Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs

Liewlaksaneeyanawin, Cherdsak; Ritland, Carol; El‐Kassaby, Yousry A.; Ritland, Kermit

doi:10.1007/s00122-004-1635-7

Cited by 145 publications

(118 citation statements)

References 30 publications

(30 reference statements)

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“…Twelve nuclear microsatellite primers developed for Pinus taeda (Elsik et al, 2000;Auckland et al, 2002;Liewlaksaneeyanawin et al, 2004;Chagn et al, 2004) and Pinus sylvestris (Soranzo et al, 1998) were selected to genotype all the individuals. The amplified microsatellite primers are PtTX2146, PtTX3107, PtTX3116, PtTX4001, PtTX4011, LOP1, LOP3, SPAC 12:5, SPAG 7:14, SPAC 11:8, SsrPt_ctg64 and Ssr_ctg4487b.…”

Section: Methodsmentioning

confidence: 99%

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

et al. 2009

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We have investigated the fine-scale spatial genetic structure in a managed Scots pine forest. For this purpose, we perform a Bayesian genetic-cluster analysis of 96 geographically mapped individual seed trees of Swedish Scots pine based on 14 microsatellite loci. The analysis was carried out with the recently developed program GENECLUST (François et al., 2006), which provides the facility to jointly incorporate both spatial information from a geographical neighborhood structure through a Potts-Dirichlet model and account for variable degrees of inbreeding within the clusters. To evaluate whether inbreeding and spatial interaction should be included in the best-fitting statistical model for our data, we used the deviance information criterion (DIC), a weighted measure of model fit that accounts for an effective number of free parameters in a model. Analysis shows that a model with a single estimated cluster, with high levels of inbreeding (0.25) and with a moderate amount of spatial dependency within the unique cluster (C ¼ 0.2-0.4), best explains the data. We also carried out Bayesian parentage analysis, which enabled us to exclude the possibility that the sample constitutes one single full-sib family.

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Section: Methodsmentioning

confidence: 99%

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

et al. 2009

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“…Total genomic DNA was isolated using E-Z 96 Plant DNA kit (OMEGA Bio-Tek, Norcross, GA) following the manufacturer's protocol. Genotypes were determined at nine nuclear SSR loci, eight developed for loblolly pine (PtTX2146, PtTX3025, PtTX3107, PtTX3116, PtTX4001 (Auckland et al 2002), SsrPt_ctg1376, SsrPt_ctg4363 (Chagne et al 2004), and LOP1 (Liewlaksaneeyanawin et al 2004)) and one, SPAC12.5, developed for Scots pine (Soranzo et al 1998). PCR amplification was performed in simplex reactions as described in Torimaru et al (2009).…”

Section: Dna Isolation and Pcr Amplificationmentioning

confidence: 99%

Mating dynamics of Scots pine in isolation tents

Funda

Wennström

Almqvist

et al. 2016

Tree Genetics & Genomes

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Seed orchards are forest tree production populations for supplying the forest industry with consistent and abundant seed crops of superior genetic quality. However, genetic quality can be severely affected by non-random mating among parents and the occurrence of background pollination. This study analyzed mating structure and background pollination in six large isolation tents established in a clonal Scots pine seed orchard in northern Sweden. The isolation tents were intended to form a physical barrier against background pollen and induce earlier flowering relative to the surrounding trees. We scored flowering phenology inside and outside the tents and tracked airborne pollen density inside and outside the seed orchard in three consecutive pollination seasons. We genotyped 5683 offspring collected from the tents and open controls using nine microsatellite loci, and assigned paternity using simple exclusion method. We found that tent trees shed pollen and exhibited maximum female receptivity approximately 1 week earlier than trees in open control. The majority of matings in tents (78.3 %) occurred at distances within two trees apart (about 5 m). Selffertilization was relatively high (average 21.8 %) in tents without supplemental pollination (SP), but it was substantially reduced in tents with SP (average 7.7 %). Pollen contamination was low in open controls (4.8-7.1 %), and all tents remained entirely free of foreign pollen. Our study demonstrates that tent isolation is effective in blocking pollen immigration and in manipulating flowering phenology. When complimented with supplemental pollination, it could become a useful seed orchard management practice to optimize the gain and diversity of seed orchard crops.

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“…Finally, high levels transferability and substantial polymorphism were observed among 23 cotton (Gossypium) species (Guo et al, 2006). In general terms, this sort of transferability is unique to EST-SSRs, with anonymous SSRs being significantly less portable (Chagne et al, 2004;Liewlaksaneeyanawin et al, 2004;Gutierrez et al, 2005;Pashley et al, 2006; but see Fitzsimmons et al, 1995;Dayanandan et al, 1997). EST-SSRs have also been shown to produce substantially 'cleaner' data (that is, easier to analyze/interpret amplification profiles) as compared to their anonymous counterparts .…”

Section: Jr Ellis and Jm Burkementioning

confidence: 99%

“…Another obvious concern is that since EST-SSRs are located within genes, and thus more conserved across species, they may be less polymorphic than anonymous SSRs. This concern has been borne out in a number of taxa, including rice (Cho et al, 2000), bread wheat (Gupta et al, 2003), pines (Liewlaksaneeyanawin et al, 2004), barley (Chabane et al, 2005) and sunflower . However, the levels of genetic diversity revealed by these markers are still considerably higher than those revealed by most alternative marker types, such as allozymes (Hamrick and Godt, 1996).…”

Section: Jr Ellis and Jm Burkementioning

confidence: 99%

“…In general, EST-SSRs have been found to be significantly more transferable across taxonomic boundaries than are traditional 'anonymous' SSRs (Chagne et al, 2004;Liewlaksaneeyanawin et al, 2004;Gutierrez et al, 2005;Pashley et al, 2006), and reports of EST-SSR transferability have become increasingly common. This is particularly true in plants, where transferability among economically important crop taxa has been demonstrated on a number of occasions (Decroocq et al, 2003;Thiel et al, 2003;Bandopadhyay et al, 2004;Saha et al, 2004;Varshney et al, 2005b).…”

Section: Introductionmentioning

confidence: 99%

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EST-SSRs as a resource for population genetic analyses

2007

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Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

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Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs

Cited by 145 publications

References 30 publications

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

Mating dynamics of Scots pine in isolation tents

EST-SSRs as a resource for population genetic analyses

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