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The mutation parameter θ is fundamental and ubiquitous in the analysis of population samples of DNA sequences. This paper presents a new highly efficient estimator of θ by utilizing the phylogenetic information among distinct alleles in a sample of DNA sequences. The new estimator, called Allelic BLUE, is derived from a generalized linear model about the mutations in the allelic genealogy. This estimator is not only highly accurate, but also computational efficient, which makes it particularly useful for estimating θ for large samples, as well as for a large number of cases, such as the situation of analyzing sequence data from a large genome project, such as the 1000 Genomes Project. Simulation shows that Allelic BLUE is nearly unbiased, with variance nearly as small as the minimum achievable variance, and in many situations, it can be hundreds- or thousands-fold more efficient than a previous method, which was already quite efficient compared to other approaches. One useful feature of the new estimator is its applicability to collections of distinct alleles without detailed frequencies. The utility of the new estimator is demonstrated by analyzing the pattern of θ in the data from the 1000 Genomes Project.

International audience; Background The major prolificacy gene FecL was first described in the Lacaune sheep meat breed Ovi-Test in 1998. A few studies estimated the effect of this gene on prolificacy but little data is available. In 2010, the Ovi-Test cooperative started genotyping FecL in all of their replacement ewe lambs. Thanks to the large amount of genotyping data that is available now, gene effects on litter size and other relevant traits can be estimated more accurately.MethodsOur study included 5775 ewes genotyped since 2010 and 1025 sires genotyped since 2002. Performances and pedigrees were extracted from the French national database for genetic evaluation and research. Analysis of the effect of the gene on different traits was based on linear or threshold genetic animal models using the ASReml software.ResultsThe female population was composed of 71% homozygous wild type ewes (++), 27% heterozygous ewes for the FecL mutation (L+) and 2% homozygous mutant (LL) ewes. On average, L + ewes produced 0.5 more lambs per lambing than ++ ewes. The FecL gene not only affected the mean litter size but also its variability, which was lower for ++ than for L + ewes. Fertility after insemination was higher for L + ewes than for ++ ewes. Lambs from ++ dams were heavier (+300 g) than the lambs of L + dams and the mortality of twin lambs born from ++ dams was lower than those from L + dams. In addition, bias in estimated breeding values for prolificacy when ignoring the existence of this major gene was quantified.ConclusionsThe effect of the FecL gene on prolificacy was estimated more accurately and we show that this gene affects both the mean and the variability of litter size and other traits. This paper also shows that ignoring the existence of this major gene in genetic evaluation of prolificacy can lead to a large overestimation of polygenic breeding values.