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Crop Improvement - Science topic

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Genome edited plants
Agricultural foods
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it is a powerful tool that, when used responsibly, can contribute significantly to the future of agriculture by creating crops that are more resilient, nutritious, and sustainable.
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Pre breeding is essential for linking genetic diversity arising from wild relatives and other unimproved materials to utilization in crop improvement. It is the main link between the germplasm conservation and its use in plant breeding for developing new varieties.
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Pre-breeding aims to isolate desired genetic traits (e.g. disease resistance) from unadapted material like CWR and introduce them into breeding lines that are more readily crossable with modern, elite varieties. Pre-breeding broadens the elite genepool by re-capturing lost beneficial genetic diversity. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this.
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In organic farming and for high-K demanding crops, K could be a problem. N source can come from compost, or animal manure; P can be supplied by bone meal or rock phosphate, but K is hard to find. Seaweeds may be a source, but could pose an invasive problem. Natural polyhalide mineral is only available in certain locations. Any suggestions are appreciated. Thanks.
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In my humble opinion, One option is soils with a heavy texture without conducting the improvement operations. In fact, It can be suitable pi-loads (case study) for conducting such an experiments due to the presence of preservative colloids and an appropriate granulation/granular (intake and uptake of the K element from the base source). Of course, It is better to the whole variables ought to considered alone or together and the comparison analysis was done for receiving the best results. This works to some extent in natural ecosystem and as above said it needs to more studies in the crop lands and agricultural ecosystems.
Regards
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In recent years, data science has emerged as a promising interdisciplinary subject, and helped understand and analyze actual phenomena with data in multiple areas. The availability and interpretation of large size data that is a vital tool for many businesses and companies has changed business models, and led to creation of new data-driven businesses.
In agriculture including crop improvement programs, both short and long term experiments are conducted, and big size data is generated. However, deep data mining, meaningful interpretation, deeper extraction of knowledge and learning from data sets are more often missing. Whether application of data science is also vital in agriculture including crop improvement for understanding and analyzing the actual phenomena and extracting deeper knowledge??
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Dear Dr Rk Naresh, Agreed with your statement; thank you so much for your inputs to the discussion.
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Please explain which is good nanoparticle in agriculture.
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I have used ZnO as foliar application
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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?
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The reason is that there are very few publications where functional characterization (cloning, overexpression, silencing, etc.) of the genes identified through GWAS has been performed. However, most of the publications on functional characterization revolve around genes identified through transcription because these are quantitative traits and are controlled by many genes and the influence of the environment is very high and the effect of each gene is weak (Minor genes) and they have small-effect genes rather than Major genes that have large -effects
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In mutation breeding with EMS, turmeric single bud chips were used. Near LD50, many sprouts started withering. But due to care in handling like helping the pseudostem to open, helping the leaves unfold in budlings, helped more budlings to survive. Further, some of sprouts withered and died due to deleterious mutations, but new sprout arose from the bud, in the nodes (generally in the opposite to original sprout). These new sprouts were given extra care to survive, by placing them at proper position in the protrays.
1. Helping pseudostem to open freely.
2. Helping budlings to open leaves freely while germinating so that budling can establish.
3. Allowing the new sprout to grow in withered budlings, by placing the new sprout at geotropically advantageous position.
All these measures helped to achieve recovery of more mutant population.
Any opinion on the utility of this method in mutation breeding.
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Mutation breeding through radiation is a way of variability creation in different crops usually those are not propagated by seeds or those are not able to produce true seeds with proper germination ability. Sometimes mutation breeding resulted better if it is given below the injury level or below the lethal dose. In Bangladesh mutation on Ginger with 5Crad Gamma radiation found better than its higher or below doses. If the dose is higher new bud may die, damaged or unable to germinate. If any shoots germinate from out side of the radiation imposed area may not have any change. However it may need keen observation and should allow time to see the result.
Thanks a lot.
