Genomics provide a tool to monitor changes in founding breeds proportions
By El Hamidi Hay and Harvey Blackburn
Composite cattle populations play an important role in global beef cattle production. They enable producers to effectively combine the desirable traits (through complementarity) of progenitor breeds (e.g., Bos taurus and Bos indicus) and take advantage of hybrid vigor and thereby increase productivity. Beef producers in the United States have been highly successful in developing new breeds/composites that have found national and global acceptance (e.g., Brahman, Brangus, Santa Gertrudis, Beefmaster).
It is important to note that composite breeding is different than crossbreeding. Once the composite is formed and stabilized with the targeted proportions of the founding breeds the resulting animals are mated like any other pure breed. The advantages of composite development are multiple purebred populations do not need to be maintained to form the crossbred, nor do they require separate breeding pastures and variable calf crops.
In dealing with current and future changes in the production landscape that include issues such as increases in temperature, incidence of parasitic diseases and alterations in plant species composition in varying parts of the country, producers and breeders alike may wish to explore whether or not there is a need for increased composite use and/or the development of new composites.
But before embarking upon such an effort it is useful to evaluate what sort of genetic changes appear to be occurring in some of our present composite populations. Prior to the work discussed below no assessment of how breed compositions in a composite have maintained themselves. For example, a composite could be formed using 50% of breed A and 50% of breed B but does that 50:50 ratio remain the same over time in subsequent generations or does one breed eventually come to dominate the genetic composition of the composite?
Before endeavoring to develop new breeds of composite cattle it is beneficial to evaluate, using new genomic tools, some of our current composite populations and how they have changed over time.
A popular composite in the United States is Brangus. This composite was started for the purpose to combine the traits of two highly successful progenitor breeds; Brahman, with its adaptation to heat and humidity found in the Gulf Coast and disease resistance and Angus with its carcass qualities and milking ability. The International Brangus Breeders Association (IBBA) started the Brangus registry in 1949 with the goal of maintaining the progenitor proportions of 62.5% Angus and 37.5% Brahman1. But a study evaluating the genetic composition of Brangus cattle in the United States, revealed the targeted proportions had changed from the original target to an average of 70.38% Angus and 29.62% Brahman (Figure 1)2.
Further, in a chromosome-by-chromosome analysis some chromosomes showed greater proportions in progenitor proportions (e.g., chromosome 15) (Figure 1). The sex chromosome Y in Brangus was shown to be all Angus. This is sensible since Angus bulls were mated to Brahman cows. The Y chromosome being all Angus will lead to decreased genetic variation in males and potentially causing inbreeding depression in male fertility traits.
In another example of composite development, the USDA Agricultural Research Service’s station in Miles City, Montana developed a composite using three Bos taurus breeds (50% Red Angus, 25% Charolais, 25% Tarentaise) referred to as Composite Gene Combination (CGC). The breeds used in developing the CGC population provided a broad range of characteristics (e.g., growth, meat quality, and maternal ability). The goal was to combine the positive attributes of each breed to raise productivity in a limited nutrient environment.
In comparing the genetic composition of CGC over time it was found that the percent of Tarentaise increased to 57%, while Charolais decreased to approximately 5% and Red Angus decreased to 38%3. Therefore, these changes in the progenitor proportions indicate that Tarentaise contributed useful attributes to the CGC population managed with limited nutritional inputs in a cool semi-arid environment.
This result was unexpected and illustrates the importance of deciding what breeds to use in developing a composite population. The decline in Charolais proportion is due to the selection against light coat color. This selection signature was detected in a region in chromosome 5 which harbors genes with metabolic properties associated with pigmentation (ErbB3, SILV)4. Although other genetic effects may influence coat color. With this decrease in Charolais proportion, attributes of this founder breed were lost in the CGC population.
As we look toward further composite breed or population development several key aspects emerge from these evaluations that breeders should consider. Once a composite has been formed, that is the desired breed combination has been reached (e.g., 3/8 and 5/8 in Brangus), it takes approximately five generations of mating within the newly composite to stabilize gene frequencies across the genome. After the fifth generation the composite develops its own unique genetic signature that is different from other breeds. After stabilization breeders can expect increases in inbreeding, but with attention to mating plans inbreeding can be controlled. Genomic information could be used for better estimation of inbreeding and more informed mating decisions.
Importantly, the genetic composition of the composite changes over time and generations. The changes in composition can be driven either by selection for specific traits, a factor that seemed to cause changes in Brangus or by natural selection which seemed to be the reason for the increase in Tarentaise in the CGC population, since no consistent long-term selection was practiced within that population.
Interestingly, breed composition across the genome is not constant suggesting contributions from the progenitor breeds deviate from the average proportions sought in the original design of such populations. The fact they are not in-line with the designed genetic proportions may be fortuitous and suggests the composite is self-adjusting to its production system. (In the CGC case the suitability of the Tarentaise in a semi-arid cold climate has become apparent).
As mentioned in the CGC population the proportion of Charolais decreased by 80% mainly driven by the selection against the light color while this change may have been beneficial in terms of cow-calf production it serves as an example of how quickly a genotype can be changed in a newly formed composite. By monitoring composite development with genomic tools such a change could have been mitigated if so desired.
Due to the dynamic changes in composite population genetics, the issue for breeders becomes one of determining whether or not the breeding program is facilitating the purpose of the composite or potentially detracting from the composites ultimate goal. With our current capacities in genomics this issue can be addressed. But it will require the development of specialized SNP panels or genotyping animals with panels that have a higher density of SNPs.
In both the Brangus and CGC example the Bovine HD chip was used. Fortunately, with the development of new low read sequencing (which has a lower cost point) more information concerning breed proportions across the genome can be estimated, particularly for traits that are not currently selected (e.g., heat or cold tolerance). Composite populations have and will likely continue to be important genetic resources for beef cattle production. The benefits composites provide, as well as the ease of management, make them very attractive to producers. However, these benefits could be lost by poor mating and selection decisions. Genomics provide a tool to monitor changes in founding breeds proportions and to control inbreeding accumulation.
References 1. Koger, M., Efective crossbreeding systems utilizing zebu cattle. Journal of Animal Science 1980, 50 (6), 1215-1220. 2. Paim, T. d. P.; Hay, E. H. A.; Wilson, C.; Thomas, M. G.; Kuehn, L. A.; Paiva, S. R.; McManus, C.; Blackburn, H., Genomic breed composition of selection signatures in Brangus beef cattle. Frontiers in genetics 2020, 11, 710. 3. Hay, E. H.; Toghiani, S.; Roberts, A. J.; Paim, T.; Kuehn, L. A.; Blackburn, H. D., Genetic architecture of a composite beef cattle population. Journal of Animal Science 2022, 100 (9), skac230. 4. Gutiérrez-Gil, B.; Wiener, P.; Williams, J. L., Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais× Holstein population. BMC genetics 2007, 8 (1), 56.
Figure 1. Proportion of Angus and Brahman measured in Brangus for various chromosomes. Red dashed line represents the original targeted proportion of Angus and green dotted line represents Brahman in the Brangus breed. Adapted from Paim et al. 2020.
Figure 2. Progenitor breed proportions of CGC animals according to their equivalent generation number.
Hay is a research geneticist with the USDA Agricultural Research Service in Miles City, Montana. Blackburn is the national coordinator of the National Animal Germplasm Program with the USDA Agricultural Research Service.
