scholarly journals Genetic mapping studies in Coffea sp using molecular marker methods Studi peta genetik pada Coffea sp. menggunakan metode penanda molekuler

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
. PRIYONO ◽  
Riza Arief PUTRANTO
Keyword(s):  
Molecular Markers ◽  
Genetic Mapping ◽  
Genetic Map ◽  
Crop Improvement ◽  
Average Density ◽  
Genetic Maps ◽  
Gene Characterization ◽  
Robusta Coffee ◽  
Dna And Rna ◽  
Genomic Comparative Analysis

AbstrakAnalisis genetik telah  menjadi alat yang penting  dalam  pemuliaan  tanaman untuk perbaikan sifat penting tanaman. Salah satu potensi terbesar dari analisis tersebut adalah identifikasi penanda molekuler yang berguna untuk pemetaan genetik. Pemetaan genetik  merupakan  salah satu langkah penting dari analisis  genetik.  Intisari  dari   semua pemetaan genetik adalah  menempatkan  koleksi  pe- nanda molekuler pada posisi tertentu dalam genom. Hal tersebut dapat kemudian digunakan untuk meng- identifikasi lokus sifat kuantitatif (QTLs) dengan memanfaatan keragaman genetik alami yang tersedia dan meningkatkan sifat-sifat penting serta berharga. Sampai saat ini, tiga belas peta genetik telah dipublikasi dan tersedia pada Coffea sp. yang menciptakan database besar untuk kerangka genetik. Sebuah peta genetik terbaru dengan akses terbuka dan berfungsi sebagai referensi telah dibangun oleh International Coffee Genomics Network (ICGN). Peta tersebut tediri dari 3230 lokus, dengan panjang peta 1471 cM (1cm ~ 500 Kb) serta kepadatan satu penanda setiap 220 Kb. Peta-peta genetik pada tanaman kopi telah digunakan dari karakterisasi gen hingga analisis komparatif genom dengan spesies tanaman yang berbeda. Saat ini, pesatnya kemajuan teknologi New Genome Sequencing (NGS) untuk sekuensing DNA dan RNA memungkinkan validasi dari peta-peta genetik untuk prediksi QTLs serta gen-gen yang membawa sifat penting Coffea sp.AbstractGenetic analysis has become an important tool in plant breeding for crop improvement. One of their greatest potential appears to be the identification of molecular markers useful for genetic mapping. Genetic mapping is one of important steps in genetic analysis. The essence of all genetic mapping is to place a collection of molecular markers onto their respective positions on the genome. Thus, it leads to identification of new quantitative trait loci (QTLs) by making benefits of natural available genetic diversity.and to improve important and valuable traits. Until present, thirteen genetic maps were published and available in Coffea sp. creating a huge database for genetic framework. One most recent and open reference genetic map for robusta coffee has been generated by the International Coffee Genomics Network (ICGN) comprising 3230 loci, genetic size 1471 cM (1cM ~500 Kb), with an average density close to one marker every 220 Kb. The Coffea genetic maps have been utilized from gene characterization to genomic comparative analysis with different plant species. Nowadays, the feasibility of NGS for DNA and RNA sequencing allow the validation of genetic map related to the prediction of QTLs and adjacent genes related to important traits for Coffea sp. 

scholarly journals Genetic mapping studies in Coffea sp using molecular marker methods Studi peta genetik pada Coffea sp. menggunakan metode penanda molekuler

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
. PRIYONO ◽  
Riza Arief PUTRANTO
Keyword(s):  
Molecular Markers ◽  
Genetic Mapping ◽  
Genetic Map ◽  
Crop Improvement ◽  
Average Density ◽  
Genetic Maps ◽  
Gene Characterization ◽  
Robusta Coffee ◽  
Dna And Rna ◽  
Genomic Comparative Analysis

