Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Matteo Cortellari,Licia Colli,Andrea Talenti,Paolo Ajmone Marsan,Elisa Somenzi,Elena Ciani,Francesca M Sarti,Stefano Frattini,Luigi Liotta,Alessio Negro,Paola Crepaldi,Fabio Pilla,Salvatore Mastrangelo,Roberta Ciampolini,Emiliano Lasagna,Arianna Bionda,Donata Marletta

doi:10.1186/s12711-021-00685-4

Abstract

BackgroundClimate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas.ResultsWe analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups.ConclusionsThese results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

Highlights

Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices
single nucleotide polymorphism (SNP) that had a missing genotype frequency higher than 0.2, or that were in unplaced scaffolds or on the X chromosome were excluded from the analysis, but we did not apply a threshold for minor allele frequency (MAF) to better identify runs of homozygosity (ROH) [18]
Argentata dell’Etna and Messinese were the breeds that, together with the Val di Livo had the lowest average value of the total ROH length per individual (31.2, 36.8, and 56.8 Mb, respectively), while the two highest values were found in Vallesana (364.6 Mb) and Maltese bred in Sicily (347.5 Mb)

Summary

Introduction

Several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. In the valleys and hilly regions, modern intensive and semi-intensive farming systems are present, which are suited to milk and cheese production and usually exploit cosmopolitan dairy goat breeds, Saanen and Alpine [6, 7] In these systems, medium-to-large flocks are mostly kept indoor with controlled feeding and limited grazing, which is generally conducted in fenced pastures near the farm [8]. The traditional extensive farms, which can be considered as low-input/low-output systems, are mainly located in the mountainous areas and depend highly on natural grazing On these farms, small flocks of local breeds are kept indoor during the winter and in pasture for the rest of the year because of extreme variations in climate and weather conditions, especially during the winter. The animals of this farming system are influenced by the climate conditions

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