Molecular Tools for Nursery Plant Production
Received Date: Oct 02, 2014 / Accepted Date: Oct 21, 2014 / Published Date: Oct 29, 2014
Breeding strategies in nursery plants is lagging behind most of the agricultural crops while molecular methods have been adopted last decade. Identification and verification of varieties for nursery plants were applied by molecular tools. Marker assisted breeding utilizes the DNA markers linked to genes of interest to achieve efficient selection strategies. Marker assisted selection (MAS) is a process whereby a marker is used for indirect selectionof genetic determinants of a trait of interest. There are different kinds of molecular markers, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), microsatellites and single nucleotide polymorphisms (SNPs). These molecular markers allow high density DNA marker maps. In this review, all of these molecular markers have been applied widely among crops and ornamentals and the advantages and disadvantages have been listed. The best molecular markers are those that distinguish multiple alleles per locus (highly polymorphic) and are co-dominant.
Keywords: Nursery; Production; Ornamentals; Molecular markers; SSR; AFLP; RFLP; RAPD; SRAP
Most of the traits of interest for plant breeding programs are quantitative traits. These traits are controlled by many genes and environmental factors. Phenotypic selection is the most common used form of selection in traditional genetic improvement programs. However, by using this method, you will not know which genes are actually being selected. With the development of molecular markers, marker assisted selection (MAS) become increasingly important in the coming years. MAS involve the selection of plants carrying genomic regions that are involved in the expression of traits of interest through molecular markers .
Molecular markers can be thought as constant landmarks in the plant genome. There are different kinds of molecular markers, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), microsatellites and single nucleotide polymorphisms (SNPs). These molecular markers allow high density DNA marker maps.
There are three types of relationships between the markers and the genes of interest. First, the molecular marker is located within the gene of interest. Second, the marker is in linkage disequilibrium (LD) with gene of interest throughout the whole population. Third, the marker is not in linkage disequilibrium with gene of interest throughout the whole population . This study will give a general review about molecular markers used in nursery plants
In genetics, a molecular marker is a fragment of DNA that associated with a certain location within the genome. Molecular markers are usually phenotypically neutral and could identify by techniques such as southern hybridization or PCR. Several different kinds of molecular marker could be applied on plant selection: such as restriction fragment length polymorphisms (RFLPs), is detected by southern hybridization. The principle of RFLPs is detecting a site in a genome where the distance between two restriction sites varies among different individuals. These sites are identified by restriction enzyme digests of chromosomal DNA. It requires a radioactive probe when do southern blotting.
Other methods involve using PCR, such as amplified fragment length polymorphisms (AFLPs) uses restriction enzymes to digestc genomic DNA . Usually this technique has three steps: first, digestion of total plant DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. Second, selective amplification of a subset of these fragments with two PCR primers that have corresponding adaptor and restriction site specific sequences. Third, run the amplicons on a gel matrix, followed by visualization of the band pattern. Random amplified polymorphic DNA (RAPDs) markers are about 10 nucleotide length DNA fragments from PCR amplification of random segments of genomic DNA. RAPDs are able to differentiate between genetically distinct individuals. In recent years, RAPD has been used to characterize the phylogeny of diverse plant and animal species . Single nucleotide polymorphisms (SNPs) refer to a single nucleotide difference in the sequence of a gene or segment of the genome . There are a variety of methods for analyzing SNPs; detection of SNPs can be done without gels, such as high resolution melting method. All of the above molecular markers have been applied widely among crops and ornamentals and the advantages and disadvantages have been listed in Table 1 . The best molecular markers are those that distinguish multiple alleles per locus (highly polymorphic) and are co-dominant (each allele can be observed).
|Molecular marker||Advantages||Disadvantages||Codominant (C) or Dominant (D)|
|Amplified fragment length Polymorphism (AFLP)||Multiple loci
High levels of polymorphism generated
|Large amounts of DNA required
|Simple sequence repeats (SSRs) or microsatellites||Technically simple
Robust and reliable
Transferable between population
|Large amounts of time and labor required for production of primers
Usually require polyacrylamide electrophoresis
|Restriction fragment length polymorphism (RFLP)||Robust
Transferable across populations
|Time-consuming, laborious and expensive
Large amount of DNA required
|Random amplified polymorphic DNA (RAPD)||Quick and simple
Multiple loci from a single primer possible
Small amounts of DNA required
|Problems with reproducibility
Generally not transferable
|Sequence-related amplified polymorphism (SRAP)||Simple
Moderate throughput ratio
Facile sequence of related bands
|Time and labor required for production of primers||C|
Table 1: Advantages and disadvantages of most commonly-used DNA markers.
Sequence-related amplified polymorphism (SRAP) is a simple marker technique aimed for the amplification of open reading frames. Based on two-primer amplification, SRAP combines simplicity, reliability, moderate throughput ratio and facile sequencing of selected bands .
