Major Breeding Programs Research Articles

Genomic signatures of strawberry domestication and diversification.

Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.

Early Performance of Selected Citrus Rootstocks Grafted with ‘Valencia’ Sweet Orange in Commercial Settings within a Citrus Greening Endemic Environment

Citrus greening or Huanglongbing (HLB) has caused sweet orange (Citrus sinensis) yield in Florida to decrease by 55% since the disease was first discovered in 2005. As a consequence, the profitability and sustainability of citrus (Citrus sp.) production in Florida have been jeopardized, as evidenced by the 62% reduction in the number of citrus growers statewide. Because there is still no effective treatment or management strategy to cure the disease, it is crucial to optimize grove practices and management. The use of improved rootstocks could increase the tolerance of citrus scions to biotic and abiotic stresses, thereby allowing growers to cope better with the impact of HLB in the field. We used yield data collected from commercial trials over the course of multiple seasons to assess the side-by-side performance of various commercially available rootstocks developed by the two major breeding programs in Florida in HLB-endemic field conditions. We found that some of the rootstocks attained not only statistically significant differences in yield relative to the control but also meaningful differences in revenue. Those estimates provide evidence regarding the effect of rootstock during the first few seasons after planting. Our findings are useful to improve growers’ decision-making processes regarding rootstock selection for new groves.

English

Soil salinity is a major abiotic stress that affects rice production. It can reduce yield drastically and result in total crop failure. The objectives of this study are to determine the genetic diversity within thirty-six rice accessions and to identify genotypes that are tolerant to salinity. Thirty-six rice accessions including three check varieties were sown in experimental pots and their leaves harvested for DNA extraction. Screening was done with 31 simple sequence repeats (SSRs) primers, of which 14 were markers for salt tolerance, 2 primers did not produce any results. 28 out of the 31 primers were polymorphic. The polymerase chain reaction (PCR) products were run and visualized on a 3% agarose gel matrix stained with ethidium bromide. Amplified bands were scored and analyzed with PowerMarker v3.25 and DARwin v5 software. The genetic diversity among the accessions assembled was high (He=0.6, I=0.516, PIC=0.471). Saltol primers RM10711 and RM10793 were the only primers able to completely discriminate tolerant genotypes from susceptible ones, hence they can be used in selections involving the genotypes. Accessions SR1, IR72, Sebota 337-1, Perfume (Short) type, Anyofula, Local Red, GR18Red, GH1580, GH1528, GH1575, NericaL23, NericaL24 and NericaL27 performed well under salinity stress in this study and were identified to be superior among the accessions used. These accessions should be incorporated into major breeding programs to improve the salt tolerance of existing commercial lines or for the production of new commercial lines. Key words: Rice, abiotic stress, agarose gel, genetic diversity, polymerase chain reaction (PCR), simple sequence repeats (SSRs) markers, salinity. &nbsp

Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events

AEI Aquaculture Environment Interactions Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AEI 8:497-509 (2016) - DOI: https://doi.org/10.3354/aei00194 Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events María Quintela1,*, Vidar Wennevik1, Anne G. E. Sørvik1, Øystein Skaala1, Ove T. Skilbrei1,†, Kurt Urdal2, Bjørn Torgeir Barlaup3, Kevin A. Glover1,4 1Institute of Marine Research, Post Box 1870, Nordnes, 5817 Bergen, Norway 2Rådgivende Biologer AS, Bredsgården, 5003 Bergen, Norway 3Uni Research Environment, PO Box 7810, 5020 Bergen, Norway 4Department of Biology, University of Bergen, 5020 Bergen, Norway *Corresponding author: maria.quintela.sanchez@imr.no †Deceased ABSTRACT: Aquaculture escapees represent a threat to the genetic integrity of native populations, may spread infectious agents and display ecological interactions with wild fish. DNA-based identification methods are well established for tracing Atlantic salmon escapees back to their farms of origin. However, traditional genetic assignment approaches are not always able to single out the farm of origin in cases where several potential farm sources rear fish from the same genetic line, and display strongly overlapping allele frequencies. We investigated whether an alternative statistical approach, which involves ad hoc identification of sibling relationships, circumvents the challenge of overlapping allele frequencies. We analysed the following samples collected in 2013: (1) 221 farmed escapees captured in several rivers in the Ryfylke region of Norway, (2) 139 farmed escapees captured some 150 km away in an upstream fish migration trap in the River Etne, and (3) 779 farmed salmon sampled from 17 cages on 10 farms in Ryfylke. Siblingship tests increased the precision of identification of escapees back to their farm of origin over genetic assignment and population statistic approaches. Together with other non-genetic data, siblingship tests were also able to connect 2 seemingly independent escape events, demonstrating that some of the salmon escaping from 1 or 2 farms in Ryfylke took approximately 1 mo to migrate 150 km northwards before entering the River Etne. Finally, we demonstrated that the genetic background of the escapees captured in the River Etne during the course of an entire season was represented by the 3 major breeding programs in Norway. KEY WORDS: Salmon farming · Aquaculture · Farmed escapees · Microsatellites · Assignment analyses · COLONY · Trap Full text in pdf format PreviousCite this article as: Quintela M, Wennevik V, Sørvik AGE, Skaala Ø and others (2016) Siblingship tests connect two seemingly independent farmed Atlantic salmon escape events. Aquacult Environ Interact 8:497-509. https://doi.org/10.3354/aei00194 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AEI Vol. 8. Online publication date: September 01, 2016 Print ISSN: 1869-215X; Online ISSN: 1869-7534 Copyright © 2016 Inter-Research.

Limits to captive breeding of mammals in zoos.

Captive breeding of mammals in zoos is the last hope for many of the best-known endangered species and has succeeded in saving some from certain extinction. However, the number of managed species selected is relatively small and focused on large-bodied, charismatic mammals that are not necessarily under strong threat and not always good candidates for reintroduction into the wild. Two interrelated and more fundamental questions go unanswered: have the major breeding programs succeeded at the basic level of maintaining and expanding populations, and is there room to expand them? I used published counts of births and deaths from 1970 to 2011 to quantify rates of growth of 118 captive-bred mammalian populations. These rates did not vary with body mass, contrary to strong predictions made in the ecological literature. Most of the larger managed mammalian populations expanded consistently and very few programs failed. However, growth rates have declined dramatically. The decline was predicted by changes in the ratio of the number of individuals within programs to the number of mammal populations held in major zoos. Rates decreased as the ratio of individuals in programs to populations increased. In other words, most of the programs that could exist already do exist. It therefore appears that debates over the general need for captive-breeding programs and the best selection of species are moot. Only a concerted effort could create room to manage a substantially larger number of endangered mammals.

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

BackgroundGenomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT).ResultsApproximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure.ConclusionThese markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

MOLECULAR ANALYSIS OF SCAB RESISTANCE IN APPLE CULTIVARS AND HYBRIDS FROM TRANSYLVANIA

Scab, caused by Venturia inaequalis, is the most important apple disease worldwide, therefore all major apple breeding programs have in cluded disease resistance as a primary goal. In Romania, especially in Transylvania climatic condit ions are extremely favorable for disease development and spread. In addition, the vast majority of the a pple cultivars in these areas are susceptible to th e infection. In this study, we analyzed 64 apple plan ts (cultivars and hybrids) cultivated in Transylvan ia in order to genotype for the Vf locus. Plants were screened using specific DNA markers for the presence of Vf resistance gene.