Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.

Maintaining diversity of small ruminant genetic resources is instrumental for sustainable agricultural production. Community-based livestock breeding programs (CBBPs) have emerged as a potential approach to implement breeding programs in smallholder farms. This study assesses the viability of CBBPs as a potential approach for conservation and improvement of indigenous small ruminants, using case studies of goat CBBPs in Malawi and Uganda. Data were collected using focus group discussions, personal interviews, and direct observations. The program promotes and empowers smallholders to have access to small ruminant feed resources through protection of existing communal pasturelands, capacity building in pasture production, and conservation of crop residues and crop by-products. Implementation of the CBBP enhances the contributions through improved animal growth performance, kids’ survival, and twinning rates leading to increased offtake rates and better prices. The existence of permanently established supporting organizations and other stakeholders provides sustainable institutional support instrumental for the establishment and growth of CBBPs. However, establishment of functional community-based institutions (producer cooperatives) and investments in institutional/policy reforms to safeguard fair trading, access to common resources by small ruminant keepers, and adoption of the CBBP model into national livestock development programs are some of the key milestones that can guarantee sustainability.