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In between Genetic and plant breeding, plant physiology, agriculture biotechnology and plant pathology which one subject have maximum contribution in crop improvement? Which one is better for research?
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Among the research areas of Genetic and plant breeding, plant physiology, agriculture biotechnology and plant pathology all of them have contribution in crop improvement but I thing Genetic and plant breeding has maximum contribution in crop improvement. Agriculture biotechnology is also better but it has to follow conventional breeding.
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Now a days, speed breeding is becoming famous for rapid varietal development through rapid generation advancement.
However, it's applicability and feasibility for everyone and everywhere is still not wider. What you think about it? How will it be useful in future breeding for crop improvement.?
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Dear Parmeshwar K. Sahu Any breeding scheme based on rapid turn over of generation cycle, ultimately resilting in rapid attainment of final outcomes may be referred to as speed breeding. Its concept is rooted in haploidy breeding through which completely homozygous lines are derived from haploids by using colchicine in a single generation. Recently Australian breeders have used it to develop a wheat variety "DS Faraday". The details of speed breeding can be accessed at the links goven below:
Thanks!
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I have  got the  negative heritability (-3%) for Harvest Index in pooled analysis for RILs. But interestingly the heritability for harvest index was  high in individual year (75% and 91%). My design was alpha lattice and 300 RILs were evaluated in two stress seasons for heat tolerance in Chickpea. Analysis was done in SAS proc Mixed model.
Could you please tell me why I got these results and if it is okay then how to interpret the results?
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Dear Paul, I recommend you to read a very good paper on negative heritability. Despite all the resistance of the scientific community to admit it, I strongly agree with those who think that negative heritability may occur in situations were individuals grouped under similar criteria like genotype are likely to have more divergent traits. Here is the reference:
On Negative Heritability and Negative Estimates of Heritability
David Steinsaltz, Andy Dahl, Kenneth W. Wachter
Genetics June 2020 215: 343-357; https://doi.org/10.1534/genetics.120.303161
Thanks
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What are the practical uses of trait heritability estimates in crop breeding programs? Does trait with high heritability mean it is of high economic value in a breeding program? How to approach or target lowly heritable traits ( traits with low heritability estimates) but of substantial economic value in crop improvement programs?
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I do agree with @Md Sarowar Alam. He gave the right answer.
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Developing superior crop varieties across environments is a very complex due to GXEXM or GXE interaction, and I want any clarification about the difference between GXEXM & GXE .
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Dear Zigale Semahegn GxExM interaction study provides a more precise picture of genotypic variation than that of simply GxE study. You can ask yourself: why one year evaluation is less reliable than two year evaluation, and why single location evaluation is less dependable than multilocation studies?? The answer to these questions would bring you towards solution to your own question that you asked at RG.
Thanks!
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Dear Colleagues,
As we know that heterosis plays an important role in crop improvement. CGMS system of hybrid rice is mostly applicable and useful approach for developing a good hybrid. However, it is very difficult to sustain the hybrids in their actual form as they show in F1. Therefore, we need to produce hybrid seeds every year. We read abkut some methods for fixation of heterosis which are not applicable in each crop.
So let's discuss about the possible techniques which could be applied for fixation of heterosis in hybrid rice. Kindly give you valuable comments in this regard.
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interested
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My greenhouse maize plants are too thin. They have strips on the leaves.
The conditions are 14h day/10h night; 26-28°C day and 20-22°C night; 60% humidity; peat soil mixed with little sand. 
I use Osmocote exact Standard 3-4 for fertilization. It is a granular and should work for 3- 4 month. It contains all important nutrients which dissolve gradually:
16% nitrogen (7,4% nitrate-N and 8,6% ammonium-N)
9% P2O5
12% K2O
2,5% MgO
0,02% B
0,056% Cu
0,45% Fe
0,06 Mn
0,025% Mo
0,02% Zn
The plants are at V4 stage now.
I think that the plants have a nutrition deficite. What is the best fertilizer for greenhouse maize? Du you have any suggestions for improvement?
