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

Abstract

Background 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. 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. Results We 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. Conclusions These 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.

Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

“…Here, we characterized the genome-wide ROH pattern in JC goats by mining information from WGS data. The number of ROHs in JC goats is much more than those in many other goat populations [ 13 , 39 , 40 , 41 ]. Although population-specific genetic composition underlies this difference, another important reason is the setting of the minimum length of ROH, which varied with the different densities of SNP maps (i.e., SNP chips vs. WGS).…”

“…Although population-specific genetic composition underlies this difference, another important reason is the setting of the minimum length of ROH, which varied with the different densities of SNP maps (i.e., SNP chips vs. WGS). Besides goats [ 13 , 39 , 40 , 41 ], previous studies using SNP chip data usually detect long ROHs (e.g., > 0.5 Mb [ 12 , 42 , 43 ] or 1 Mb [ 11 , 44 , 45 , 46 ]) in a variety of livestock populations. In contrast, the WGS data usually yield millions of SNPs and enable us to detect short ROH with a length of < 500 kb, as demonstrated in cattle [ 47 ], goats [ 14 ], and sheep [ 32 ].…”

“…Accordingly, ROHs with different lengths can reflect historical inbreeding events at different generations, which is an advantage of ROH-based estimates of inbreeding compared with other molecular inbreeding estimates, mainly including those derived from genomic kinship matrixes [ 9 ]. Therefore, ROH-based inbreeding coefficients are now widely used in a variety of animal species, such as pigs [ 10 ], cattle [ 11 ], sheep [ 12 ], and goats [ 13 , 14 ]. Furthermore, ROH islands (i.e., ROHs are common between individuals) at the population level can be an indicator of the identification of signatures of selection [ 10 , 12 , 14 , 15 ], demonstrating that ROH is a versatile statistic.…”

Genome‐wide survey on three local horse populations with a focus on runs of homozygosity pattern

“…Moreover, the estimate of the number of ROH and the length of these segments may be useful for conservation programmes in endangered populations and can contribute to improving mating strategy and management. For example, animals that have the high levels of ROH (with long segments) could be excluded from mating schemes or assigned lower priority to minimize the loss of genetic diversity and maintain or increase the effective population size (Cortellari et al, 2021; Mastrangelo, Ciani, Marsan et al, 2018; Metzger et al, 2015; Purfield et al, 2012; Schiavo, Bovo, Bertolini, Tinarelli et al, 2020). Our results showed that the Arab horses had the highest levels of F ROH , followed by Purosangue Orientale Siciliano.…”

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

“…Continuous stretches of homozygous sequences, i.e., Runs of homozygosity (ROHs), were scored on the two Montecristo nuclei to assess population demographic history. ROHs were computed with PLINK v1.9 [ 20 ] as described in [ 31 ]. Number of ROHs per animal, average ROH length and ROH distribution across length classes (0–2 Mb, 2–4 Mb, 4–8 Mb, 8–16 Mb, and >16 Mb; see Supplementary Table S2 ) were calculated.…”