Maize Germplasm Conservation in Southern California's Urban Gardens: Introduced Diversity Beyond ex situ and in situ Management.

Contemporary germplasm conservation studies largely focus on ex situ and in situ management of diversity within centers of genetic diversity. Transnational migrants who transport and introduce landraces to new locations may catalyze a third type of conservation that combines both approaches. Resulting populations may support reduced diversity as a result of evolutionary forces such as genetic drift, selection, and gene flow, yet they may also be more diverse as a result of multiple introductions, selective breeding and cross pollination among multiple introduced varietals. In this study, we measured the amount and structure of maize molecular genetic diversity in samples collected from home gardens and community gardens maintained by immigrant farmers in Southern California. We used the same markers to measure the genetic diversity and structure of commercially available maize varieties and compared our data to previously reported genetic diversity statistics of Mesoamerican landraces. Our results reveal that transnational dispersal creates an opportunity for the maintenance of maize genetic diversity beyond its recognized centers of diversity

Chytrid fungus infection in alpine tree frogs is associated with individual heterozygosity and population isolation but not population-genetic diversity

Chytridiomycosis, a disease caused by the emerging fungus Batrachochytrium dendrobatidis (Bd), has been implicated in the decline of over 500 amphibian species. Population declines could have important genetic consequences, including reduced genetic diversity. We contrasted genetic diversity among both long-Bd-exposed and unexposed populations of the south-east Australian alpine tree frog (Litoria verreauxii alpina) across its range. At the population level, we found no significant differences in genetic diversity between Bd-exposed and unexposed populations. Encouragingly, even Bd-infected remnant populations that are now highly isolated maintain genetic diversity comparable to populations in which Bd is absent. Spatial genetic structure among populations followed an isolation-by-distance pattern, suggesting restricted movement among remnant populations. At the individual level, greater heterozygosity was associated with reduced probability of infection. Loss of genetic diversity in remnant populations that survived chytridiomycosis epidemics does not appear to be a threat to L. v. alpina. We suggest several factors underpinning maintenance of genetic diversity: (1) remnant populations have remained large enough to avoid losses of genetic diversity; (2) many individuals in the population are able to breed once before succumbing to disease; and (3) juveniles in the terrestrial environment have low exposure to Bd, providing an annual ‘reservoir’ of genetic diversity. The association between individual heterozygosity and infection status suggests that, while other work has shown all breeding adults are typically killed by Bd, males with greater heterozygosity may survive longer and obtain fitness benefits through extended breeding opportunities. Our results highlight the critical role of life history in mitigating the impacts of Bd infection for some amphibian species, but we infer that increased isolation as a result of disease-induced population extirpations will enhance population differentiation and thus biogeographic structure

Genetic diversity of Koala retrovirus (KoRV) env gene subtypes: Insights into northern and southern koala populations

Koala retrovirus (KoRV) is a recently endogenised retrovirus associated with neoplasia and immunosuppression in koala populations. The virus is known to display sequence variability and to be present at varying prevalence in different populations, with animals in southern Australia displaying lower prevalence and viral loads than northern animals. This study used a PCR and next generation sequencing strategy to examine the diversity of the KoRV env gene in both proviral DNA and viral RNA forms in two distinct populations representative of the “northern” and “southern” koala genotypes. The current study demonstrated that the full range of KoRV subtypes is present across both populations, and in both healthy and sick animals. KoRV-A was the predominant proviral subtype in both populations, but there was marked diversity of DNA and RNA subtypes within individuals. Many of the northern animals displayed a higher RNA viral diversity than evident in their proviral DNA, indicating relatively higher replication efficiency of non-KoRV-A subtypes. The southern animals displayed a lower absolute copy number of KoRV than the northern animals as reported previously and a higher preponderance of KoRV-A in individual animals. These discrepancies in viral replication and diversity remain unexplained but may indicate relative protection of the southern population from KoRV replication due to either viral or host factors and may represent an important protective effect for the host in KoRV’s ongoing entry into the koala genome

Genetic diversity and population structure of Peronosclerospora sorghi isolates of Sorghum in Uganda

Sorghum is the third most important staple cereal crop in Uganda after maize and millet. Downy mildew disease is one of the most devastating fungal diseases which limits the production and productivity of the crop. The disease is caused by an obligate fungus, Peronosclerospora sorghi (Weston & Uppal) with varying symptoms. Information on the genetic diversity and population structure of P.sorghi in sorghum is imperative for the screening and selection for resistant genotypes and further monitoring possible mutant(s) of the pathogen. Isolates of P. sorghi infecting sorghum are difficult to discriminate when morphological descriptors are used. The use of molecular markers is efficient, and reliably precised for characterizing P. sorghi isolates. This study was undertaken to assess the level of genetic diversity and population structure that exist in P. sorghi isolates in Uganda. A total of 195 P. sorghi isolates, sampled from 13 different geographic populations from 10 different regions (agro-ecological zones) was used. Eleven (11) molecular markers, comprising of four Random amplified microsatellite (RAM) and seven (7) Inter-Simple Sequence Repeat (ISSR) markers were used in this study. The analysis of molecular variation (AMOVA) based on 11 microsatellite markers showed significant (P < 0.001) intra-population (88.9 %, PhiPT = 0.111) and inter-population (8.4 %, PhiPR = 0.083) genetic variation, while the genetic variation among regions (2.7 %, PhiRT = 0.022) was not significant. The highest genetic similarity value (0.987 = 98.7 %) was recorded between Pader and Lira populations and the lowest genetic similarity (0.913 = 91.3 %) was observed between Namutumba and Arua populations. The mean Nei's genetic diversity index (H) and Shannon Information Index (I) were 0.308 and 0.471 respectively. Seven distinct cluster groups were formed from the 195 P. sorghi isolates based on their genetic similarity. Mantel test revealed no association between genetic differentiation and geographical distance (R2 = 0.0026, p = 0.02) within the 13 geographic populations

Genetic Diversity and Trait Association Analysis of Indonesian Rice (Oryza Sativa L.) Germplasm Using Ssr Markers

Generating a new crop variety with certain desirable traits requires germplasm collection with wide genetic diversity to facilitate accelerated development of improved cultivars. This study was conducted to characterize genetic diversity of Indonesian rice accessions using SSR markers and their agro-morphological characters to allow the identification of Marker Trait Association (MTA). A survey of genetic diversity among 72 traditional landraces of 15 provinces in Indonesia and 24 improved varieties was conducted using four multiplex panels of 14 fluorescent-labeled SSR markers and 22 agro-morphological characters. A total of 140 alleles with an average of 10 alleles per locus and Polymorphism Information Content (PIC) values at 0.73. The population structure identified five subgroups. A total of 4 highly significant MTA were identified. One character with highly significant MTA was number of panicle associated with RM277. Based on SSR marker, RM105 had two MTAs for auricle color and ligule shape. After validation, these MTAs may be deployed to improve rice productivity