Development and testing of new gene‐homologous EST‐SSRs for <i>Eucalyptus gomphocephala</i> (Myrtaceae)

Bradbury, Donna; Smithson, Ann; Krauss, Siegfried L.

doi:10.3732/apps.1300004

Cited by 13 publications

(8 citation statements)

References 13 publications

(14 reference statements)

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“…In addition, all individuals were genotyped using 11 EST‐SSRs previously optimized for E. gomphocephala ( EGM09 , EGM12 , EGM14 , EGM24 , EGM25 , EGM30 , EGM35 , EGM37 , EGM46 , EGM47 and EGM48 ) (Bradbury et al . ). These loci were developed from eucalypt homologs of annotated genes involved in diverse functions including flowering‐time regulation, desiccation tolerance and heat shock (Table ).…”

Section: Methodsmentioning

confidence: 97%

“…All 18 SSR loci were amplified in multiplex PCR and genotyped as described for EST‐SSRs in Bradbury et al . (), with some exceptions (Table ).…”

Section: Methodsmentioning

confidence: 99%

“…or contig number of source EST (from Bradbury et al . ); Eucalyptus grandis locus ID, locus name in E. grandis genome ( E. grandis Genome Project 2010, http://www.phytozome.net/eucalyptus); Location, location of the SSR repeat in E. grandis (UTR, untranslated region; CDS, coding region); Gene, top gene annotation (source: Bradbury et al . ); Size range, range of observed allele sizes; A T , total number of alleles observed; S , number of private alleles; H O , observed heterozygosity; H E , expected heterozygosity; F , fixation index; F ST , among‐population differentiation.…”

Section: Methodsmentioning

confidence: 99%

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Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

2013

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Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.

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Section: Methodsmentioning

confidence: 97%

“…All 18 SSR loci were amplified in multiplex PCR and genotyped as described for EST‐SSRs in Bradbury et al . (), with some exceptions (Table ).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

2013

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“…A total of 2,400 samples were genotyped at 14 microsatellite loci: EGM30, EGM47, EGM14, EGM12, EGM34, EMBRA10, EMBRA7, EMBRA20, EMBRA18, EMCRC11, EV22, EV23, EV28 and ES140 (Bradbury, Smithson, & Krauss, 2013;Brondani, Brondani, Tarchini, & Grattapaglia, 1998;Glaubitz, Emebiri, & Moran, 2001;Nevill et al, 2013;Steane et al, 2001). Details of DNA extraction, polymerase chain reaction conditions and scoring of electropherogram profiles are provided in Bezemer (2018).…”

Section: Study Species Sample Collection and Microsatellite Genotymentioning

confidence: 99%

Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial

et al. 2019

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Historically fragmented and specialized habitats such as granite outcrops are understudied globally unique hot spots of plant evolution. In contrast to predictions based on mainstream population genetic theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long‐lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south‐western Australia. To quantify population to landscape‐level genetic structure, we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterized by low levels of genetic diversity, small absolute population sizes, localized clonality and strong fine‐scale genetic subdivision. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographic neighbours separated by up to 20 km. Paradoxically, other pairs of neighbouring stands as little as 7 km apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provide some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly resprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.

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“…Microsatellite loci were amplified using nine primer pairs developed in other eucalypts (EGM25, EGM30, EGM47, EGM14, EGM12, EGM34, EGM35, EMBRA10 and EMBRA7) (Steane et al, 2001;Bradbury et al, 2013a) using the QIAGEN Multiplex PCR Kit (QIAGEN, Venio, Limburg, The Netherlands) as per the manufacturer's instructions. PCR conditions were as follows: 95°C for 5 min, then 30 cycles of 95°C for 30 s, 58°C for 1 min 30 s and 72°C for 30 s, followed by 60°C for 30 min.…”

Section: Microsatellite Genotypingmentioning

confidence: 99%

Paternity analysis reveals wide pollen dispersal and high multiple paternity in a small isolated population of the bird-pollinated Eucalyptus caesia (Myrtaceae)

et al. 2016

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Optimal foraging behaviour by nectavores is expected to result in a leptokurtic pollen dispersal distribution and predominantly near-neighbour mating. However, complex social interactions among nectarivorous birds may result in different mating patterns to those typically observed in insect-pollinated plants. Mating system, realised pollen dispersal and spatial genetic structure were examined in the bird-pollinated Eucalyptus caesia, a species characterised by small, geographically disjunct populations. Nine microsatellite markers were used to genotype an entire adult stand and 181 seeds from 28 capsules collected from 6 trees. Mating system analysis using MLTR revealed moderate to high outcrossing (t m = 0.479-0.806) and low estimates of correlated paternity (r p = 0.136 ± s.e. 0.048). Paternity analysis revealed high outcrossing rates (mean = 0.72) and high multiple paternity, with 64 different sires identified for 181 seeds. There was a significant negative relationship between the frequency of outcross mating and distance between mating pairs. Realised mating events were more frequent than expected with random mating for plants o40 m apart. The overall distribution of pollen dispersal distances was platykurtic. Despite extensive pollen dispersal within the stand, three genetic clusters were detected by STRUCTURE analysis. These genetic clusters were strongly differentiated yet geographically interspersed, hypothesised to be a consequence of rare recruitment events coupled with extreme longevity. We suggest that extensive polyandry and pollen dispersal is a consequence of pollination by highly mobile honeyeaters and may buffer E. caesia against the loss of genetic diversity predicted for small and genetically isolated populations.

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Development and testing of new gene‐homologous EST‐SSRs for Eucalyptus gomphocephala (Myrtaceae)

Cited by 13 publications

References 13 publications

Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial

Paternity analysis reveals wide pollen dispersal and high multiple paternity in a small isolated population of the bird-pollinated Eucalyptus caesia (Myrtaceae)

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