Molecular Plant Breeding - Science topic

State the reasons in the case of  non crop plants, which is a timber yielding one?

I need CEL1 enzyme to use it in my laboratory work to complete my PhD thesis. Unfortunately, I didn't find it anywhere. So I'm waiting for any request about companies name where is available or anyone who sell it for me.

thank you.

Dear All

I need a reference (proofed study) that report the minimum number of markers for GWAS.

Recently, I have read so many papers on GWAS which were published in high-profile international journals. I have found a wide range of markers that were used in GWAS extending from 200 to up to 1,000,000 SNPs.

what are the economics, social and environmental value of conventional and molecular plant breeding?

What bioinformatics tools are available to help analyze and interpret large-scale molecular data generated from crop research?

How can you identify and isolate specific genes involved in crop yield or disease resistance?

When we are doing selfing or crossing in castor we are only getting 1-2 capsules. Are there any methods to increase the seed setting after selfing or crossing?

We have SSR marker (150) based genotypic data of 190 rice landraces. Want to prepare a research article. Which kind of analysis may be performed with these data? Kindly give your opinion and suggestions.

Regards

Parmeshwar

What open-source softwares are available to generate a heat map of the Jaccard similarity coefficient for SSR diversity from the available data set?

There is very little publication where functional characterization(cloning, overexpression, silencing, etc.) of genes identified through GWAS has been performed. However, most of the publications on functional characterization are on genes identified through transcriptome. Why is this? I doubt whether there is any usefulness of GWAS on crop improvement or not? if yes then give me some successful publication examples?

Large germplasm collections may have several duplicates which need to be removed from the set. DUS characterization based on morphological traits are the best way to differentiate them. But it is very tough to DUS characters in large germplasm lines. Is there any method in molecular breeding to identify the duplicates in huge germplasm collections of rice? Kindly give your opinion and suggestions.

As SSR are most widely used markers in major cereals. They are highly reliable (i.e. reproducible), co-dominant in inheritance, relatively simple and cheap to use and generally highly polymorphic. What other factors can affect polymorphism in case of SSR markers?

If a journal Impact factor in SCI

But no impact factor as per Journal citation reports .

Is SCI valid

This is just a hypothetical question. For example, you genotyped 500 BC3F2 rice plants, phenotypes them and conduct GWAS. Then, two generations later, you genotyped the BC3F4 plants and you got interesting phenotypic results. Would it be possible to do GWAS using the phenotypic data from BC3F4 plants but using the genotyping data from BC3F2 plants?

In the process of preparing scions for grafting, it is seldom a practice to trim the leaves on the scion while still on the mother plant. The implication of this is that after few days, the petiole snaps off easily, after which it can be severed for onward grafting to an understock. What could be physiologically responsible for this phenomenon in plants? Thank you.

Many QTLs are being reported in rice for salinity tolerance using bi-parental populations and n number of traits. I am looking for QTLs with LOD more than 5 and variance more than 15-20 %

Scientific community is now facing a new threat of unethical publications in predatory journals.

How someone can identify the predatory journal?

Scientific community is now facing a new threat of unethical publications in predatory journals.

How someone can identify the predatory journal?

Is there any authenticate list of predatory journals available?

Which mapping function is preferred for linkage map construction; Haldane's or Kosambi mapping function?

What are the effects of each one on the resulted linkage groups?

I need to collect leaf samples for DNA extraction very far from the lab station so i was advised about drying the leaves in silica gel. How exactly do I do it?

Seeds obtained from heterozygous T0 mutants obtained through CRISPR CAS9 were sown and the plants raised were properly genotyped. Following normal segregation pattern, T1 generation had WT, heterozygous and homozygous plants. The homozygous were not producing normal seeds but strangely few (2 in many) produced more than 50% normal seeds, when those seeds and the plants raised from them were genotyped they were found to be heterozygous. In T1 I ignored this (thinking that T0 plants from CRISPR CAS9 might carry chimeric mutation for the gene).

To get T2 generation, seeds obtained from T1 heterozygous were planted, but T2 homozygous plants also had such plants. The situation even continued to the next generations. I am wondering what might be the cause. I know that cross pollination in rice occurs to small extent but if that is the cause then all homozygous plants must bear small number of such seeds. In this case homozygous usually don’t produce normal seeds at all, unusually few homozygous bear normal heterozygous seeds. Your suggestions will be highly appreciated to explain this situation. Thanks.

I make Hoagland solution and I added Sodium silicate in it, but I saw White precipitate on the perineum.Why?

As we do not know how many markers are required for screening of background during marker assisted breeding and if we cover the whole chromosome with marker still it will not impart accurate results. According to me intermittent phenotyping is important aspect in MABB.