AbstrakAnalisis genetik telah  menjadi alat yang penting  dalam  pemuliaan  tanaman untuk perbaikan sifat penting tanaman. Salah satu potensi terbesar dari analisis tersebut adalah identifikasi penanda molekuler yang berguna untuk pemetaan genetik. Pemetaan genetik  merupakan  salah satu langkah penting dari analisis  genetik.  Intisari  dari   semua pemetaan genetik adalah  menempatkan  koleksi  pe- nanda molekuler pada posisi tertentu dalam genom. Hal tersebut dapat kemudian digunakan untuk meng- identifikasi lokus sifat kuantitatif (QTLs) dengan memanfaatan keragaman genetik alami yang tersedia dan meningkatkan sifat-sifat penting serta berharga. Sampai saat ini, tiga belas peta genetik telah dipublikasi dan tersedia pada Coffea sp. yang menciptakan database besar untuk kerangka genetik. Sebuah peta genetik terbaru dengan akses terbuka dan berfungsi sebagai referensi telah dibangun oleh International Coffee Genomics Network (ICGN). Peta tersebut tediri dari 3230 lokus, dengan panjang peta 1471 cM (1cm ~ 500 Kb) serta kepadatan satu penanda setiap 220 Kb. Peta-peta genetik pada tanaman kopi telah digunakan dari karakterisasi gen hingga analisis komparatif genom dengan spesies tanaman yang berbeda. Saat ini, pesatnya kemajuan teknologi New Genome Sequencing (NGS) untuk sekuensing DNA dan RNA memungkinkan validasi dari peta-peta genetik untuk prediksi QTLs serta gen-gen yang membawa sifat penting Coffea sp.AbstractGenetic analysis has become an important tool in plant breeding for crop improvement. One of their greatest potential appears to be the identification of molecular markers useful for genetic mapping. Genetic mapping is one of important steps in genetic analysis. The essence of all genetic mapping is to place a collection of molecular markers onto their respective positions on the genome. Thus, it leads to identification of new quantitative trait loci (QTLs) by making benefits of natural available genetic diversity.and to improve important and valuable traits. Until present, thirteen genetic maps were published and available in Coffea sp. creating a huge database for genetic framework. One most recent and open reference genetic map for robusta coffee has been generated by the International Coffee Genomics Network (ICGN) comprising 3230 loci, genetic size 1471 cM (1cM ~500 Kb), with an average density close to one marker every 220 Kb. The Coffea genetic maps have been utilized from gene characterization to genomic comparative analysis with different plant species. Nowadays, the feasibility of NGS for DNA and RNA sequencing allow the validation of genetic map related to the prediction of QTLs and adjacent genes related to important traits for Coffea sp. 

scholarly journals Unlocking Genetic Diversity in Selected Chickpea Genotypes Using Morphological and Molecular Markers

2017 ◽  
Vol 5 (1) ◽  
pp. 50-57
Author(s):  
Rupsanatan Mandal ◽  
Suprakash Pal ◽  
Nonigopal Shit
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Coefficient Of Variation ◽  
Block Design ◽  
Crop Improvement ◽  
Research Work ◽  
Genetic Maps ◽  
Quantitative Character ◽  
Moderate Degree ◽  
Improvement Program

