Extended haplotype homozygosity analysis reveals positive selection patters in 6 Spanish goat breeds

Abstract

Goats are a major livestock resource in Spain. Their adaptability and resilience in adverse environments and their increased productivity even in intensive schemes make them valuable livestock resources. For this reason, several local breeds were developed, focused on meat or dairyproduction during the last decades. In this study, we determined the presence of selection fingerprints in dairy (n = 2) and meat (n = 3) Spanish goat breeds, by estimating the integrated haplotype score (iHS) of the extended haplotype homozygosity (EHH) analysis using SNP array information. Samples from178 Spanish individuals including 46 Malagueña (MLG), 43 Florida (FLO) and 25 Murciano-Granadina (MUR) dairy goats, and 24 Bermeya (BER), 20 Mallorquina (MLL) y 20 Blanca de la Rasquera (RAS) were genotyped using the Illumina GoatSNP50 BeadChip (55,000markers). Data were pruned by LD and MAF using PLINK and analyzed (per breed) using the REHH package of the statistical environment R. Finally, candidate regions (selection sweeps, SS) were selected based on the iHS P-value with a minimum length of 1Mb. Results showed a clear anddistinctive iHS peak in the CHI12, despite their productive ability. This selective signature, located in a chromosome previously associated with adaptability, could be related to a genetic ability to cope with the Spanish environment, in which all these breeds were bred during the last 50 years, characterized as harsh and with low levels of forage lands. In addition, meat breeds showed an increased number of selective sweeps but more diffuses than dairy breeds (19 vs 11 on average). In particular, the less selected breeds (RAS and MLL) showed more than 20 small selective sweeps located in 15 different chromosomes, whereas the most selected breed (FLO) showed only 8 candidate regions located in 5 different chromosomes, including a clear peak in CHI6. Overall, we demonstrated that iHS could be an interesting tool to analyze differences in adaptability and selection process in Spanish goats. Further research, including functional analysis of the regions detected, is necessary to obtain more precise conclusions.