I am having a problem running PHASE. The error that appears to me is that the number of alleles is too large, that I need to increase the KMAX value in constants.h and recompiling. It is not explained in the manual how to do this. I have seen an archive called constants.hpp within the folder phase-master\src\phase.2.1.1.source, but it does not work to change the Kmax number here.

Could you help me with this issue?

I do not know how to do it in MS-DOS

Thank you for your help

I'm an Ph.D student doing molecular work. i was unable find proper procedure of preparing dNTPS and taq polymerase. i'm having dNTP set, 100 mM from GeNei and Tag polymerase from Himedia MBT060C for 1000 units. can some one let me know about how to prepare these.

In Tag polymerase they have given 10X HiBuffer S and 10X HiBuffer A. for what these buffers are used and how to use these buffers.

I want to work on PBS in molecular breeding and want to know are their any genes or tightly linked markers available for PBS in Corn. I want use these in our breeding programme.

Hello everyone,

Using CRISPR CAS9, I got homozygous +1 mutants for a rice gene. The CAS9 target lies in the middle of the gene. After mutation there is no stop codon in gene body. Only one in UTR region is observed. Now my question is that this gene will normally be transcribed (so I can not use RT PCR to confirm the knock out). Also as the newly observed stop codon lies a little ahead of the original stop codon in UTR region (So I presume that we cant not use western to confirm knockout). I have just sown the plants and am looking to observe some phenotype associated with mutation. Your suggestions regarding confirming the knockout of the gene will be highly appreciated. Thanks!

Hi everybody!

My doubt is with the terms allele and gene dosage. I would like to know if they are synonymous. 

Let's see by this example if the application of the terms is correct.

Example: Supposing that we have a homozygous  genotype (AA) that expresses 20 grams of a determined protein and a hemizygous genotype (A-) that expresses 10 grams of the same protein. Each "A" allele contributes with 10 grams.

 

Is it correct if I say that the increment of allele "A" or increase of the gene dosage in a hemizygous genotype will confer a homozygous genotype with 20 grams of protein expression?  

Recently I tried to knock out a gene in rice using CRISPR CAS9. I got heterozygous plants with different mutations combination like (-3,-1) and (-6,-2) in T0 (I confirmed the genotype of T0 by TA cloning). After selfing the T0 transgenic plants (-3,-1), in T1 generation, I got only (-3, -3) homozygous plants. There were no heterozygous (-3,-1) or homozygous (-1.-1). The homozygous (-1.-1) may be lethal but I don’t understand how I could not get heterozygous plants (-3,-1). I completely lost (-1) mutation in T1 progeny. Any possible explanation for this???

In general, I think wild types has a higher organized genome compared with their cultivated counterparts, and this may be related to breeding and domestication practices that highly affected the genome architecture, genetically and/or epigenetically! Am I right?

I’m trying to extract RNA from anther of GMS  line of cotton. I’ve  used trazol method and modified CTAB but I didn’t get result.

Is there any suggestion?

Dear all

I am working on wheat which has long generation time and developing different genetic background with recurrent line takes long time. Please share some ideas about validating QTLs other than different genetic background.

Thanks in advance.

I have intention to group cultivars of a root crop into various heterotic groups. Could this be achieved through the analysis of combined historical data in the breeding program? Or do I need to establish a design experiment to achieve this? What kind of analysis is appropriate to classify the cultivars into heterotic groups? Do I need to base the analysis on yield and yield related components?

I would like to request researchgate people to comment on the following abstract. Does this report any findings, or convey a message? What are the weakness of this abstract?

Bacillus thuringiensis (Bt) insecticidal toxin protein encoded by Cry gene is a widely used technology to control insect pest in the crop field. However, development of insect resistant to Cry genes has appeared as a major threat to the durability of this approach, and thus urgent action is required to overcome this problem. Out of many available approaches, stacking of multiple Cry genes in the same plant is thought as the best strategy to delay the development of insect resistant to Cry genes. Here we report the insecticidal activity of a genetically engineered Bt gene stack consisting of Cry1B/Cry1C genes in the model plant Arabidopsis. Cry1B/Cry1C genes were designed to produce a novel version which is free of IP. Components which have the freedom to operate were used to test the insecticidal activity of the modified Cry1B/Cry1C gene stack. Availability of technology that does not require licensing agreement to use, is one of the main barrier to develop GM crops by public sector organizations in the developing countries. Thus, it is expected that the modified Cry1B/Cry1C gene stack will be a valuable tool to develop GM crops for public or humanitarian use in the developing nations.

