Cost-effective microsatellite markers for Banksia integrifolia (Proteaceae).
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ABSTRACT:
SUBMITTER: Fatemi M
PROVIDER: S-EPMC4105364 | biostudies-literature | 2013 Feb
REPOSITORIES: biostudies-literature
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Project description:Microsatellite markers were developed and cross-species transferability assessed for two Persoonia species to evaluate genetic diversity and population genetic structure of these broadly distributed southwest Australian tree species. • Microsatellite-enriched libraries and 454 GS-FLX shotgun sequencing were used to identity nine microsatellite loci for P. elliptica (one 454; eight cloning) and six for P. longifolia (three 454; three cloning). These loci were screened for variation in individuals from populations in southwestern Australia. In P. elliptica, observed and expected heterozygosities ranged from 0.46 to 0.93 and 0.42 to 0.88, respectively. For P. longifolia, observed and expected heterozygosities ranged from 0.04 to 0.88 and 0.04 to 0.84, respectively. • The microsatellites identified in this study will enable the examination of population and spatial structuring of genetic diversity in P. elliptica and P. longifolia, two priority species for mine site restoration in southwestern Australia.
| S-EPMC4103465 | biostudies-literature
Project description:BackgroundThe large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information. To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741.ResultsOver 95 gigabases of DNA and RNA-seq sequence data were de novo assembled and annotated. The draft assembly has a total length of 518 Mb and spans approximately 79% of the estimated genome size. Following annotation, 35,337 protein-coding genes were predicted of which over 90% were expressed in at least one of the leaf, shoot or flower tissues examined. Gene family comparisons with five other eudicot species revealed 13,689 clusters containing macadamia genes and 1005 macadamia-specific clusters, and provides evidence for linage-specific expansion of gene families involved in pathogen recognition, plant defense and monoterpene synthesis. Cyanogenesis is an important defense strategy in the Proteaceae, and a detailed analysis of macadamia gene homologues potentially involved in cyanogenic glycoside biosynthesis revealed several highly expressed candidate genes.ConclusionsThe gene space of macadamia provides a foundation for comparative genomics, gene discovery and the acceleration of molecular-assisted breeding. This study presents the first available genomic resources for the large basal eudicot family Proteaceae, access to most macadamia genes and opportunities to uncover the genetic basis of traits of importance for adaptation and crop improvement.
| S-EPMC5114810 | biostudies-literature
Project description:PremiseRecent habitat fragmentation is posing a risk to the wavy-leaved smokebush, Conospermum undulatum (Proteaceae), a rare plant species endemic to southwestern Western Australia. Microsatellite markers are required to characterize the genetic diversity and structure of the species for conservation purposes and to facilitate ecological studies.Methods and resultsIllumina MiSeq high-throughput sequencing was used to develop 20 novel microsatellite markers for C. undulatum. Polymorphism at each locus was assessed using 72 individuals from three natural populations. Nineteen markers were polymorphic, with the number of alleles per locus ranging from two to 21, and observed and expected heterozygosity ranging from 0.000 to 1.000 and 0.117 to 0.919, respectively. All markers successfully amplified in three congeneric species (C. stoechadis, C. canaliculatum and C. triplinervium).ConclusionsThe microsatellite markers will be useful for revealing patterns of genetic diversity, dispersal dynamics, and hybridization events for C. undulatum to inform future conservation efforts.
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Project description:BackgroundHotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself.ResultsAlthough Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone.ConclusionsThe geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.
| S-EPMC3751403 | biostudies-literature
Project description:Background and aimsPollen limitation is most prevalent among bee-pollinated plants, self-incompatible plants and tropical plants. However, we have very little understanding of the extent to which pollen limitation affects fruit set in mass-flowering trees despite tree crops accounting for at least 600 million tons of the 9200 million tons of annual global food production.MethodsWe determined the extent of pollen limitation in a bee-pollinated, partially self-incompatible, subtropical tree by hand cross-pollinating the majority of flowers on mass-flowering macadamia (Macadamia integrifolia) trees that produce about 200 000-400 000 flowers. We measured tree yield and kernel quality and estimated final fruit set. We genotyped individual kernels by MassARRAY to determine levels of outcrossing in orchards and assess paternity effects on nut quality.Key resultsMacadamia trees were pollen-limited. Supplementary cross-pollination increased nut-in-shell yield, kernel yield and fruit set by as much as 97, 109 and 92 %, respectively. The extent of pollen limitation depended upon the proximity of experimental trees to trees of another cultivar because macadamia trees were highly outcrossing. Between 84 and 100 % of fruit arose from cross-pollination, even at 200 m (25 rows) from orchard blocks of another cultivar. Large variations in nut-in-shell mass, kernel mass, kernel recovery and kernel oil concentration were related to differences in fruit paternity, including between self-pollinated and cross-pollinated fruit, thus demonstrating pollen-parent effects on fruit quality (i.e. xenia).ConclusionsThis study is the first to demonstrate pollen limitation in a mass-flowering tree. Improved pollination led to increased kernel yield of 0.31-0.59 tons ha-1, which equates currently to higher farm-gate income of approximately $US3720-$US7080 ha-1. The heavy reliance of macadamia flowers on cross-pollination and the strong xenia effects on kernel mass demonstrate the high value that pollination services can provide to food production.
