scholarly journals DNA Dizileme Temelli Haplotip Analizlerinde Kullanılan Bazı Yazılımlar

2019 ◽  
Vol 7 (sp1) ◽  
pp. 107
Author(s):  
Emel Tüten Sevim ◽  
Kemal Karabağ
Keyword(s):  
Sequence Analysis ◽  
Haplotype Analysis ◽  
Initial Step ◽  
Molecular Methods ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Genetic Potential ◽  
Pcr Technology ◽  
Selection Of

Determination of genetic resources and their diversity constitutes are the initial step of the breeding programs. Before starting to the selection of the desired properties, many molecular methods are used to determine the existing genetic potential and determine the genotypic values. Many molecular methods (RAPD, RFLP, AFLP, SSR and DNA sequencing etc.) based on PCR technology are used to identify populations, identify genes related to yield and resistance, and demonstrate phylogenetic relationships. Many software’s for the analysis of molecular datasets obtained from molecular methods have been developed and the field of bioinformatics was born. In this study, after DNA sequence analysis; it is aimed to give information about haplotype analysis by determining SNPs (Single Nucleotide Polymorphism's) in individuals of populations, calculation of the genetic distance among populations and within populations, and software and analysis used for phylogenetic tree drawing.

scholarly journals Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1424
Author(s):  
Magdalena Cieplak ◽  
Sylwia Okoń ◽  
Krystyna Werwińska
Keyword(s):  
Genetic Diversity ◽  
Avena Sativa ◽  
Genetic Similarity ◽  
Breeding Programs ◽  
Central European ◽  
Cereal Species ◽  
Genetic Pool ◽  
Selection Of ◽  
High Genetic Similarity

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

scholarly journals DNA-type results of Landrace sows for RYR1-gene and its association with productivity

2020 ◽  
Vol 11 (3) ◽  
pp. 431-437
Author(s):  
O. M. Tsereniuk ◽  
O. M. Bobrytska ◽  
O. S. Miroshnikova ◽  
O. V. Danchuk
Keyword(s):  
Mutant Allele ◽  
Dna Typing ◽  
Ryr1 Gene ◽  
Reproductive Ability ◽  
Genetic Potential ◽  
Net Profit ◽  
Two Generations ◽  
Almost All ◽  
Selection Of

Recently the assessment of QTL genes has been a relevant focus of research. Among other genes, the RYR1 is one of the most important. Research on this gene for Landrace sows of Ukrainian selection has been insufficient. This fact confirms the need for our work. A total of 63 Landrace sows from different families were evaluated by reproductive qualities for two generations. A comprehensive assessment of the sows’ reproductive ability was performed using the SIRQS-index. Determination of polymorphism in the RYR1 gene in pigs was performed by using DNA-typing of animals. Genetic potential was calculated between two generations “mother-daughter”. By assessment of polymorphism of the RYR1 gene, it was found that 6.3% of the Landrace sows were the carriers for the mutant allele of the RYR1 gene. No animals with the RYR1nn genotype were detected. Accordingly, animals with the RYR1NN genotype accounted for 93.6%. The frequency of the N allele of the RYR1 gene was 0.97, the n frequency of the RYR1 gene allele was 0.03. Sows with RYR1NN genotype had a higher level of reproductive ability compared to the RYR1Nn genotype. RYR1NN genotype also had a higher level of genetic potential. The greatest progress was established between generations of Landrace sows which were carriers for the mutant allele. The highest values of this progress were by the NBA, the lowest – by the NW. On the contrary, there was regression between populations for part of the population (Landrace sows of Ukrainian selection of RYR1Nn genotype) by the all estimated indicators of reproductive ability. Sows that were free of the mutant allele of the RYR-1 gene had high SIRQS index. The phenotypic consolidation coefficients by the NBA were lower for sows free of the mutant allele than for its carrier. The advantage of sows free of the mutant allele of the RYR-1 gene over its carrier sows was established in almost all assessed indicators of reproductive ability. No significant differences in the level of consolidation of reproductive ability between sows with different allelic variants of the RYR-1 gene were established. The higher productive level of sows with RYR1NN genotype is reflected in the indicators of economic efficiency of production. It allows higher levels of profitability to be obtained and net profit to be increased by 1093 UAH compared to sows with RYR1Nn genotype. The further monitoring of the studied gene and the gradual elimination of carriers of the mutant allele is a promising direction in breeding work.