I am trying to identify and elucidate the function of a gene (let say X) in Brassica napus that control flower development in Arabidopsis. Using the sequence of Arabidopsis X, I conducted a phlyogenetic analysis based on protein sequence data. Phylogenetic analysis revealed that there is a single X in Brassica napus genome. After phylogenetic analysis, I isolated the cDNA sequence of X from Brassica napus by RT-PCR and then sequenced 20 randomly selected clone. When the coding sequences of these clones were compared, they revealed two unique sequence which were highly homologous except single nucleotide variation in some position of the coding sequence. When the two unique sequences of Brassica napus X were compared to its progenitor (Brassica rapa and Brassica oleracea X), I found that both of them are highly similar to the sequence of their progenitor X both at nucleotide and amino acid sequence level. The identity between Brassica napus X and Brassica rapa X were 98% (nucleotide level) and 93% (amino acid sequence). The similarity between Brassica napus X and Brassica oleracea X were 100% both at nuclotide and amino acid sequence level. My question is

1. What will be the possible explanation of presence of a single Arabidopsis X in Brassica npaus genome given the fact that Brassica napus is a tetraploid crop?

2. Are the two unique sequences of X found Brassica napus genome represent two different allele or two different genes?

3. I would also welcome any other explanation on this result.

I have cloned amplified PCR fragments of a genomic maize sample into plasmids. I obtained six plasmids containing the same region. The genomic maize sample belonged to a single maize grain. The cloned region had 180 bp. Two of the obtained plasmids had the expected wild type while four plasmids had different base substitutions. Two plasmids carried a C→A substitution at the same position, one plasmid had a G→T substitution at another position, and another one had a C→T substitution (again at another position). Direct sequencing of the amplified PCR product of the mentioned genomic maize sample showed wild type. How should I interpret the cloning results? I used Phusion Hot Start II DNA Polymerase (Biozym) and 1,5 mM MgCl2 concentrations for PCR. Are the base subsitutions due to PCR/cloning error or true? How can I interpret the results?

M6 (Reg. No. GP-1, BS 228) is a diploid self-compatible

inbred line of the potato wild relative Solanum chacoense. Could you please let me know if you have successfully transformed this line using Agrobacterium? I would really appreciate if you could share the protocol. I want to transform this line for CRISPR/Cas9 research. Thanks.

-everybody knew on breeding against late blight (monogenic resistant dominant gene and simple inheritance.

-There is increased demand of purple potato due to high level of anthocyanins

-germplasm is available but there may be a difficult during introgression of the respective gene

-pros and cons on a use of diploid potato in breeding instead of tetraploids?

-what could be your suggestion????

I was given a maize SNP dataset in the HapMap format and I was curious how I can infer the genotype given this particular format (see picture below). I understand that for HapMAp data the second column contains the allele information (i.e. all possible alleles at this locus) and that columns 12 and onward contain the appropriate allele for the sequenced individual. However, I'm unsure of how to derive the genotype of a diploid when only one allele is given. I realise there is a function in R for reading raw HapMap data (see http://svitsrv25.epfl.ch/R-doc/library/snpMatrix/html/read.HapMap.data.html) but I'm not even sure it's still operational. Any information would be a help. Much thanks! 

Can we perform in vitro asexual cross breeding of plants by tissue culture?

Parents X F1s = Backcross

Parents X DH = ??

DH population,

its use in developing NIL population,

F1,

Recurrent parents

Is it required that we target all four alleles of a gene in tetraploid potato desiree for knockout studies using CRISPR/Cas9 technology? How effective is CRISPR/Cas9 vector transformation in Desiree? Is bombardment more preferable? If someone has done any research on CRISPR/Cas9 technology on Desiree, kindly let me know.

Im working on fruit tree breeding and I would like to do controlled crossing among a selection of parents. What is the ideal pollen donor:female ratio to minimize selfing in isolation plots?

Making inbreds is the most important step to develop hybrids, and it is not always easy to find genetic variations, so, some researchers try to get some new inbreds from same old inbred, by selfing  different plants in color, stature, ear length,...etc which character is better to start on , quantitative or qualitative ?

Are their microsatellite markers used as marker assisted selection in wheat, rice or barley for commercial breeding program?

microsatellite markers used as marker assisted selection (MAS) in wheat, rice or barley for commercial breeding program

which is the perfect allele size 

What design of molecular techniques says about  the functional quality of a plant? Say for example if the plant is a timber yielding by its economics?

Ideally one for european cultivars

When plantlets are obtained by direct organogenesis from nodal explants, is there a need to confirm its genetic fidelity to mother plant by means of ISSR or PCR? 

I got some of the seed without fertilization in cucurbit wide hybridization (fluorescent study) but i don't know which part of embryo sac involved in seed development, if any one knows the methods/techniques to study this aspect. and how to confirm the apomixis is actually involved in seed development.

what is the best combination of media and procedure that could help in identifying the viable/germinated pollen of pumpkin. We experienced bursting of pollen that's why we cannot identify wither germinated or not.Anyone please?

