Sire selection after genomics: fertility traits, inbreeding and sexed semen

Between roughly 1960 and 2000, selection weighted heavily towards yield produced a well-documented antagonistic decline in female fertility, quantified for the Holstein population by Lucy (2001) and others. The response — adding daughter fertility, health and survival traits to national indices from the early 2000s, and then the arrival of genomic evaluation in 2009 — has reversed the trend. Current genetic trends for daughter pregnancy rate in the major Holstein populations are positive and have been for over a decade.

Two fertility traits, often confused

• Daughter fertility (DPR, fertility index, or the national equivalent) predicts how readily a bull's daughters will conceive as cows. It is a long-term herd investment.
• Sire conception rate or non-return rate predicts how readily semen from that bull produces a pregnancy now. It affects this season's pregnancy rate.
• They are largely independent. A bull can be excellent on one and poor on the other, and a herd with a short-term fertility problem should be looking at the second while still selecting on the first.

Inbreeding is the live risk

Genomic selection compressed the generation interval, which accelerated genetic gain and simultaneously accelerated the accumulation of relatedness. Genomic inbreeding coefficients now rise faster than pedigree-based ones suggested, and the depression is measurable in exactly the traits that matter reproductively — conception, stillbirth and calf survival (Doekes et al., 2019; Makanjuola et al., 2020). Practical management means using genomic relationship-based mating software rather than pedigree rules of thumb, and keeping a deliberate spread of sire families rather than concentrating on the top three bulls of the moment.

Allocating semen across the herd

The standard modern structure is straightforward: sexed semen on the genetically superior fraction of the herd and on well-grown heifers, where conception is highest; conventional semen on the middle; beef semen on the bottom fraction, which both removes low-merit females from the replacement pool and adds calf value. The size of each band is decided by the herd's replacement requirement, not by preference. Sexed-semen conception is now close enough to conventional in heifers that the old rule of restricting it to heifers only no longer holds for well-managed lactating cows.

Selecting for your own system

National indices are weighted for national average production systems. A grazing herd in Ireland, a robot herd in the Netherlands and a housed herd in Sweden are not the same selection problem. The defensible approach is to start from the relevant national index and adjust weightings for the traits your system stresses hardest — feet and legs and grazing behaviour in a walking herd, udder conformation and milking speed in a robot herd, heat tolerance where summer THI is rising.