Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing
-
Published:2013-08-08
Issue:1
Volume:14
Page:
-
ISSN:1471-2156
-
Container-title:BMC Genetics
-
language:en
-
Short-container-title:BMC Genet
Author:
Dockter Rhyan B,Elzinga David B,Geary Brad,Maughan P Jeff,Johnson Leigh A,Tumbleson Danika,Franke JanaLynn,Dockter Keri,Stevens Mikel R
Abstract
Abstract
Background
Penstemon’s unique phenotypic diversity, hardiness, and drought-tolerance give it great potential for the xeric landscaping industry. Molecular markers will accelerate the breeding and domestication of drought tolerant Penstemon cultivars by, creating genetic maps, and clarifying of phylogenetic relationships. Our objectives were to identify and validate interspecific molecular markers from four diverse Penstemon species in order to gain specific insights into the Penstemon genome.
Results
We used a 454 pyrosequencing and GR-RSC (genome reduction using restriction site conservation) to identify homologous loci across four Penstemon species (P. cyananthus, P. davidsonii, P. dissectus, and P. fruticosus) representing three diverse subgenera with considerable genome size variation. From these genomic data, we identified 133 unique interspecific markers containing SSRs and INDELs of which 51 produced viable PCR-based markers. These markers produced simple banding patterns in 90% of the species × marker interactions (~84% were polymorphic). Twelve of the markers were tested across 93, mostly xeric, Penstemon taxa (72 species), of which ~98% produced reproducible marker data. Additionally, we identified an average of one SNP per 2,890 bp per species and one per 97 bp between any two apparent homologous sequences from the four source species. We selected 192 homologous sequences, meeting stringent parameters, to create SNP markers. Of these, 75 demonstrated repeatable polymorphic marker functionality across the four sequence source species. Finally, sequence analysis indicated that repetitive elements were approximately 70% more prevalent in the P. cyananthus genome, the largest genome in the study, than in the smallest genome surveyed (P. dissectus).
Conclusions
We demonstrated the utility of GR-RSC to identify homologous loci across related Penstemon taxa. Though PCR primer regions were conserved across a broadly sampled survey of Penstemon species (93 taxa), DNA sequence within these amplicons (12 SSR/INDEL markers) was highly diverse. With the continued decline in next-generation sequencing costs, it will soon be feasible to use genomic reduction techniques to simultaneously sequence thousands of homologous loci across dozens of Penstemon species. Such efforts will greatly facilitate our understanding of the phylogenetic structure within this important drought tolerant genus. In the interim, this study identified thousands of SNPs and over 50 SSRs/INDELs which should provide a foundation for future Penstemon phylogenetic studies and breeding efforts.
Publisher
Springer Science and Business Media LLC
Subject
Genetics(clinical),Genetics
Reference74 articles.
1. St Hilaire R, Arnold MA, Wilkerson DC, Devitt DA, Hurd BH, Lesikar BJ, Lohr VI, Martin CA, McDonald GV, Morris RL, Pittenger DR, Shaw DA, Zoldoske DF: Efficient water use in residential urban landscapes. HortScience. 2008, 43: 2081-2092. 2. Martin CA: Landscape water use in Phoenix, Arizona. Desert Plants. 2001, 17: 26-31. 3. Bradley BA, Blumenthal DM, Early R, Grosholz ED, Lawler JJ, Miller LP, Sorte CJB, D’Antonio CM, Diez JM, Dukes JS, Ibanez I, Olden JD: Global change, global trade, and the next wave of plant invasions. Front Ecol Environ. 2012, 10: 20-28. 10.1890/110145. 4. Burt JW, Muir AA, Piovia-Scott J, Veblen KE, Chang AL, Grossman JD, Weiskel HW: Preventing horticultural introductions of invasive plants: potential efficacy of voluntary initiatives. Biol Invasions. 2007, 9: 909-923. 10.1007/s10530-007-9090-4. 5. Broderick SR, Stevens MR, Geary B, Love SL, Jellen EN, Dockter RB, Daley SL, Lindgren DT: A survey of Penstemon’s genome size. Genome. 2011, 54: 160-173. 10.1139/G10-106.
Cited by
10 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|