scholarly journals Developing Microsatellite DNA Markers in Pecan

2003 ◽  
Vol 128 (3) ◽  
pp. 374-380 ◽  
Author(s):  
L.J. Grauke ◽  
Muhammad J. Iqbal ◽  
Avutu S. Reddy ◽  
Tommy E. Thompson

A microsatellite-enriched library was developed from `Halbert', a native pecan [Carya illinoinensis (Wangenh.) K. Koch] selection from Coleman County, Texas. A genomic library enriched for simple sequence repeats (SSR) containing 6144 clones was archived in 384 well plates for screening. In total, 439 clones were identified after Southern hybridization using di- and tri-nucleotide repeats as probes. In total, 125 positive clones were sequenced and primers were designed for 24 repeats. The SSR markers chosen for analysis include di-(CT and GA) and tri-nucleotide repeats (CTT, GAA and GAT). Of the 24 primer pairs tested, 19 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the National Clonal Germplasm Repository (NCGR) Carya collections. The 19 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing polymorphism. The number of fragments amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. Evaluation of the data confirms the utility of the microsatellites in delimiting known relationships.

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 293-297 ◽  
Author(s):  
Muhammad H Rahman ◽  
S Dayanandan ◽  
Om P Rajora

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. Key words: poplar, microsatellites, genetic mapping, simple sequence repeat (SSR) markers, DNA fingerprinting.


Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1083-1094 ◽  
Author(s):  
Muhammad H Rahman ◽  
Om P Rajora

Accurate identification of Populus clones and cultivars is essential for effective selection, breeding, and genetic resource management programs. The unit of cultivation and breeding in poplars is a clone, and individual cultivars are normally represented by a single clone. Microsatellite DNA markers of 10 simple sequence repeat loci were used for genetic fingerprinting and differentiation of 96 clones/cultivars and varieties belonging to six Populus species (P. deltoides, P. nigra, P. balsamifera, P. trichocarpa, P. grandidentata, and P. maximowiczii) from three sections of the genus. All 96 clones/cultivars could be uniquely fingerprinted based on their single- or multilocus microsatellite genotypes. The five P. grandidentata clones could be differentiated based on their single-locus genotypes, while six clones of P. trichocarpa and 11 clones of P. maximowiczii could be identified by their two-locus genotypes. Twenty clones of P. deltoides and 25 clones of P. nigra could be differentiated by their multilocus genotypes employing three loci, and 29 clones of P. balsamifera required the use of multilocus genotypes at five loci for their genetic fingerprinting and differentiation. The loci PTR3, PTR5, and PTR7 were found to be the most informative for genetic fingerprinting and differentiation of the clones. The mean number of alleles per locus ranged from 2.9 in P. trichocarpa or P. grandidentata to 6.0 in P. balsamifera and 11.2 in 96 clones of the six species. The mean number of observed genotypes per locus ranged from 2.4 in P. grandidentata to 7.4 in P. balsamifera and 19.6 in 96 clones of the six species. The mean number of unique genotypes per locus ranged from 1.3 in P. grandidentata to 3.9 in P. deltoides and 8.8 in 96 clones of the six species. The power of discrimination of the microsatellite DNA markers in the 96 clones ranged from 0.726 for PTR4 to 0.939 for PTR7, with a mean of 0.832 over the 10 simple sequence repeat loci. Clones/cultivars from the same species showed higher microsatellite DNA similarities than the clones from the different species. A UPGMA cluster plot constructed from the microsatellite genotypic similarities separated the 96 clones into six major groups corresponding to their species. Populus nigra var. italica clones were genetically differentiated from the P. nigra var. nigra clones. Microsatellite DNA markers could be useful in genetic fingerprinting, identification, classification, certification, and registration of clones, clultivars, and varieties as well as genetic resource management and protection of plant breeders' rights in Populus.Key words: Populus, simple sequence repeat markers, clonal identification, genetic fingerprinting, clone–cultivar relationships.


2012 ◽  
Vol 40 (2) ◽  
pp. 261 ◽  
Author(s):  
Mohammad Nazrul ISLAM ◽  
Md. Rezwan MOLLA ◽  
Md. Motiar ROHMAN ◽  
Mirza HASANUZZAMAN ◽  
Shah Mohammad Naimul ISLAM ◽  
...  

DNA fingerprinting and genetic diversity analysis helps direct selective breeding and conservation of plant species. Since simple sequence repeats (SSR) markers are co-dominant, they can predict level of genetic diversity and thereby protect plant genetic resources of a region. Keeping the aforesaid rationale in mind, we worked on molecular characterization of eight cotton varieties in Bangladesh using simple sequence repeat (SSR) or microsatellite DNA markers. All the three microsatellite DNA markers were found to be polymorphic, extracting a total of eight alleles with an average of 2.67 alleles per locus in the present study. Allele sizes were as 149-155 bp, 178-198 bp and 140-202 bp for the loci BNL1551, BNL1721 and BNL2960, respectively. Polymorphism Information Content (PIC) values were ranged from 0.469 to 0.531. UPGMA dendrogram separated 8 varieties of cotton into two clusters. One cluster contained six varieties CB-1, CB-2, CB-3, CB-7, CB-9 and CB-10 while other two varieties CB-5 and HC 1 formed another cluster. The findings of this study would provide a useful guide for selecting specific germplasm with distinct genetic background for diversifying cotton breeding program in Bangladesh.


Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 15-21 ◽  
Author(s):  
L Perera ◽  
J R Russell ◽  
J Provan ◽  
W Powell

We have used eight pairs of simple sequence repeat (SSR) primers to analyse the genetic diversity in 130 individuals of coconut (Cocos nucifera L.) comprising 75 tall individuals and 55 dwarf individuals, representing 94 different coconut ecotypes throughout the world. A total of 51 alleles were detected, with an average of 6.4 alleles per locus. Fifty alleles were detected in tall coconuts (talls; mean alleles/locus 6.3) compared with only 26 (mean/ locus 3.3) in dwarfs, and the average diversity value in talls (0.589) was also significantly higher than that in dwarfs (0.348). Using the eight SSRs we were able to uniquely discriminate 116 of the 130 individuals. A phenetic tree based on DAD (absolute distance) values clustered individuals into five groups, each mainly composed of either talls or dwarfs. These results provide evidence in support of previous hypotheses concerning the dissemination of coconut, as well as important new information for conservation and breeding purposes. Key words: coconut, Cocos nucifera, microsatellites, SSR, genetic diversity.


2018 ◽  
Vol 51 ◽  
pp. 185-192
Author(s):  
S. Kruhlyk ◽  
V. Dzitsiuk ◽  
V. Spyrydonov

Genetic variability of domestic dogs is a source for effective process of breed formation and creating unique gene complexes. In the world, for preservation of genetic resources of dogs, there are dog training associations which have great confidence: American Club Dog Breeders (AKC), the British Kennel Club (KC) and the Federation Cynologique Internationale (FCI), aimed at protecting breeding dogs, standards creation, registration of a breed, and issuance of accurate pedigrees. Evaluation of the genetic diversity of dog breeds is able to significantly complement and improve their breeding programs. Since breeds of dog differ in morphological and economic characteristics, the problem of finding of the breed features in the genome of animals is becoming more topical. From this point of view, French Bulldog is an interesting breed of dog (FRANC.BULLDOGGE, FCI standard number 101) which belongs by the classification of breeds, adopted in FCI, to the group IX – a dog-companion for health and fun, but to a subgroup of fighting dogs of a small format. French Bulldog breed has been researched slightly not only in Ukraine and also abroad, as the main work of all dog association is focused on solving theoretical and practical issues of breeding, keeping, feeding, veterinary protection and others. The study was conducted at Research Department of Molecular Diagnostic Tests of Ukrainian Laboratory of Quality and Safety of Agricultural Products. 33 animals of French Bulldog breed, admitted to use in dog breeding of Ukrainian Kennel Union (UKU), were involved for the genetic analysis using DNA markers. The materials of the research were buccal epithelial cells, selected before the morning feeding of animals by scraping mucous membrane of oral cavity with disposable, dry, sterile cotton swab. Genomic DNA was extracted using KIT-set of reagents for DNA isolation according to the manufacturer's instructions. PEZ1, PEZ3, PEZ6, PEZ8, FHC 2010, FHC 2054 markers, recommended by International Society for Animal Genetics (ISAG), ACN, КC and FCI, were used for research. As a result of research 25 alleles for all the loci were detected in the experimental sample of dogs. The average number of alleles at the locus Na, obtained by direct counting, was 4.16. The most polymorphic loci for this breed were PEZ6 and PEZ3 with 8 and 6 allelic variants. Monomorphic loci were PEZ8 and FHC 2054 which had 4 and 3 alleles and the lowest level of polymorphism was observed for PEZ 1 and FHC 2010 loci in which only 2 alleles were identified. On analyzing the molecular genetic characteristics of dogs of French Bulldog breed, we found a high variability of genotype on rare alleles, which included alleles: M, C, D, E, J, K, L, O, N and representing 60% of the total number of the identified alleles. C, D, E alleles for PEZ3 locus and O allele at PEZ6 locus are unique to the sampling of dogs because they are not repeated in other loci. Typical alleles: N, F, R, I, P, K, M are 40% of the total. But F, R alleles for PEZ3 locus and P allele for locus PEZ6 are not repeated either in standard allelic variants or in rare one, indicating a high information content of these alleles and loci to be used for further monitoring of allele pool, genetic certification and identification of dogs. Microsatellite DNA loci were analyzed as a result of investigations of French Bulldogs and the most informative: PEZ3, PEZ6 and PEZ8 were found, which have high efficiency in individual and breed certification of dogs due to high variability. These data allow further monitoring of the state of genetic diversity of the breed and the development of measures for improvement of breeding to preserve the structure of breeding material. The study of individual and population genetic variability is advisable to continue for breeding of French Bulldogs "in purity" and preserving valuable gene complexes. The results are the basis for further monitoring of the proposed informative panels of microsatellite DNA markers for genotyping dog of French Bulldog breed and their complex evaluation.


2008 ◽  
Vol 16 (2) ◽  
pp. 156
Author(s):  
Liao Xinjun ◽  
Chang Hong ◽  
Zhang Guixiang ◽  
Wang Donglei ◽  
Song Weitao ◽  
...  

2010 ◽  
Vol 34 (2) ◽  
pp. 169-177
Author(s):  
Fu-ping LIU ◽  
Jun-jie BAI ◽  
Hong-mei SONG ◽  
Xing YE ◽  
Sheng-jie LI ◽  
...  

2014 ◽  
Vol 6 (3) ◽  
pp. 689-691 ◽  
Author(s):  
Melissa A. Millar ◽  
Margaret Byrne ◽  
David J. Coates ◽  
J. Dale Roberts

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