| S-EPMC8796667 | biostudies-literature
Project description:BackgroundSequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has burgeoned, leading to well-supported angiosperm phylogenies. However, some relationships, particulary among early-diverging lineages, remain unresolved. The diverse Southern Hemisphere plant family Proteaceae arose on the ancient supercontinent Gondwana early in angiosperm history and is a model group for adaptive radiation in response to changing climatic conditions. Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses.ResultsThe chloroplast genome of the Australian nut crop tree Macadamia integrifolia was assembled de novo from Illumina paired-end sequence reads. Three contigs, corresponding to a collapsed inverted repeat, a large and a small single copy region were identified, and used for genome reconstruction. The complete genome is 159,714 bp in length and was assembled at deep coverage (3.29 million reads; ~2000 x). Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo. Genome structure and content followed the ancestral angiosperm pattern and were highly conserved in the Proteales, whilst size differences were largely explained by the relative contraction of the single copy regions and expansion of the inverted repeats in Macadamia.ConclusionsThe Macadamia chloroplast genome presented here is the first in the Proteaceae, and confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales. It provides a high-quality reference genome for future evolutionary studies and will be of benefit for taxon-rich phylogenomic analyses aimed at resolving relationships among early-diverging angiosperms, and more broadly across the plant tree of life.
| S-EPMC4290595 | biostudies-literature
Project description:BACKGROUND: Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conservation management, no species-specific microsatellite marker has been reported. METHODS: We adopted next-generation sequencing (NGS) to elucidate the microsatellite markers of Korean water deer and overcome these impediments on marker developments. We performed genotyping to determine the efficiency of this method as applied to population genetics. RESULTS: We obtained 98 Mbp of nucleotide information from 260,467 sequence reads. A total of 20,101 di-/tri-nucleotide repeat motifs were identified; di-repeats were 5.9-fold more common than tri-repeats. [CA](n) and [AAC](n)/[AAT](n) repeats were the most frequent di- and tri-repeats, respectively. Of the 17,206 di-repeats, 12,471 microsatellite primer pairs were derived. PCR amplification of 400 primer pairs yielded 106 amplicons and 79 polymorphic markers from 20 individual Korean water deer. Polymorphic rates of the 79 new microsatellites varied from 2 to 11 alleles per locus (H(e): 0.050-0.880; H(o): 0.000-1.000), while those of known microsatellite markers transferred from cattle to Chinese water deer ranged from 4 to 6 alleles per locus (H(e): 0.279-0.714; H(o): 0.300-0.400). CONCLUSIONS: Polymorphic microsatellite markers from Korean water deer were successfully identified using NGS without any prior sequence information and deposited into the public database. Thus, the methods described herein represent a rapid and low-cost way to investigate the population genetics of endangered/non-model species.
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Project description:The frequency and intensity of drought events are predicted to increase because of climate change, threatening biodiversity and terrestrial ecosystems in many parts of the world. Drought has already led to declines in functionally important tree species, which are documented in dieback events, shifts in species distributions, local extinctions, and compromised ecosystem function. Understanding whether tree species possess the capacity to adapt to future drought conditions is a major conservation challenge. In this study, we assess the capacity of a functionally important plant species from south-eastern Australia (Banksia marginata, Proteaceae) to adapt to water-limited environments. A water-manipulated common garden experiment was used to test for phenotypic plasticity and genetic adaptation in seedlings sourced from seven provenances of contrasting climate-origins (wet and dry). We found evidence of local adaptation relating to plant growth investment strategies with populations from drier climate-origins showing greater growth in well-watered conditions. The results also revealed that environment drives variation in physiological (stomatal conductance, predawn and midday water potential) and structural traits (wood density, leaf dry matter content). Finally, these results indicate that traits are coordinated to optimize conservation of water under water-limited conditions and that trait coordination (phenotypic integration) does not constrain phenotypic plasticity. Overall, this study provides evidence for adaptive capacity relating to drought conditions in B. marginata, and a basis for predicting the response to climate change in this functionally important plant species.
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