Journal club of one: ”Genomic predictions for crossbred dairy cattle”

A lot of dairy cattle is crossbred, but genomic evaluation is often done within breed. What about the crossbred individuals? This paper (VanRaden et al. 2020) describes the US Council on Dairy Cattle Breeding’s crossbred genomic prediction that started 2019.

In short, the method goes like this: They describe each crossbred individual in terms of their ”genomic breed composition”, get predictions for each them based on models from all the breeds separately, and then combine the results in proportion to the genomic breed composition. The paper describes how they estimate the genomic breed composition, and evaluated accuracy by predicting held-out new data from older data.

The genomic breed composition is a delightfully elegant hack: They treat ”how much breed X is this animal” as a series of traits and run a genomic evaluation on them. The training set: individuals from sets of reference breeds with their trait value set to 100% for the breed they belong to and 0% for other breeds. ”Marker effects for GBC [genomic breed composition] were then estimated using the same software as for all other traits.” Neat. After some adjustment, they can be interpreted as breed percentages, called ”base breed representation”.

As they already run genomic evaluations from each breed, they can take these marker effects and then animal’s genotypes, and get one estimate for each breed. Then they combine them, weighting by the base breed representation.

Does it work? Yes, in the sense that it provides genomic estimates for animals that otherwise wouldn’t have any, and that it beats parent average estimates.

Accuracy of GPTA was higher than that of [parent average] for crossbred cows using truncated data from 2012 to predict later phenotypes in 2016 for all traits except productive life. Separate regressions for the 3 BBR categories of crossbreds suggest that the methods perform equally well at 50% BBR, 75% BBR, and 90% BBR.

They mention in passing comparing these estimates to estimates from a common set of marker effects for all breeds, but there is no detail about that model or how it compared in accuracy.

The discussion starts with this sentence:

More breeders now genotype their whole herds and may expect evaluations for all genotyped animals in the future.

That sounds like a reasonable expectation, doesn’t it? Before what they could do with crossbred genotypes was to throw it away. There are lots of other things that might be possible with crossbred evaluation in the future (pulling in crossbred data into the evaluation itself, accounting for ancestry in different parts of the genome, estimating breed-of-origin of alleles, looking at dominance etc etc).

My favourite result in the paper is Table 8, which shows:

Example BBR for animals from different breeding systems are shown in Table 8. The HO cow from a 1964 control line had 1960s genetics from a University of Minnesota experimental selection project and a relatively low relationship to the current HO population because of changes in breed allele frequencies over the past half-century. The Danish JE cow has alleles that differ somewhat from the North American JE population. Other examples in the table show various breed crosses, and the example for an animal from a breed with no reference population shows that genetic contributions from some other breed may be evenly distributed among the included breeds so that BBR percentages sum to 100. These examples illustrate that GBC can be very effective at detecting significant percentages of DNA contributed by another breed.

Literature

VanRaden, P. M., et al. ”Genomic predictions for crossbred dairy cattle.” Journal of Dairy Science 103.2 (2020): 1620-1631.

Paper: ”Mixed ancestry and admixture in Kauai’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs”

We have a new paper almost out (now in early view) in Molecular Ecology about the chickens on the Pacific island Kauai. These chickens are pretty famous for being everywhere on the island. Where do they come from? If you use your favourite search engine you’ll find an explanation with two possible origins: ancient wild birds brought over by the Polynesians and escaped domestic chickens. This post on Kauaiblog is great:

Hawaii’s official State bird is the Hawaiian Goose, or Nene, but on Kauai, everyone jokes that the “official” birds of the Garden Island are feral chickens, especially the wild roosters.

Wikepedia says the “mua” or red jungle fowl were brought to Kauai by the Polynesians as a source of food, thriving on an island where they have no real predators. /…/
Most locals agree that wild chickens proliferated after Hurricane Iniki ripped across Kauai in 1992, destroying chicken coops and releasing domesticated hens, and well as roosters being bred for cockfighting. Now these brilliantly feathered fowl inhabit every part of this tropical paradise, crowing at all hours of the day and night to the delight or dismay of tourists and locals alike.

In this paper, we look at phenotypes and genetics and find that this dual origin explanation is probably true.

jeff_trimble_kauai_chickens_cc_by_nc_sa

(Chickens on Kauai. This is not from our paper, but by Jeff Trimble (cc:by-sa-nc) published on Flickr. There are so many pretty chicken pictures there!)

Dom, Eben, and Pamela went to Kauai to photograph, record to and collect DNA from the chickens. (I stayed at home and did sequence bioinformatics.) The Kauai chickens look and sound like mixture of wild and domestic chickens. Some of them have the typical Junglefowl plumage, and other have flecks of white. Their crows vary in the length of the characteristic fourth syllable. Also, some of them have yellow legs, a trait that domestic chickens seem to have gotten not from the Red but from the Grey Junglefowl.

We looked at DNA sequences by massively parallel (SOLiD) sequencing of 23 individuals. We find mitochondrial sequences that fall in two haplogroups: E and D. The presence of the D haplogroup, which is the dominating one in ancient DNA sequences from the Pacific, means that there is a Pacific component to their ancestry. The E group, on the other hand, occurs in domestic chickens. It also shows up in some ancient DNA samples from the Pacific, but not from Kauai (and there is a scientific debate about these sequences). The nuclear genome analysis is pretty inconclusive. I think what we would need is some samples of possible domestic source populations (Where did the escapee  chickens came from? Are there other traditional domestic sources?) and a better sampling of Red Junglefowl to make better sense of it.

When we take the plumage, vocalisation and mitochondrial DNA together, it looks like this is a feral admixed population of either Red Junglefowl or traditional Pacific chickens mixed with domestics. A very interesting population indeed.

Kenneth Chang wrote about the paper in New York Times; includes quotes from Eben and Dom.

E Gering, M Johnsson, P Willis, T Getty, D Wright (2015) Mixed ancestry and admixture in Kauai’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs. Molecular ecology