@article{lozada-soto_tiezzi_jiang_cole_vanraden_maltecca_2022, title={Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle}, volume={105}, ISSN={["1525-3198"]}, url={https://doi.org/10.3168/jds.2022-22116}, DOI={10.3168/jds.2022-22116}, abstractNote={Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (FPED), marker-based using a genomic relationship matrix (FGRM), and segment-based using ROH (FROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using FPED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using FGRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using FROH. In addition, the effective population size at past generations (5-100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.}, number={11}, journal={JOURNAL OF DAIRY SCIENCE}, author={Lozada-Soto, Emmanuel A. and Tiezzi, Francesco and Jiang, Jicai and Cole, John B. and VanRaden, Paul M. and Maltecca, Christian}, year={2022}, month={Nov}, pages={8956–8971} }
 @article{lozada-soto_lourenco_maltecca_fix_schwab_shull_tiezzi_2022, title={Genotyping and phenotyping strategies for genetic improvement of meat quality and carcass composition in swine}, volume={54}, ISSN={["1297-9686"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85131500498&partnerID=MN8TOARS}, DOI={10.1186/s12711-022-00736-4}, abstractNote={Abstract}, number={1}, journal={GENETICS SELECTION EVOLUTION}, author={Lozada-Soto, Emmanuel Andre and Lourenco, Daniela and Maltecca, Christian and Fix, Justin and Schwab, Clint and Shull, Caleb and Tiezzi, Francesco}, year={2022}, month={Jun} }
 @article{fabbri_dadousis_tiezzi_maltecca_lozada-soto_biffani_bozzi_2021, title={Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity}, volume={16}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85117913573&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0248087}, abstractNote={In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.}, number={10}, journal={PLOS ONE}, author={Fabbri, Maria Chiara and Dadousis, Christos and Tiezzi, Francesco and Maltecca, Christian and Lozada-Soto, Emmanuel and Biffani, Stefano and Bozzi, Riccardo}, year={2021}, month={Oct} }
 @article{lozada-soto_maltecca_lu_miller_cole_tiezzi_2021, title={Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection}, volume={53}, ISSN={["1297-9686"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85108104621&partnerID=MN8TOARS}, DOI={10.1186/s12711-021-00644-z}, abstractNote={Abstract}, number={1}, journal={GENETICS SELECTION EVOLUTION}, author={Lozada-Soto, Emmanuel A. and Maltecca, Christian and Lu, Duc and Miller, Stephen and Cole, John B. and Tiezzi, Francesco}, year={2021}, month={Jun} }
 @article{lozada-soto_tiezzi_lu_miller_cole_maltecca_2020, title={30 Inbreeding in American Angus cattle before and after the implementation of genomic selection}, volume={98}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.1093/jas/skaa278.026}, DOI={10.1093/jas/skaa278.026}, abstractNote={Abstract}, number={Supplement_4}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Lozada-Soto, Emmanuel A and Tiezzi, Francesco and Lu, Duc and Miller, Stephen P and Cole, John B and Maltecca, Christian}, year={2020}, month={Nov}, pages={14–14} }