scholarly journals Mapping QTL for spike fertility related traits in two double haploid wheat (Triticum aestivum L.) populations

2020 ◽  
Author(s):  
Nicole Pretini ◽  
Leonardo S. Vanzetti ◽  
Ignacio I. Terrile ◽  
Guillermo Donaire ◽  
Fernanda G. González
Keyword(s):  
Double Haploid ◽  
Snp Array ◽  
Triticum Aestivum L ◽  
Yield Potential ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Grain Number Per Spike ◽  
Fertility Traits ◽  
Major Qtl ◽  
Selection Of

AbstractIn breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with a higher grain number per spike (GN) and occasionally higher grain weight (GW) (main numerical components of the yield). This task could be facilitated with the use of molecular markers such us single nucleotide polymorphism (SNP). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two double haploid (DH) populations (Baguette Premium 11 x BioINTA 2002 and Baguette 19 x BioINTA 2002, BP11xB2002 and B19xB2002). Both populations were genotyped with the iSelect 90K SNP array and evaluated in four (BP11xB19) or five (B19xB2002) environments. We identify a total of 305 QTL for 14 traits, however 28 QTL for 12 traits were considered significant with an R2 > 10% and stable for being present at least in three environments. There were detected eight hotspot regions on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B were at least two major QTL sheared confident intervals. QTL on two of these regions have previously been described, but the other six regions were never observed, suggesting that these regions would be novel. The R5A1 (QSL.perg-5A, QCN.perg-5A,QGN.perg-5A) and R5A.2 (QFFTS.perg-5A, QGW.perg-5A) regions together with the QGW.perg-6B resulted in a final higher yield suggesting them to have high relevance as candidates to be used in MAS to improve yield.Author contribution statementKey message28 stable and major QTL for 12 traits associated to spike fertility, GN and GW were detected. Two regions on 5A Ch., and QGW.perg-6B showed direct pleiotropic effects on yield.

Evaluation of Ethiopian chickpea (Cicer arietinum L.) germplasm accessions for symbio-agronomic performance

2012 ◽  
Vol 28 (4) ◽  
pp. 338-349
Author(s):  
Gemechu Keneni ◽  
Endashaw Bekele ◽  
Fassil Assefa ◽  
Muhammad Imtiaz ◽  
Tolessa Debele ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
Seed Size ◽  
Agronomic Performance ◽  
Agronomic Characters ◽  
Fixed Nitrogen ◽  
Breeding Programs ◽  
Legume Crop ◽  
Genetic Potential ◽  
Germplasm Accessions ◽  
Selection Of

AbstractChickpea (Cicer arietinum L.) is an economically and ecologically important food legume crop. Ethiopia has a large collection of chickpea germplasm accessions; but, it has not been extensively characterized for desirable sources of agronomic and symbiotic significance for use in breeding programs. A study was conducted at two locations (Ambo and Ginchi) in 2009/2010 to characterize and evaluate Ethiopian chickpea germplasm accessions for symbiotic and agronomic performance. One hundred and thirty-nine germplasm accessions were evaluated with 16 other genotypes including non-nodulating reference checks. Differences among genotypes, locations and genotype by location interaction effects were significant for a number of characters. A number of accessions better performing over the improved genotypes were identified for both symbiotic and agronomic characters. The amount of fixed nitrogen ranged from 13 to 49% in foliage, 30 to 44% in grain and 28 to 40% in total above-ground biomass. Grain yield performance varied from 31 to 70 g per 5 plants and seed size ranged from 82 to 288 g per 1000 seeds. For both symbiotic and agronomic characters, landraces were found to be overwhelmingly superior to introduced genotypes, except for seed size, where the best genotypes were all from exotic sources. The result indicated that Ethiopian chickpea landraces have better genetic potential for improving a number of symbiotic and agronomic characters over the varieties currently in use. Selection of best individuals within and among the accessions would be expected to be effective.

