Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

Biscarini, Filippo; Mastrangelo, Salvatore; Catillo, G.; Senczuk, Gabriele; Ciampolini, Roberta

doi:10.3390/ani10122285

Cited by 55 publications

(98 citation statements)

References 53 publications

(78 reference statements)

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“…Genomic regions under selection can be defined as highly homozygous (

islands) and heterozygous (

islands) regions [ 28 ]. The

and

islands were obtained based on the SNP frequency (times that each SNP was detected in a run divided by the number of animals) within

and

, respectively.…”

Section: Methodsmentioning

confidence: 99%

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Hidalgo

Cesarani

Garcia

et al. 2021

Animals

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The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

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“…Genomic regions under selection can be defined as highly homozygous (

islands) and heterozygous (

islands) regions [ 28 ]. The

and

islands were obtained based on the SNP frequency (times that each SNP was detected in a run divided by the number of animals) within

and

, respectively.…”

Section: Methodsmentioning

confidence: 99%

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Hidalgo

Cesarani

Garcia

et al. 2021

Animals

View full text Add to dashboard Cite

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“…To date, few studies have been done comparing the performance of software used for ROH detection and the ways of determining appropriate parameters ( Howrigan et al, 2011 ). Actually, a standard methodology for ROH detection is still ambiguous ( Biscarini et al, 2020 ). In our study, we used PLINK software with default parameters to detect ROH; the same method has been applied in several published works ( Peripolli et al, 2018 ; Xu et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Fang

Hao

et al. 2021

Front. Genet.

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Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

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“…Genotypes at loci in the Bovine SNP50K v2 BeadChip (Illumina Inc., San Diego, CA, United States) for 146 Maremmana (135 females and 11 males) and 174 pooled samples from seven other Podolian-derived Italian breeds (Marchigiana, Romagnola, Chianina, Calvana, Podolica, Cinisara and Modicana) were retrieved from previously published studies ( Mastrangelo et al, 2018 ; Biscarini et al, 2020 ; Senczuk et al, 2020 ). In general, methods for the detection of selection signatures are designed to analyze non-related animals ( Zhao et al, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

“…Genotyping Data, Quality Control, and Relatedness Filtering (Mastrangelo et al, 2018;Biscarini et al, 2020;Senczuk et al, 2020). In general, methods for the detection of selection signatures are designed to analyze non-related animals (Zhao et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

“…In fact, about 11,800 animals are recorded in the herdbook in 2019, including 6,853 cows and 213 bulls reared in 250 herds for beef production. 1 Previous studies have investigated genetic diversity and population structure of Maremmana and its relationship with other breeds (e.g., Ajmone-Marsan et al, 2002;Moioli et al, 2004;Pariset et al, 2010;Maretto et al, 2012;Catillo et al, 2018;Biscarini et al, 2020;Senczuk et al, 2020), but to the best of our knowledge, there is no information on trait-specific selection signatures for this breed. Such information may contribute to improve our understanding of how selection affects livestock phenotypes, thus allowing important insights into the evolutionary history and the genetic architecture of the selected traits.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

et al. 2021

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The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.

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Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

Cited by 55 publications

References 53 publications

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

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