The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

Abstract

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations

“…Such approach was most suitable given the low number of individuals per breed (between 1 and 4), which is the direct consequence of the threatened population size of most of these breeds (http://edepot.wur.nl/424249). Even though (slightly) different breeds were grouped into the same population, we expect potential bias to be minimal, as already shown in Bortoluzzi et al () when using genome‐wide SNP chip data.…”

“…The recent creation of neo‐bantam breeds involved, on top of domestication, an additional population bottleneck. As we showed in our previous study, the reduced N e and parent–offspring mating pursued within a neo‐bantam breed to consolidate favourable traits considerably increased the level of inbreeding (Bortoluzzi et al, ). Although we expect the recent and sudden bottleneck to have acted differently on the accumulation of deleterious variants relative to the domestication bottleneck experienced by historical breeds, its effect on genome‐wide patterns of deleterious variation remains unclear.…”

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

“…Originally conceived to improve the accuracy of homozygosity mapping of recessive Mendelian diseases, ROH have formed the foundation of studies investigating the contribution of recessive deleterious variants to the genetic risk for complex diseases and to the determination of complex traits. 1 Moreover, they have provided unique insights into the demographic and sociocultural processes 1 that have shaped genomic variation patterns in contemporary worldwide human populations, [2][3][4][5][6][7][8] ancient hominins, [9][10][11][12] non-human primates, 13,14 woolly mammoths, 15 livestock, [16][17][18][19][20][21] birds, 22,23 felines, 24 and canids. [25][26][27][28][29][30][31] Recent population bottlenecks, cultural preferences for endogamy or consanguineous marriage, and natural selection can create increased rates of ROH in individual genomes, substantially increasing overall homozygosity in such populations.…”

Short Communication: Duration and volume of crowing of Pelung chickens of West Java, Indonesia

“…In general, chicken diversity is a result of demographic migration (Sartika et al 2004) and farmer preferences (Komiyama et al 2016;Bortoluzzi et al 2018). Farmer preferences contribute significantly in developing chickens for specific uses such as for entertainment purposes (Komiyama et al 2016;Bortoluzzi et al 2018).…”