Validation of doubled haploid plants by enzymatic mismatch cleavage

Plant Methods

Bradley J Till²  Jochen Kumlehn¹  Ingrid Otto¹  Andrea Müller¹  Joanna Jankowicz-Cieslak²  Owen A Huynh²  Bernhard J Hofinger² 

[1] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany;Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria

关键词: Loss of heterozygosity;    Single-strand-specific nuclease;    TILLING;    Polymorphism discovery;   

Others  :  805713
DOI  :  10.1186/1746-4811-9-43

 received in 2013-08-07, accepted in 2013-11-01,  发布年份 2013

【 摘 要 】

Background

Doubled haploidy is a fundamental tool in plant breeding as it provides the fastest way to generate populations of meiotic recombinants in a genetically fixed state. A wide range of methods has been developed to produce doubled haploid (DH) plants and recent advances promise efficient DH production in otherwise recalcitrant species. Since the cellular origin of the plants produced is not always certain, rapid screening techniques are needed to validate that the produced individuals are indeed homozygous and genetically distinct from each other. Ideal methods are easily implemented across species and in crops where whole genome sequence and marker resources are limited.

Results

We have adapted enzymatic mismatch cleavage techniques commonly used for TILLING (Targeting Induced Local Lesions IN Genomes) for the evaluation of heterozygosity in parental, F1 and putative DH plants. We used barley as a model crop and tested 26 amplicons previously developed for TILLING. Experiments were performed using self-extracted single-strand-specific nuclease and standard native agarose gels. Eleven of the twenty-six tested primers allowed unambiguous assignment of heterozygosity in material from F1 crosses and loss of heterozygosity in the DH plants. Through parallel testing of previously developed Simple Sequence Repeat (SSR) markers, we show that 3/32 SSR markers were suitable for screening. This suggests that enzymatic mismatch cleavage approaches can be more efficient than SSR based screening, even in species with well-developed markers.

Conclusions

Enzymatic mismatch cleavage has been applied for mutation discovery in many plant species, including those with little or no available genomic DNA sequence information. Here, we show that the same methods provide an efficient system to screen for the production of DH material without the need of specialized equipment. This gene target based approach further allows discovery of novel nucleotide polymorphisms in candidate genes in the parental lines.