Proficiency and organization of the genetic variability in cultivated and wild relatives are pivotal for a particular crop improvement program. In the present scenario there has been noteworthy improvement in the development of novel genetic tools such as DNA or molecular markers and genetic maps profiling techniques. In this study, seven chickpea (Cicer arietinum L.) genotypes including some cultivars were considered (Collection Id of the seven genotypes are TZCP-1, TZCP-2, TZCP-3, TZCP-4, TZCP-5, TZCP-6 and TZCP-7). The experiment was conducted out in Random Complete Block Design (RCBD) having three replications. All the quantitative characters were collected for assessing the diversity and to find key characters in chickpea cultivars. The statistical analysis was done for all the quantitative character (viz. plant height, number of branches per plant, number of pod per plant, number of seeds per pod, test weight, seed length, seed width, days to 50% flowering, days to 50% maturity and grain yield). Analysis of variance divulged significant differences among the genotypes for all the 10 characters. An extensive range of diversity was displayed by most of the characters under study. The magnitude of phenotypic coefficient of variation (1.23% - 33.71%) in the present study was slightly wider than genotypic coefficient of variation (1.13% - 33.02%) suggesting that environmental factors have high contribution to the observed variation among chickpea accessions. The first four PC axes from the principal component analysis accounted for 91.63% of the multivariate variation among entries indicating a moderate degree of correlation among characters for these entries. The genotypic data generated through RAPD profiling of seven chickpea genotypes were used to study genetic diversity or interrelationship. The pair wise Jaccard’s similarity coefficient ranged from 0.47 (TZCP-3 and TZCP-5) to 0.87 (TZCP-2 and TZCP-4). Finally, this research work helped with the analysis of genetic diversity in chickpea by using different approaches such as morphological and molecular marker system.

scholarly journals Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry

2005 ◽  
Vol 130 (5) ◽  
pp. 722-728 ◽  
Author(s):  
Eric T. Stafne ◽  
John R. Clark ◽  
Courtney A. Weber ◽  
Julie Graham ◽  
Kim S. Lewers
Keyword(s):  
Molecular Markers ◽  
Genetic Mapping ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Maps ◽  
Black Raspberry ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
Simple Sequence ◽  
Mapping Populations

Interest in molecular markers and genetic maps is growing among researchers developing new cultivars of Rubus L. (raspberry and blackberry). Several traits of interest fail to express in seedlings or reliably in some environments and are candidates for marker-assisted selection. A growing number of simple sequence repeat (SSR) molecular markers derived from Rubus and Fragaria L. (strawberry) are available for use with Rubus mapping populations. The objectives of this study were to test 142 of these SSR markers to screen raspberry and blackberry parental genotypes for potential use in existing mapping populations that segregate for traits of interest, determine the extent of inter-species and inter-genera transferability with amplification, and determine the level of polymorphism among the parents. Up to 32 of the SSR primer pairs tested may be useful for genetic mapping in both the blackberry population and at least one of the raspberry populations. The maximum number of SSR primer pairs found useable for mapping was 60 for the raspberry population and 45 for the blackberry population. Acquisition of many more nucleotide sequences from red raspberry, black raspberry, and blackberry are required to develop useful molecular markers and genetic maps for these species. Rubus, family Rosaceae, is a highly diverse genus that contains hundreds of heterozygous species. The family is one of the most agronomically important plant families in temperate regions of the world, although they also occur in tropical and arctic regions as well. The most important commercial subgenus of Rubus is Idaeobatus Focke, the raspberries, which are primarily diploids. This subgenus contains the european red raspberry R. idaeus ssp. idaeus L., as well as the american black raspberry R. occidentalis L. and the american red raspberry R. idaeus ssp. strigosus Michx. Interspecific hybridization of these, and other raspberry species, has led to greater genetic diversity and allowed for the introgression of superior traits such as large fruit size, fruit firmness and quality, disease resistance, and winter hardiness.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junjie Cui ◽  
Jiazhu Peng ◽  
Jiaowen Cheng ◽  
Kailin Hu
Keyword(s):  
Genetic Map ◽  
Average Density ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Map Construction ◽  
Indel Markers ◽  
Genome Wide ◽  
Indel Polymorphisms ◽  
Molecular Marker Development ◽  
Development And Validation

Abstract Background The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

scholarly journals An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 282-295 ◽  
Author(s):  
Elizabeth S Jones ◽  
Natalia L Mahoney ◽  
Michael D Hayward ◽  
Ian P Armstead ◽  
J Gilbert Jones ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Linkage Map ◽  
Genetic Map ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Genetic Linkage Map ◽  
Population Based ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

Sign in / Sign up

Export Citation Format

Share Document