Current status of applications of molecular markers in nursery plants production
Molecular marker technologies have been widely used in ornamental plants. Most of the traits of ornamental importance are quantitative traits with complex inheritance and regulated by several genes, the environment and their interactions. Moreover, improving polygenic traits through MAS is a complex process . Because more than one gene is involved in a quantitative trait, these genes have smaller individual effects on the phenotype. So the effect of the individual genes cannot be easily identified. In the following tables, the reader can find a brief summary of the current status regarding application of MAS in the different ornamentals. Gene-markers associated for important traits in ornamentals are listed in Table 2. Furthermore, marker selections in ornamentals by using amplified fragment length polymorphisms (AFLPs) method are showed in Table 3.
|Capsicum annuum L||Erect versus pendant orientated fruit||108 F2:3 individuals||Bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP)||Saengryeog 211 (pendant), Saengryeog 213 (erect)||A2C79||2008|
|Oil Palm||Genetic diversity||6 Cultivars||Simple sequence repeat (SSR)||20 SSR markers||2012|||
|Mei (Prunus mume Sieb. Et Zucc.)||Genome-wide characterization and linkage mapping||mei genome||Genome-wide characterization of simple sequence repeats (ssrs)||188,149 ssrs occurring at a frequency of 794 SSR/Mb.||2013|||
|Ornamental kale (Brassica oleracea L. Var. Acephala)||Artistic diversiform leaf color||500 F2 individuals||Sequence related amplified polymorphism (SRAP)||Re (red leaf)||Me8Em4 Me8Em17Me9Em11||2013|||
|Cherry plum (myrobalan plum)||Resistance to root-knot nematodes (RKN)||Ma1 and Ma3||SCAL19690 and SCAFLP2202||2004|||
|Paeonia||Genetic diversity||29 cultivars||Sequence related amplified polymorphism (SRAP)||24 primers||Me8/Em8 Me8/Em1||2008|||
|Dendrobium (Orchidaceae)||Genetic diversity||31 Chinese Dendrobium species||Sequence-related amplified polymorphism (SRAP)||14 primers||727 loci||2013|||
|Aechmea gomosepala||Genetic divergence of bromeliad hybrids||Sequence related amplified polymorphism (SRAP)||16 primers||265 loci||2012|||
Table 2: Selected examples of gene-marker associated for important traits in ornamentals.
|Heather (Calluna vulgaris)||Genetic mapping of the "bud-flowering"||Single mapping population||535 AFLP markers||2013|||
|Evergreen azalea||Genetic diversity||130 genotypes||3 primers (408 polymorphic fragments)||2013|||
|Mei (Prunus mume Sieb.et Zucc.)||Genetic diversity||65 accessions||64 -primer combination||2012|||
|Sinningia speciosa||Genetic diversity||24 accessions of S. Speciosa||16 primers||2012|||
|Viburnum||Interspecific cross||5 primers||2012|||
|Sacred lotus||Genetic diversity||58 accessions||20 primers||2012|||
|Spring orchid (Cymbidium goeringii)||Genetic diversity||Two wild populations||15 primer sets||2011|||
|Aquilegia (Ranunculaceae)||Genetic diversity||64 accessions||16 primers||2011|||
|Viola suavis||Parallel evolution of white-flowered morphotypes||36 populations||3 primers||2008|||
|Berberis thunbergii||Influence of invasive populations||85 plants representing five invasive populations.||6 primers||2008|||
|Ginkgo biloba||Genetic diversity||21 cultivars||64 primers||2006|||
|Yellow camellia (Camellia nitidissima)||Genetic diversity||6 populations||8 primers||2006|||
|Aglaonema||Genetic diversity||54 culivars||53 primers||2004|||
Table 3: Selected examples of amplified fragment length polymorphisms (AFLPs) marker assisted selection in ornamentals.
In nursery plants production, the majority of application of molecular marker is used for genetic diversity studies. However, MAS for quantitative traits is a difficult task in ornamentals, as with many other crops. Further advances in molecular technology and genome programs will soon create a wealth of information that can be exploited for the genetic improvement of ornamental crops. High-throughput genotyping, for example, will allow direct selection on marker information based on population-wide LD. Methods to effectively analyze and use this information in selection are still to be developed. The eventual application of these technologies in practical breeding programs will be on the basis of economic grounds, which, along with cost-effective technology, will require further evidence of predictable and sustainable genetic advances using MAS. Until complex traits can be fully dissected, the application of MAS will be limited to genes of moderate-to large effect and to applications that do not endanger the response to conventional selection. Until then, observable phenotype will remain an important component of genetic improvement programs, because it takes account of the collective effect of all genes.
- Young ND (1999) A cautiously optimistic vision for marker-assisted breeding. Mol Breeding, 5: 505-510.