【 授权许可】

   
2013 Hofinger et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Blakeslee AF, Belling J, Farnham ME, Bergner AD: A Haploid Mutant in the Jimson Weed, “Datura Stramonium”. Science 1922, 55(1433):646-647.
• [2]Maluszynski M, Kasha KJ, Szarejko I: Published doubled haploid protocols in plant species. In Doubled Haploid Production in Crop Plants, A Manual. Edited by Maluszynski M, Kasha KJ, Forster BP, Szarejko I. Dordecht: Kluwer Academic Publishers; 2003:309-335.
• [3]Forster BP, Heberle-Bors E, Kasha KJ, Touraev A: The resurgence of haploids in higher plants. Trends Plant Sci 2007, 12(8):368-375.
• [4]Kasha KJ, Kao KN: High frequency haploid production in barley (Hordeum vulgare L.). Nature 1970, 225(5235):874-876.
• [5]Pickering RA, Morgan PW: The influence of temperature on chromosome elimination during embryo development in crosses involving Hordeum spp., wheat (Triticum aestivum L.) and rye (Secale cereale L.). Theor Appl Genet 1985, 70:199-206.
• [6]Hoekstra S, VanZijderveld MH, Louwerse JD, Heidekamp F, Van der Mark F: Anther and microspore culture of Hordeum vulgare L. Cv. Igri. Plant Sci 1992, 86:89-96.
• [7]Coronado MJ, Hensel G, Broeders S, Otto I, Kumlehn J: Immature pollen-derived doubled haploid formation in barley cv. Golden Promise as a tool for transgene recombination. Physiol Plantarum. Acta Physiol Plant 2005, 27:591-599.
• [8]Oleszczuk S, Sowa S, Zimny J: Androgenic response to preculture stress in microspore cultures of barley. Protoplasma 2006, 228(1–3):95-100.
• [9]Gonzalez-Melendi P, Ramirez C, Testillano PS, Kumlehn J, Risueno MC: Three dimensional confocal and electron microscopy imaging define the dynamics and mechanisms of diploidisation at early stages of barley microspore-derived embryogenesis. Planta 2005, 222(1):47-57.
• [10]Daghma DS, Kumlehn J, Hensel G, Rutten T, Melzer M: Time-lapse imaging of the initiation of pollen embryogenesis in barley (Hordeum vulgare L.). J Exp Bot 2012, 63(16):6017-6021.
• [11]Stein N, Perovic D, Kumlehn J, Pellio B, Stracke S, Streng S, Ordon F, Graner A: The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.). Plant J 2005, 42(6):912-922.
• [12]Kumlehn J, Serazetdinova L, Hensel G, Becker D, Loerz H: Genetic transformation of barley (Hordeum vulgare L.) via infection of androgenetic pollen cultures with Agrobacterium tumefaciens. Plant Biotechnol J 2006, 4(2):251-261.
• [13]Kapusi E, Ma L, Teo CH, Hensel G, Himmelbach A, Schubert I, Mette MF, Kumlehn J, Houben A: Telomere-mediated truncation of barley chromosomes. Chromosoma 2012, 121(2):181-190.
• [14]Kapusi E, Hensel G, Coronado MJ, Broeders S, Marthe C, Otto I, Kumlehn J: The elimination of a selectable marker gene in the doubled haploid progeny of co-transformed barley plants. Plant Mol Biol 2013, 81(1–2):149-160.
• [15]Ravi M, Chan SW: Haploid plants produced by centromere-mediated genome elimination. Nature 2010, 464(7288):615-618.
• [16]Geiger HH, Gordillo GA: Doubled haploids in hybrid maize breeding. Maydica 2009, 54:485-499.
• [17]Munyon IP, Hubstenberger JF, Phillips GC: Origin of plantlets and callus obtained from chile pepper anther cultures. In Vitro Cell Dev Biol 1989, 25:293-296.
• [18]Jankowicz-Cieslak J, Huynh OA, Bado S, Matijevic M, Till BJ: Reverse-genetics by TILLING expands through the plant kingdom. Emirates Journal of Food and Agriculture 2011, 23(4):290-300.
• [19]Till BJ, Zerr T, Comai L, Henikoff S: A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 2006, 1(5):2465-2477.
• [20]Till BJ, Jankowicz-Cieslak J, Sagi L, Huynh OA, Utsushi H, Swennen R, Terauchi R, Mba C: Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling. Theor Appl Genet 2010, 121(7):1381-1389.
• [21]Jankowicz-Cieslak J, Huynh OA, Brozynska M, Nakitandwe J, Till BJ: Induction, rapid fixation and retention of mutations in vegetatively propagated banana. Plant Biotechnol J 2012, 10(9):1056-1066.
• [22]Slade AJ, McGuire C, Loeffler D, Mullenberg J, Skinner W, Fazio G, Holm A, Brandt KM, Steine MN, Goodstal JF, et al.: Development of high amylose wheat through TILLING. BMC Plant Biol 2012, 12:69. BioMed Central Full Text
• [23]Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M: TILLING - a shortcut in functional genomics. J Appl Genet 2011, 52(4):371-390.
• [24]Sato Y, Shirasawa K, Takahashi Y, Nishimura M, Nishio T: Mutant Selection from Progeny of Gamma-ray-irradiated Rice by DNA Heteroduplex Cleavage using Brassica Petiole Extract. Breed Sci 2006, 56(2):179-183.
• [25]Till BJ, Burtner C, Comai L, Henikoff S: Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 2004, 32(8):2632-2641.
• [26]Garvin MR, Gharrett AJ: DEco-TILLING: an inexpensive method for single nucleotide polymorphism discovery that reduces ascertainment bias. Mol Ecol Notes 2007, 7(5):735-746.
• [27]Raghavan C, Naredo MEB, Wang HH, Atienza G, Liu B, Qiu FL, McNally KL, Leung H: Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol Breeding 2007, 19(2):87-101.
• [28]Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, et al.: Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 2004, 37(5):778-786.
• [29]Dunwell JM, Wilkinson MJ, Nelson S, Wening S, Sitorus AC, Mienanti D, Alfiko Y, Croxford AE, Ford CS, Forster BP, et al.: Production of haploids and doubled haploids in oil palm. BMC Plant Biol 2010, 10:218. BioMed Central Full Text
• [30]Murovec J, Stajner N, Jakse J, Javornik B: Microsatellite Marker for Homozygosity Testing of Putative Doubled Haploids and Characterization of Mimulus Species Derived by a Cross-genera Approach. J Am Soc Hortic Sci 2007, 132(5):659-663.
• [31]Nelson MN, Mason AS, Castello MC, Thomson L, Yan G, Cowling WA: Microspore culture preferentially selects unreduced (2n) gametes from an interspecific hybrid of Brassica napus L. x Brassica carinata Braun. Theor Appl Genet 2009, 119(3):497-505.
• [32]Chani E, Veilleux RE, Boluarte-Medina T: Improved androgenesis of interspecific potato and efficiency of SSR markers to identify homozygous regenerants. Plant Cell Tiss Org Cult 2000, 60:101-112.
• [33]Varshney RK, Marcel TC, Ramsay L, Russell J, Roder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A: A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 2007, 114(6):1091-1103.
• [34]Szurman-Zubrzycka M: Identification of new alleles of genes potentially related to root system development in Hordeum vulgare and their functional analysis. PhD thesis. Katowice. Poland: University of Silesia; 2013.
• [35]Gottwald S, Bauer P, Komatsuda T, Lundqvist U, Stein N: TILLING in the two-rowed barley cultivar ‘Barke’ reveals preferred sites of functional diversity in the gene HvHox1. BMC Res Notes 2009, 2:258. BioMed Central Full Text
• [36]Mejlhede N, Kyjovska Z, Backes G, Burhenne K, Rasmussen SK, Jahoor A: EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley. Plant Breed 2006, 125(5):461-467.
• [37]Till BJ, Zerr T, Bowers E, Greene EA, Comai L, Henikoff S: High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res 2006, 34(13):e99.
• [38]Bulgarelli D, Biselli C, Collins NC, Consonni G, Stanca AM, Schulze-Lefert P, Vale G: The CC-NB-LRR-type Rdg2a resistance gene confers immunity to the seed-borne barley leaf stripe pathogen in the absence of hypersensitive cell death. PLoS One 2010, 5:9.
• [39]Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, et al.: TILLING to detect induced mutations in soybean. BMC Plant Biol 2008, 8:9. BioMed Central Full Text