Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

ABSTRACTKlebsiella aerogenesis an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens,K. aerogenespopulation structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidateK. aerogenesclonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure ofK. aerogenesbased on 97 publicly available genomes by using both, multilocus sequence typing and single nucleotide polymorphisms extracted from core genome. We also assessed virulence and resistance profiles using VFDB and CARD, respectively. We show thatK. aerogeneshas an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least ten CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow and extended spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profile due to the presence of the toxin-encodingclboperon and the siderophore production genes,irpandybt.Notably, CC3 comprises the majority ofK. aerogenesisolates associated with hospital outbreaks, emphasizing the importance of its constant monitoring. Collectively, our results can be useful in the development of new therapeutic and surveillance strategies worldwide.

Origins and genetic legacies of the Caribbean Taino

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

How to make a domesticate

Crop domestication is an adaptive process that transforms a wild plant into a domesticated species that can reared and maintained for human use. Though there are hundreds of thousands of flowering plant species, only a small fraction has ever been domesticated. Successful domestication is likely influenced by a number of key plant characteristics, including its life history, the usefulness of a crop for early societies, and the maintenance of a large effective population size. Although many studies have sought to identify individual loci with large effects on domestication traits, we argue that relevant phenotypes are likely controlled by a large number of loci, most of relatively small effect. Most of these alleles were probably selected from standing genetic variation present in the wild ancestor rather than new mutations. Both archaeological evidence and quantitative genetics suggest that the process of domestication was in most cases gradual, likely lasting several millennia. We end by discussing how these findings from the past may inform future efforts to domesticate new species.

How to make a domesticate

Crop domestication is an adaptive process that transforms a wild plant into a domesticated species that can reared and maintained for human use. Though there are hundreds of thousands of flowering plant species, only a small fraction has ever been domesticated. Successful domestication is likely influenced by a number of key plant characteristics, including its life history, the usefulness of a crop for early societies, and the maintenance of a large effective population size. Although many studies have sought to identify individual loci with large effects on domestication traits, we argue that relevant phenotypes are likely controlled by a large number of loci, most of relatively small effect. Most of these alleles were probably selected from standing genetic variation present in the wild ancestor rather than new mutations. Both archaeological evidence and quantitative genetics suggest that the process of domestication was in most cases gradual, likely lasting several millennia. We end by discussing how these findings from the past may inform future efforts to domesticate new species.

Black Bass Diversity: Multidisciplinary Science for Conservation

<em>Abstract.</em>—The Florida Fish and Wildlife Conservation Commission (FWC) has applied guidelines outlined in its genetic policy for the release of finfishes in Florida to the conservation and management of Florida Bass <em>Micropterus floridanus</em>. A statewide genetic study was initiated after interspecific hybrids with nonnative Largemouth Bass <em>M. salmoides </em>were found in 10% of a bass sample collected in 1999 from Lake Parker, which is located 150 km south of the previously recognized intergrade zone. Using allozyme polymorphisms, mitochondrial DNA restriction fragment length polymorphisms, and microsatellite genotypes, genetic structure was resolved among 48 widely distributed populations of bass across Florida, some containing pure Florida Bass and others containing intergrades with Largemouth Bass. The FWC defined four geographic regions of Florida as genetic management units and prohibited government agencies from moving Florida Bass, Largemouth Bass, or hybrids between regions. All broodfish at the state’s Florida Bass Conservation Center hatchery are now genetically certified as pure Florida Bass prior to spawning, and wild fish are regularly added to the spawning stock to avoid the accumulation of domesticated traits. A large effective population size (about 100 or more breeders per spawning group) of hatchery broodfish is kept at the hatchery to maintain adequate genetic diversity of production fingerlings. A Florida statute was created making the nonnative Largemouth Bass and their hybrids a conditional nonnative species south and east of the Suwannee River; as such, it is currently illegal to possess them within the native range of Florida Bass without an FWC permit. Standards were also developed to genetically authenticate and manage the broodstock from private fish hatcheries requesting a FWC permit to possess, sell, or transport cultured Florida Bass within the regulated region of the state. Similar guidelines were developed for private pond management companies and other organizations that request a permit to relocate and stock wild bass in Florida. The FWC has taken two important steps forward in protecting the genetic integrity of Florida Bass: (1) developing genetic markers and applying them to bass conservation (particularly the genetic testing of broodfish), and (2) enabling fishery managers to develop and implement the rules and practices necessary for conservation of Florida’s black bass <em>Micropterus </em>spp. populations.