Directions

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A Goal of Farm Animal Genomics

• To select the farm animals for better Semen
  quality traits by genetic markers
• Requirements for the selection of animals
• Variability in reproductive traits (Different
  fertility rate)
• Heritabilities (0.15-0.301)
• QTLs or chromosomal regions that explain the
  variation in phenotypes
• Breeding strategies
• Evaluation of selection response

Low to moderate heritability traits can be
improved by marker assisted selection
1. Druet et al., 2009
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Identified QTL for Semen Quality Traits in Cattle
Trait No. of QTL Chromosome
Percentage of abnormal sperm (ABSP) 3 20, 21, 27
Percentage of live sperm after osmotic stress 1 23
Percentage of livesperm after thawing 2 23, 27
Semen Volume 4 4, 11, 15, 22
Sperm acrosome integrity rate 1 2
Sperm average path velocity 1 25
Sperm counts 3 4,11, 27
Sperm motility 6 4,7, 11, 27
Need to identify Further possible QTL
Functional annotation of genes in the QTL
A total of only 21 QTL in AnimalQTLdb
www.animalgenome.org/cgi-bin/QTLdb/BT/summary
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Methodology In-Silico Analysis for Cattle ABSP
Extraction of chromosomal coordinates for the QTL
from Cattle tracks from UMD3.1 Genome
Extraction of annotated genes from Ensembl
Cattle UMD 3.1 genome
Reported QTL (n 3) from AnimalQTLdb
NO
Get gene name if gt 80 homology
NCBI BLAST for the Protein/ nucleotide sequence
Gene names known
YES
Total Gene List (n 134)
Single Site Analysis (SSA) by oPPOSUM 3.0 for
common orthologous transcription factors (oTF)
based on human genome (Z score gt 10 Fisher score
gt 7)
Functional annotation by Panther 9.0 based on
cattle database
Putative regulative (Trans) QTL based on
significant oTF gene co-ordinates in cattle
genome
ABSP Percentage of Abnormal Sperm
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Results Molecular Functions of Genes at reported
QTL for Cattle ABSP
1
36.6
32.7
5.0
6.9
No. of Genes
6.9
5.0
4.0
6.9
Category
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Results Protein Class of Genes at reported QTL
for Cattle ABSP
1.0
4.0
2.0
3.0
5.0
8.9
3.0
14.9
2.0
1.0
4.0
15.8
No. of Genes
3.0
2.0
7.9
7.9
8.9
1.0
6.9
2.0
4.0
1.0
Category
5.0
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Results Biological Functions of Genes at
Reported QTL for Cattle ABSP
3.0
5.9
16.8
4.0
41.6
13.9
11.9
No. of Genes
13.9
52.50
8.9
2.0
9.9
Category
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Results Cellular Locations of Genes at reported
QTL for Cattle ABSP
7.9
3.0
4.0
No. of Genes
2.0
2.0
4.0
Category
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Results Pathway Analysis of Genes at reported
QTL for Cattle ABSP
1.0
2.0
1.0
4.0
No. of Genes
1.0
Category
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Results Orthologous Transcription Factors for
Genes at Reported QTL for Cattle ABSP
A total of 178 TF were predicted to be regulating
at least 2 genes within 5000 bp up- or
down-stream of a gene.
TF Target gene hits Target gene non hits Background gene hits Background gene non hits Target TFBS hits Target TFBS nucleotide rate Background TFBS hits Background TFBS nucleotide rate Z-Score Fisher Score
ELF3 66 33 12278 12474 246 0.0186 40428 0.0146 13.93 7.684
FOXA2 45 54 6534 18218 94 0.00931 14127 0.0067 13.42 10.23
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Results Functional Role of ELF3
Biological Function
Molecular Function
Cellular Location

• Blastocyst Development
• Transcription From RNA Polymerase II Promoter
• Inflammatory Response
• Multicellular Organismal Development
• Epidermis Development
• Extracellular Matrix Organization
• Epithelial Cell Differentiation
• Negative Regulation Of Transcription,
  DNA-templated
• Positive Regulation Of Transcription,
  DNA-templated
• Positive Regulation Of Transcription From RNA
  Polymerase II Promoter
• Mammary Gland Involution

• Sequence-specific DNA Binding Transcription
  Factor Activity
• Transcription Coactivator Activity
• Protein Binding
• Sequence-specific DNA Binding

• Nucleus
• Nucleolus
• Cytoplasm
• Golgi Apparatus

First in-slilico report for possible role of ELF3
in abnormal sperm percentage in cattle
http//severus.dbmi.pitt.edu/wiki-pi/index.php/gen
e/view/3170
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Results Functional Role of FOXA2
Cellular Location
Molecular Function
Biological Function

• Nucleus
• Transcription Factor Complex
• Cytoplasm

• RNA Polymerase II Core Promoter Proximal Region
  Sequence-specific DNA Binding
• DNA Binding
• Double-stranded DNA Binding
• Sequence-specific DNA Binding Transcription
  Factor Activity
• RNA Polymerase II Distal Enhancer
  Sequence-specific DNA Binding Transcription
  Factor Activity
• Transcription Factor Binding
• DNA Binding, Bending
• Protein Domain Specific Binding
• Transcription Regulatory Region DNA Binding

• In Utero Embryonic Development
• Ectoderm Formation
• Regulation Of Transcription From RNA Polymerase
  II Promoter
• Pattern Specification Process
• Adult Locomotory Behavior
• Regulation Of Blood Coagulation
• Glucose Homeostasis

First in-slilico report for possible role of
FOXA2 in abnormal sperm percentage in cattle
http//severus.dbmi.pitt.edu/wiki-pi/index.php/gen
e/view/3170
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Results Orthologous Transcription Factors for
Genes at Reported QTL for Cattle ABSP
Earlier reported QTL for ABSP were on Chr 20, 21
and 27
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Conclusions

• Many genes in the reported QTL for ABSP are
  involved in cellular (42), metabolic (53),
  binding (37) and catalytic (33) activities.

• Pathway analysis found that 25 genes are involved
  in 21 pathways with a major contribution of GnRH
  pathway members (follistatin, PTGER4, ISL1 and
  MAP3K1)

• ELF3 (Chr 16 at 70.8 Mb) and FOXA2 (Chr 13 at
  41.9 Mb) loci could be probable putative trans
  QTL for abnormal sperm percentage in cattle by
  In-silico analysis.

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Future Directions
Association studies have to be conducted for
abnormal sperm percentage by using the genetic
markers located at ELF3 and FOXA2 gene loci to
confirm their possible association with this ABSP
in cattle.
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• Thank you!!