Source: TEXAS A&M UNIVERSITY submitted to
HORN GROWTH IN CATTLE: GENOMIC STRUCTURE, EXPRESSION AND REGULATION OF THE POLL LOCUS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0193658
Grant No.
2003-35205-12825
Project No.
TEX08931
Proposal No.
2002-03468
Multistate No.
(N/A)
Program Code
43.1
Project Start Date
Nov 15, 2002
Project End Date
Nov 14, 2005
Grant Year
2003
Project Director
Gill, C. A.
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
ANIMAL SCIENCE
Non Technical Summary
Bruises cost the US fed beef industry more than $22 million every year. Bruising on carcasses is one of the top ten concerns of producers and packers. A major cause of bruising is horns. One in five cattle shipped to packing plants still have horns. Horn growth takes place primarily after birth and the absence of horns is due to single gene acting as a dominant inhibitor of horn growth. The POLL locus has been mapped to bovine chromosome one, but it is not known how the gene affects the developmental pathway for horns. Our long-term goals are to identify transcription factors affecting horn development, understand how they function to control broad genetic programs, and develop novel strategies to improve cattle management in terms of dehorning. The overall objective of this application is to identify a strong candidate for the bovine POLL locus and to establish the genomic organization of POLL. We expect to identify a genomic rearrangement (micro-deletion or insertion) in polled cattle that would disrupt the function of the POLL gene. The rationale that underlies the proposed research is that understanding horn development in cattle is expected to lead to new knowledge of gene regulation in bone development. These results will be significant, because they are expected to provide new markers for POLL that can be applied by producers to select against horns.
Animal Health Component
100%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310104025%
3033310108025%
3043310104025%
3043310108025%
Knowledge Area
303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3310 - Beef cattle, live animal;

Field Of Science
1080 - Genetics; 1040 - Molecular biology;
Goals / Objectives
Our long-term goals are to identify transcription factors affecting horn development, understand how they function to control broad genetic programs, and develop novel strategies (marker-assisted selection or therapeutics) to improve cattle management in terms of dehorning. The overall objective of this application, which is the next step toward achieving our long-term goal, is to identify a strong candidate for the bovine POLL locus. Our research objective is to establish the genomic organization of the POLL locus. We expect to identify a genomic rearrangement (micro-deletion or insertion) in polled cattle that would disrupt the function of the POLL gene.
Project Methods
We have identified three transcription factors that are positional candidates for POLL. We expect one of these three genes or their associated regulatory elements to contain a mutation that explains the dominant polled condition. The goal for this research objective is to identify a genomic rearrangement in polled cattle versus horned cattle with inheritance consistent to explain polledness. The approach will be to build a contig of Angus and Longhorn BACs for the critical interval, in conjunction with targeted sequencing. Overlapping Angus and Longhorn BACs will be identified by PCR-based screening with primers designed from BAC end sequences. The physical order of the BAC ends will be verified using a 12000rad bovine-hamster whole-genome radiation hybrid panel. BACs will be sized, fingerprinted and analyzed with FPC software to confirm and specify overlaps. New microsatellite markers will also be developed for these BACs. Haplotype and linkage disequilibrium analyses of genotypes will be performed to refine the critical region. In addition to standard methods, we will use our novel approach for analyzing categorical Mendelian traits. This novel method will be extended to produce multipoint likelihoods and power will be compared to standard methods via simulation. We will also sequence the three transcription factors that are positional candidates for POLL. Up to 20kb of regulatory sequence will be evaluated. PCR products generated from Angus and Longhorn BAC DNA will be the template for sequencing. Detected differences in genomic sequence will be further investigated by sequencing in a breed panel. Sequences will be based called, trimmed and automatically ported to our bioinformatics pipeline for sequence similarity searches on a SGI-ORIGIN 3800 48 processor supercomputer.

Progress 11/15/02 to 11/14/05

Outputs
Our preliminary data placed POLL in a 1.7cM interval between IFNAR and SOD1 on bovine chromosome one. By comparison to human chromosome 21, we identified three positional candidates encoding transcription factors within this interval. We expected one of these three genes or their associated regulatory elements to contain a mutation that explained the dominant polled condition. Our approach was to build a contig of Angus and Horned Hereford BACs for the critical interval containing these genes, in conjunction with targeted sequencing. We used BAC clones isolated in preliminary studies as seeds to complete the Angus contig. In addition, we contributed our BAC clones and associated mapping data to the International Bovine BAC Map Consortium and were able to recover corresponding contigs containing Horned Hereford BACs. A content map was constructed by screening 78 markers across the BACs and a single contig spanning ~3Mb was assembled. BAC end sequences and other markers were also aligned to the 6x bovine genome sequence. Horned Hereford sequence traces and quality data were recovered for comparison to Angus traces to facilitate the identification of single nucleotide polymorphisms (SNPs) from across the critical interval. Only one of the three positional candidate genes, GCFC, was expressed in bovine neonatal horn buds. To characterize the gene further, we assembled bovine whole-genome shotgun, BAC, and in house sequence data into a contig spanning approximately 150,000 bases to include GCFC, its promoter, and its 3' end. This contig served as a reference sequence for SNP discovery. A panel of DNA was assembled with at least eight animals per breed (Angus, Brahman, Horned Hereford, Polled Hereford, Simmental, Ankole, and Nellore). Approximately 45,000 base pairs of sequence was generated for each animal. SNPs within breeds were characterized and then consensus sequences were compared between breeds. Across breeds there were 156 SNPs or small deletions identified within GCFC.

