Project : USDA ARS

ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Research Project #442591

Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

2023 Annual Report

Accomplishments
1. Creation of the first complete, ungapped sex chromosome assemblies for cattle, sheep, and goat. Sex chromosomes (X and Y in mammals) harbor important genes affecting sex-specific traits and lack of high-quality assemblies have hampered genetic and genomic research in livestock species. Sex chromosomes have been very difficult to assemble from DNA sequence due to the presence of highly repetitive sequence arrays that can extend for millions of base pairs. ARS scientists at Clay Center, Nebraska, and Beltsville, Maryland, collaborated with researchers at the University of Idaho, Utah State University, University of Missouri, and the National Institutes of Health, to create and analyze complete sex chromosomes from cattle, sheep, and goat. The group produced the first complete sex chromosomes for any livestock species and identified surprising differences between gene content and arrangement between the ruminant species and between ruminants and primates. This work opens the door for improved analysis of sex-specific trait expression in three important livestock species. Genetic improvement programs with sex-specific inheritance patterns will now have higher accuracy. Beef cattle producers will benefit through an increased rate of genetic progress for important traits in these livestock species.

2. DNA pooling technique to reveal genetic connections between seedstock and commercial sectors of the beef industry. Genetic evaluation of seedstock cattle could benefit from commercial data as there are hidden relationships between commercial and seedstock sectors because many commercial producers buy bulls from the seedstock sector. Single nucleotide polymorphism genotypes could reveal these hidden relationships; however, genotyping can be cost prohibitive. The cost of commercial data capture could be decreased by pooling DNA, which is a method to genotype groups of animals to use their data in genetic evaluation. ARS researchers in Clay Center, Nebraska, constructed DNA pools with portions of shared unrelated animals to determine whether it is possible to reveal genetic connections between seedstock and commercial sectors, thus enabling the beef industry to produce cattle that better fit commercial production systems, as genetic evaluation of seedstock cattle could benefit from commercial data. DNA pools were created to mimic the results of DNA pools sharing relatives with the same degree of shared genomes. For example, a DNA pool of progeny and a DNA pool of the dams of the pooled progeny would produce the same result as two DNA pools sharing 50% overlap of unrelated animals. Knowing the relationship between seedstock cattle and DNA pools of commercial cattle may allow commercial data to enhance genetic evaluation of seedstock animals ultimately resulting in beef cattle with superior performance and efficiencies. Cattle that fit optimally in their production system have better health, are more environmentally sustainable and are more efficient, leading to more sustainable beef production.

3. Birth weight and postweaning gain of cattle from the Germplasm Evaluation project. Birth weight and postweaning gain of cattle from the Germplasm Evaluation project, that had been sequenced at low coverage (~0.5x) and had sequence-level genotypes imputed, were examined by ARS researchers in Clay Center, Nebraska, to estimate the amount of variation explained by sequence variants. Genotypes for single nucleotide polymorphism (SNP), a common type of genomic marker, on commercial SNP chips as well as variants within and near protein-coding genes were extracted and divided into sets according to expected functional consequences. Genomic relationship matrices were constructed for each marker subset to estimate variance components to see which portions explain the most variation. Fitting all markers explained the most variation in both birth weight and postweaning gain, followed by the modifier variants which are close to genes but do not alter the protein-coding sequence. Little variation was attributable to high impact variants, which can cause loss of gene function. Further refinement of markers using similar methods will identify marker sets that are more robust across breeds and improve our ability to use genomic markers in genomic improvement programs for important industry traits. Beef cattle producers will benefit from faster rates of genetic improvement as a result.

4. Evaluation of breed differences and heterosis for mature cow body composition and weight. Body condition score (BCS) and mature weight are both important indicators of mature cow efficiency and, subsequently, feed requirements. While a higher-condition score may result in heavier mature weights, the relationship is not guaranteed across breeds or animals within breeds. ARS researchers at Clay Center, Nebraska, with collaborators at the University of Nebraska, estimated breed differences for 16 different breeds as well as heterosis and genetic relationships between BCS and mature weight. Both traits were moderately heritable across cow parities and genetic relationships between the parities ranged from 0.3 to 0.6 indicating that although the traits are moderately related, selection for one trait is possible without changing the other. These results will help producers select breeds or individuals with lower maintenance energy requirements and will enable decision support tools for producers seeking to reduce cow maintenance requirements, which contribute to feed costs. These results are already being utilized in one large multibreed evaluation program in the United States (International Genetic Solutions).

U.S. DEPARTMENT OF AGRICULTURE

Genetics and Animal Breeding: Clay Center, NE