scholarly journals ReferenceSeeker: rapid determination of appropriate reference genomes

2019 ◽  
Author(s):  
O. Schwengers ◽  
T. Hain ◽  
T. Chakraborty ◽  
A. Goesmann
Keyword(s):  
Rapid Determination ◽  
Single Nucleotide ◽  
Microbial Genomes ◽  
Polymorphism Detection ◽  
Command Line Tool ◽  
Subsequent Calculation ◽  
In Silico Analyses ◽  
Reference Genomes ◽  
Selection Of

AbstractSummaryThe large and growing number of microbial genomes available in public databases makes the optimal selection of reference genomes necessary for many in-silico analyses, e.g. single nucleotide polymorphism detection, scaffolding and comparative genomics, increasingly difficult. Here, we present ReferenceSeeker, a novel command line tool combining a fast kmer profile-based database lookup of candidate reference genomes with subsequent calculation of highly specific average nucleotide identity (ANI) values for the rapid determination of appropriate reference genomes. Pre-built databases for bacteria, archaea, fungi, protozoa and viruses based on the RefSeq database are provided for download.Availability and ImplementationReferenceSeeker is open source software implemented in Python. Source code and binaries are freely available for download at https://github.com/oschwengers/referenceseeker under the GNU GPL3 [email protected]

scholarly journals Inheritance of flower traits in ornamental pepper

2018 ◽  
Vol 39 (1) ◽  
pp. 50
Author(s):  
Angela Maria dos Santos Pessoa ◽  
Elizanilda Ramalho do Rêgo ◽  
Cristine Agrine Pereira dos Santos ◽  
Michelle Gonçalves de Carvalho ◽  
Júlio Carlos Polimeni de Mesquita ◽  
...  
Keyword(s):  
Morphological Analysis ◽  
Gene Action ◽  
Diallel Analysis ◽  
Breeding Programs ◽  
Petal Length ◽  
Anther Length ◽  
Flower Traits ◽  
Flower Diameter ◽  
Selection Of

Diallel crosses provide estimates of useful parameters in the selection of parents for hybridization. They also help in understanding the gene action behind the determination of characters of interest. The objective of this study was to determine the genetic control of flower traits in ornamental pepper based on a complete diallel with parents F1’s and reciprocal crosses. The experiment was conducted in a greenhouse at Laboratório de Biotecnologia Vegetal, Centro de Ciências Agrárias, Universidade Federal da Paraíba (CCA-UFPB). Seven accessions of ornamental pepper belonging to the CCA-UFPB Germplasm Bank UFPB001, UFPB004, UFPB77.3, UFPB099, UFPB134, UFPB137 and UFPB390 were used. The morphological analysis was performed on following quantitative Capsicum descriptors: days for flowering (DFL), flower diameter (FD), petal length (PL), number of petals (NP), number of stamens (NS), anther length (AL) and fillet length (FL). The data were previously submitted to analysis of variance and then to diallel analysis. All evaluated traits were adequate to the additive-dominant model. There are possibilities of genetic gains in breeding programs, for the NP, NS, AL and FL in ornamental peppers.

Beef productivity of steers of Simmental breed of different constitutional types

2021 ◽  
pp. 11-18
Author(s):  
N. G. Fenchenko ◽  
N. I. Khairullina ◽  
D. Kh. Shamsutdinov ◽  
R. F. Galimov ◽  
F. M. Shagaliev ◽  
...  
Keyword(s):  
Live Weight ◽  
Postnatal Period ◽  
The Body ◽  
Body Type ◽  
Internal Organs ◽  
Genetic Potential ◽  
Constitutional Type ◽  
Intensive Rearing ◽  
Selection Of

