Management of lethal recessive alleles in beef cattle through the use of mate selection software

Abstract

Background Recessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions. Methods Two beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0–100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping. Results With full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring ( aa ) as compared to indiscriminate selection against carrier parents ( Aa ). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses. Conclusions Genotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding.

Symposium review: Exploiting homozygosity in the era of genomics—Selection, inbreeding, and mating programs

“…These quantities are the average (pedigree/genomic) inbreeding expected when a bull is mated to a random sample of cows in the population so that the higher the ratio of expected to genomic future inbreeding, the more related the bull is to the current population (VanRaden et al, 2011b). Minimization of progeny inbreeding (Pryce et al, 2012), linear programming (Weigel, 2001), look-ahead mate selection (Shepherd, 2005), selection against lethal alleles (Van Eenennaam and Kinghorn, 2014;Cole et al, 2016;Upperman et al, 2019), index selection including Mendelian variance (Santos et al, 2019), and genomic selection including dominance (Sun et al, 2014) have all been proposed as methods to controlling inbreeding.…”

Comparison of Genetic Merit for Weight and Meat Traits between the Polled and Horned Cattle in Multiple Beef Breeds

“…Hence, loss of genetic diversity and consequently elevated levels of inbreeding may occur in the progeny of closely related polled animals. Inbreeding depression in production traits, as well as the potential increase of detrimental allelic homozygosity [ 32 ] and associated diseases (e.g., Pompes), are risks [ 33 , 34 ]. Generally, in livestock species, a 0.137% decrease of the mean of a trait has been estimated for every unit (1%) increase in inbreeding and the loss was larger (0.351%) for production traits [ 34 ]: Zebu cattle decreased by 0.269% for weight traits [ 35 ].…”

Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing

“…The 13-bp deletion in DNAH17 adds to a catalogue of sequence variants that cause male-factor infertility in pigs (Sironen et al, 2011), (Sironen et al, 2006), (Noskova et al, 2020). It remains an open question how an increasing number of undesired recessive alleles may be considered appropriately in livestock populations (Cole, 2015), (Upperman et al, 2019). Although the newly identified 13bp deletion does neither compromise the welfare of homozygous animals nor result in huge economic losses, it's frequency should be kept at a low level to prevent the birth of homozygous boars that manifest a sterilizing sperm tail disorder.…”