Impacts
New markers closely associated with POLL, when applied by producers, will help the beef industry to meet their targets for reducing the incidence of horns.

Publications

  • Black, S.G., K.R. Wunderlich, C.A. Abbey, and C.A. Gill. 2006. Comparative analysis of splice variants of putative transcription factor GCFC. Plant and Animal Genome XIV, San Diego, California, USA (Abstract #P821).
  • Wunderlich, K.R., S.G. Black, C.A. Abbey, and C.A. Gill. 2006. A survey of gene expression in the POLL critical interval. Plant and Animal Genome XIV, San Diego, California, USA (Abstract #P543).
  • Rakowitz, K.R., Abbey, C.A. and Gill, C.A. (2005) Haplotype analysis within the POLL critical interval on bovine chromosome one. Plant and Animal Genome XIII, San Diego, California, USA (Abstract #P533).
  • Chiu, R., Bosdet, I., Mathewson, C., Wye, N., Lee, D., Barber, S., Yang, G., Stott, J., Abbey, C., Motta de Carmo Costa, M., Gill, C., Hansen, C., Keele, J., Larkin, D., Meng, Y., Osoegawa, K., Schibler, L., Siddiqui, A., Snelling, W., Williams, J.L., Adelson, D., Archibald, A., Benkel, B., Caetano, A.R., Eggen, A., Holt, R., Jones, S., de Jong, P.J., Lewin, H., McEwan, J.C., Moore, S., Tellam, R., Zhao, S., Kappes, S., Marra, M. and Schein, J. (2004) A BAC physical map of the bovine genome. Plant and Animal Genome XII, San Diego, California, USA.


Progress 01/01/04 to 12/31/04

Outputs
In order to identify the causative mutation for POLL, we have refined the linkage map and have constructed a 3 Mb BAC contig and STS content map of the POLL critical interval. Three candidate genes encoding transcription factors were annotated within this region. Only one of the three genes, GCFC, is expressed in the horn buds. To characterize the gene further, we assembled bovine whole-genome shotgun, BAC, and in house sequence data into a contig spanning approximately 150,000 bases to include GCFC, its promoter, and its 3' end. This contig served as a reference sequence for SNP discovery. A panel of DNA was assembled with at least eight animals per breed (Angus, Brahman, Horned Hereford, Polled Hereford, Simmental, Ankole, and Nellore). Approximately 45,000 base pairs of sequence was generated for each animal. SNPs within breeds were characterized and then consensus sequences were compared between breeds. The number of confirmed SNPs within GCFC for each individual breed varied from 7 to 68 with an average ratio of 1:5.75 for transitions vs. transverions.

Impacts
New markers closely associated with POLL, when applied by producers, will help the beef industry to meet their targets for reducing the incidence of horns.

Publications

  • Rakowitz, K.R., Abbey, C.A., Schein, J., Adelson, D.L. and Gill, C.A. (2004) A 3Mb BAC contig and STS content map of the POLL critical interval on bovine chromosome one. Proceedings of the 29th International Conference on Animal Genetics, Tokyo, Japan, Sept. 11-16.


Progress 01/01/03 to 12/31/03

Outputs
We have identified three positional candidates for POLL and we expect one of these three genes or their associated regulatory elements to contain a mutation that explains the dominant polled condition. Our approach was to build a contig of Angus and Horned Hereford BACs for the critical interval containing these genes, in conjunction with targeted sequencing. We used BAC clones isolated in preliminary studies as seeds to complete the Angus contig. In addition, we contributed our BAC clones and associated mapping data to the International Bovine BAC Map Consortium and were able to recover corresponding contigs containing Horned Hereford BACs. A content map was constructed by screening 54 markers across the BACs and a single contig spanning 3Mb was assembled. Targeted sequencing of BACs containing the three candidate genes has commenced. Nested primers designed from either EST sequences or multiple species alignments have been used to generate more than 10kb of sequence to date. Primers have been subsequently developed from the generated sequence to screen across a breed panel. Haplotypes for ten animals from nine different breeds are being characterized for consistency with the inheritance pattern of horns. So far, no mutations have been identified in coding regions but a number of breed specific SNPs have been identified in introns.

Impacts
New markers closely associated with POLL, when applied by producers, will help the beef industry to meet their targets for reducing the incidence of horns.

Publications

  • No publications reported this period