In order to ensure the growth of beef production, it is necessary to rationally use all available reserves and, fi rst of all, the allocation of intra-breed types and lines that ensure the improvement of herds and breeds of animals with high genetic potential under specifi c natural conditions. Therefore when breeding cattle of dual purposes breeds important role should be attached to the selection of animals of diff erent lines, body types, related groups that provide high fattening, and beef indicators with good adaptive traits. In relation with the above, it has been considered relevant to study the formation of beef productivity of steers of diff erent exterior and constitutional intra-breed types of Simmental breed with the determination of the energy and biological value of products under intensive rearing. As well as the infl uence of feeding conditions and maintenance of young animals of Simmental breed, taking into account the exterior and constitutional type, on the formation of live weight in the postnatal period, with a comparative assessment of the growth intensity depending on the body type. As a result of the research, the association between the live weight and the weight of the most active internal organs: heart, lungs, kidneys, which characterize the level and nature of metabolic processes that have a positive eff ect on the formation of beef productivity of experimental Simmental steers of domestic selection depending on the exterior and constitutional types. It has been found that to increase the production of high-quality beef, it is advisable to intensively rear Simmental steers of medium and compact types up to 18 months of age with a live weight of 460,2–517,8 kg, a carcass weight of 252,3–282,4 kg, a slaughter yield of 58,1–59,4 % and expenditures of feed of 3,7–4,0 thousand tons of EFU per 1 head.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide

ESTIMASI NILAI HERITABILITAS BOBOT IKAN MAS VARIETAS PUNTEN DALAM PROGRAM SELEKSI INDIVIDU

2016 ◽  
Vol 11 (3) ◽  
pp. 217
Author(s):  
Estu Nugroho ◽  
Budi Setyono ◽  
Mochammad Su’eb ◽  
Tri Heru Prihadi
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Base Population ◽  
Breeding Programs ◽  
Male And Female ◽  
Body Weight Trait ◽  
Population Selection ◽  
Selection For ◽  
Weight Trait ◽  
Selection Of

Program pemuliaan ikan mas varietas Punten dilakukan dengan seleksi individu terhadap karakter bobot ikan. Pembentukan populasi dasar untuk kegiatan seleksi dilakukan dengan memijahkan secara massal induk ikan mas yang terdiri atas 20 induk betina dan 21 induk jantan yang dikoleksi dari daerah Punten, Kepanjen (delapan betina dan enam jantan), Kediri (tujuh betina dan 12 jantan), Sragen (27 betina dan 10 jantan), dan Blitar (15 betina dan 11 jantan). Larva umur 10 hari dipelihara selama empat bulan. Selanjutnya dilakukan penjarangan sebesar 50% dan benih dipelihara selama 14 bulan untuk dilakukan seleksi dengan panduan hasil sampling 250 ekor individu setiap populasi. Seleksi terhadap calon induk dilakukan saat umur 18 bulan pada populasi jantan dan betina secara terpisah dengan memilih berdasarkan 10% bobot ikan yang terbaik. Calon induk yang terseleksi kemudian dipelihara hingga matang gonad, kemudian dipilih sebanyak 150 pasang dan dipijahkan secara massal. Didapatkan respons positif dari hasil seleksi berdasarkan bobot ikan, yaitu 49,89 g atau 3,66% (populasi ikan jantan) dan 168,47 g atau 11,43% (populasi ikan betina). Nilai heritabilitas untuk bobot ikan adalah 0,238 (jantan) dan 0,505 (betina).Punten carp breeding programs were carried out by individual selection for body weight trait. The base population for selection activities were conducted by mass breeding of parent consisted of 20 female and 21 male collected from area Punten, eight female and six male (Kepanjen), seven female and 12 male (Kediri), 27 female and 10 male (Sragen), 15 female and 11 male (Blitar). Larvae 10 days old reared for four moths. Then after spacing out 50% of total harvest, the offspring reared for 14 months for selection activity based on the sampling of 250 individual each population. Selection of broodstock candidates performed since 18 months age on male and female populations separately by selecting based on 10% of fish with best body weight. Candidates selected broodstocks were then maintained until mature. In oder to produce the next generation 150 pairs were sets and held for mass spawning. The results revealed that selection response were positive, 49.89 g (3.66%) for male and 168.47 (11.43%) for female. Heritability for body weight is 0.238 (male) and 0.505 (female).

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