- Babu R, Nair SK, Prasanna, BM, Gupta HS (2004) Integrating marker-assisted selection in crop breeding - Prospects and challenges. Current Science. 87: 607-619.
- Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12: 106-117.
- Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27: 617-631.
- Liu CG, Zhang GQ (2006) Single nucleotide polymorphism (SNP) and its application in rice. Yi Chuan 28: 737-744.
- Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica, 142: 169-196.
- Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet, 103: 455-461.
- Nakaya A, Isobe SN (2012) Will genomic selection be a practical method for plant breeding? Ann Bot 110: 1303-1316.
- Lee HR, Cho MC, Kim HJ, Park SW, Kim BD (2008) Marker development for erect versus pendant-orientated fruit in Capsicum annuum L. Mol Cells, 26: 548-553.
- Zaki NM, Singh R, Rosli R, Ismail I (2012) Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae. Int J Mol Sci. 13: 4069-4088.
- Sun L, Yang W, Zhang Q, Cheng T, Pan H, et al. (2013) Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.). PLoS One 8: e59562.
- Wang YS, Liu ZY, Li YF, Zhang Y, Yang XF, Feng H (2013) Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala). Genet Mol Res, 12: 870-877.
- Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N et al. (2004) Microsatellite genetic linkage maps of myrobalan plum and an almond-peach hybrid--location of root-knot nematode resistance genes. 109: 827-38.
- Hao Q, Liu ZA, Shu QY, Zhang R, De Rick J, et al. (2008) Studies on Paeonia cultivars and hybrids identification based on SRAP analysis. Hereditas 145: 38-47.
- Hao Q, Liu ZA, Shu QY, Zhang R, De Rick J, et al. (2008) Studies on Paeonia cultivars and hybrids identification based on SRAP analysis. Hereditas 145: 38-47.
- Feng SG, Lu JJ, Gao L, Liu JJ, Wang HZ (2014) Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China. Biochem Genet 52: 127-136.
- Zhang F, Ge YY, Wang WY, Shen XL, Yu XY (2012) Assessing genetic divergence in interspecific hybrids of Aechmea gomosepala and A. recurvata var. recurvata using inflorescence characteristics and sequence-related amplified polymorphism markers. Genet Mol Res, 11: 4169-4178.
- Behrend A, Borchert T, Spiller M, Hohe A (2013) AFLP-based genetic mapping of the "bud-flowering" trait in heather (Calluna vulgaris). BMC Genet 14: 64.
- Zhou H, Liao J, Xia YP, Teng YW (2013) Determination of genetic relationships between evergreen azalea cultivars in China using AFLP markers. J Zhejiang Univ Sci B, 14: 299-308.
- Zaitlin D (2012) Intraspecific diversity in Sinningia speciosa (Gesneriaceae: Sinningieae), and possible origins of the cultivated florist's gloxinia. AoB Plants 2012: pls039.
- Al-Niemi T, Weeden NF, McCown BH, Hoch WA (2012) Genetic analysis of an interspecific cross in ornamental Viburnum (Viburnum). J Hered 103: 2-12.
- Hu J, Pan L, Liu H, Wang S, Wu Z, et al. (2012) Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers. Mol Biol Rep 39: 3637-3647.
- Huang JL, Zeng CX, Li HT, Yang JB (2011) Isolation and characterization of 15 microsatellite markers from the spring orchid (Cymbidium goeringii) (Orchidaceae). Am J Bot 98: e76-77.
- Zhu RR, Gao YK, Xu LJ, Zhang QX (2011) Genetic diversity of Aquilegia (Ranunculaceae) species and cultivars assessed by AFLPs. Genet Mol Res 10: 817-827.
- Mereda P Jr, Hodálová I, Mártonfi P, Kucera J, Lihová J (2008) Intraspecific variation in Viola suavis in Europe: parallel evolution of white-flowered morphotypes. Ann Bot 102: 443-462.
- Lubell JD, Brand MH, Lehrer JM, Holsinger KE (2008) Detecting the influence of ornamental Berberis thunbergii var. atropurpurea in invasive populations of Berberis thunbergii (Berberidaceae) using AFLP1. Am J Bot 95: 700-705.
- Wang L, Xing SY, Yang KQ, Wang ZH, Guo YY, et al. (2006) Genetic relationships of ornamental cultivars of Ginkgo biloba analyzed by AFLP techniques. Yi Chuan Xue Bao 33: 1020-1026.
- Tang S, Bin X, Wang L, Zhong Y (2006) Genetic diversity and population structure of yellow camellia (Camellia nitidissima) in China as revealed by RAPD and AFLP markers. Biochem Genet, 44: 449-461.
Citation: Jiang P (2014) Molecular Tools for Nursery Plant Production. Adv Crop Sci Tech 2:146. Doi: 10.4172/2329-8863.1000146
Copyright: © 2014 Jiang P. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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