I have to isolate more than 2500 wheat leaf samples for screening. Even we use robotic system, dna isolation is very time consuming and costly. We will use only 2 primer pair for screening. I wish to perform directly PCR by skipping DNA isolation. Phire Plant Direct PCR kit is also available but not cheap. If any alternative to the kit, I will try it. 

Thanks in advance. 

I've crossed transgenic Arabidopsis, a mutant (dominant mutation) and reporter lines. I am wondering if there's faster way to select homozygous from T2 generation aside from using resistance marker (and planting them until the 4th generation)?  I probably cannot use PCR since it's caused by a point mutation and I don't know where the insert been. Thank you for your expertise. 

many cytoplasms have been comibined with T. aestivum nucleus, but which of them give good results in combination. Do you know any site where I can get more information on A. kotschyi.

Maize is protandrous in nature but it has been noticed that silking occurs earlier than taselling in some cases.

I mean if we want to conduct a  research experiment on Integrated application of  Nitrogen levels  with Humic acid on growth and phonological development of maize hybrids and open pollinated varieties. Can we recommend the out comes of this experiment for both hybrid and OPV?

cotton 

Kindly suggest me regarding the protocol and tools for mining of the SNPs by using fastq files.

Thanks

Anyone working on anther culture or any tissue culture related work on pomegranate... I have a major issue regarding phenolic production in culture which becomes almost black even after using antioxidants and charcoal...

Advices are welcome....

I am trying to Isolate small RNA from cotton anther, I used trizol method and mirvana kit but I didn't get the result, now I am moving to Qiagene kit, has anyone already used this Kit? 

Hello all, 

I'm looking an adjustable multichannel pipette for our studies. There are some alternatives mettler toledo and voyager brands. 

Is there any experienced with these brands? Or any alternative brand? 

Thanks in advance. 

Is it right to say that the transgenic maize hybrids are hemizygous for the transgenic trait, once the parents were one transgenic homozygous inbred line while the other is a non-GM inbred line?

For example:

Homozygous transgenic inbred line (TT) crossed with non-GM inbred line (_ _), i.e. doesn't have any allele variations, because conventional maize doens't have the gene that comes from another species.  

The outcome of this cross is a plant with only one transgenic allele (T_) given by the transgenic inbred line, a hemizygous plant. 

I would be interested in blocking mRNA degradation in Arabidopsis. Someone would know some drug? Thank you!

can you also suggest the procedure of mutation in in-vitro conditions and level of mutagens?

Hi all I am working on cross pollinated crop of Jatropha Curcas. in this i want to map the QTLs for yield related traits, to this I have selected two inbred lines at self generation 6(S6) level and two heterozygous lines. Designed crosses like inbred X Inbred and Heterozygous X Inbred. The heterozygous lines are contrasting and geographically different and inbreeds are having les contrast and high homozygosis. So let me know which cross combination is good and what generation need to be mapped

I want to cloning 3 plant genes with different plant origen in E.coli Nissle 1917, but I know E.coli has a negative feedback and if the expression of these gene were increesed, are expression of them be suppressed?

what is the best method to isolate protoplasts from edible fungi, mushroom Hypsizygus marmoreus?

Can someone share agro bacterium mediated transformation protocol for pCAMBIA 1305.1 in wheat please? I am using Bobwhite cultivar and C58C1 agro strain but the regeneration rate is very poor. 

Hi folks - I am trying to run a Joint Scaling test but am having difficulties finding a step-by-step description of how to run one. Does anyone have a great go-to book? (Please note, my university library doesn't have a copy of the Lynch & Walsh (1998) textbook.) Any suggestions of where to look/read, would be much appreciated!

I am planning to map QTLs for drought and it's related traits in maize using SNP's. Want to know What would be the minimum or optimum, mapping population size for QTL identification for the drought trait / any other complex trait in maize. The number of plants per line @ F6 generation? On what basis we will say we require 250-300 population size?

Hii.. All..

I have screened sets of wheat genotypes against bipolaris  sorokiniana under epiphytotic field conditions. I have taken 5 disease phenotypic scores at weekly intervals and calculated Area Under disease progress curve(AUDPC). 

My question is whether we consider AUDPC is a measure of classify genotypes into susceptible and resistant genotypes?

The presence and magnitude of genetic variability in a gene pool is the pre-requisite of a breeding programme.

With the help of plant breeding, Biotechnology and plant physiology.

I have 145 genotypes and I would like to analyze them as lattice design. Can I design my experiment with 29 partial blocks with 5 genotyeps in each?

Can in vitro grown seedling be transferred to a suspension medium containing some stress factor to asses its effect on plant volatiles (Headspace analysis)

I am having SNP data of RIL populations and the Phenotypic data. Now I want to construct the linkage map using JoinMap. As I have no expertise of join map it would be nice if someone could provide a step by step procedure which I should follow. Thank you for giving valuable inputs in advance.