Thanks!
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Different kinds of Isotopes are playing very important roles in agriculture. They are used to detect different nutrient elements in soil and other crop improvement program. But which isotopes and how can they preserve agricultural products?
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Fertilizers labelled with radioactive isotopes such as phosphorus-32 and nitrogen-15 have been used to study the uptake, retention and utilization of fertilizers. Excessive use of fertilizers effects biodiversity and damages the environment.
Cobalt-60 is desirable because: It is easily made by irradiating normal cobalt in a research nuclear reactor or a power reactor. Cobalt itself is cheap. It has two high energy gamma rays that can penetrate the entire lot of food.
How does Food Irradiation work? Food is exposed to a carefully measured amount of intense ionizing radiation. With food irradiation, radiant energy (electrons, gamma rays, or x-rays) breaks chemical bonds, leaving the food still like-fresh, but with specific benefits, depending on treatment level.
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Turmeric is a polyploid and vegetatively propagated crop. Usually, F1 populations are used to identify QTLs. As this crop generally has no viable seed, what is the best approach to genarate QTLs.
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An F1 clonal propagated population should work fine for qtl mapping.
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Kindly suggest the name of free softwares available for LxT analysis and heterosis estimation in crop plants.
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You can run a Line x Tester Analysis
Directly, online
Use the link
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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.
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Several parameters require to be optimized in a marker aided background selection program viz. at least a few hundred highly polymorphic and evenly distributed markers with a reasonable genome coverage and a minimal marker density, no dependency of the markers to genetic background, minimum number of individuals for detecting recombinants in a given marker interval, and minimum number of data points to achieve fast completion of backcross program.
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Long juvenaility of citrus hybrid seedlings is the major hindrance in crop improvement programme. Apart from rootstock, other innovation methods should be discussed.
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Dear Gurteg, try to give a zygotic F1 seedlings two vegetation period and rest.
Sincerely. Boris Krška.
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I just want to know: the breeding techniques in the production of hybrid seed, composite seed and synthetic seed as well as the advantage and disadvantage of using each of the variety in crop improvement program
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Dear Solanki Bal:
Thank you for your answers and comments.
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In term of bolting garlic may be three types non-bolting, incomplete bolting and complete bolting. In case of complete bolting it may be used for genetic exchange (crop improvement) but what is practical use non-bolting and incomplete bolting garlic genotype genetic diversity study.
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The other two types of garlic may contain transgressive traits that will also be useful to improvement of your trait of interest. As Suzuki correctly and succinctly stated, "There are no qualitative traits". Some loci explain much more of the genetic variation in a given trait than other loci, but every trait has multiple loci that impinge upon the final phenotype. Also, without the comparators of the other two classes of garlic, how would you know if allelic uniformity at a suspected beneficial locus was significant or not? One needs to include as much phenotypic diversity as possible in breeding programs. You will inevitably narrow the pool down later after understanding what you have to work with.
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Hi! I am looking for researchers or scientists that are from the Philippines, especializing in crop improvement, plant protection or any related field.
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IRRI would be a good place to search for such scientists/ faculties
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In what condition back cross utilized in crop improvement in plant breeding?
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Back-crossing is a very common and popular breeding method. It is used to overcome a bottleneck of any of the popular cultivar by transferring of genes. By using back-crossing we can develop isogenic lines i.e. identical lines having a single or few gene differences. Suppose you are having a very good crop variety, say 'A', which is very popular among farmers but it has become susceptible to any of the deadly disease or insect-pest for which gene and source of resistance, say 'B', is known. In this condition you can improve that particular variety through back cross method. You have to cross AxB first using 'A' as 'recipient' or female parent and source of resistance i.e. 'B' as 'donor' or male parent. It will give rise to F1 which will have 50% of the genome of both A and B. Now if you back cross F1 with A genotype i.e. F1xA, it will give rise to the BC1F1 generation which will have75% (50%+25%) genome of A. But here we have to check for resistance gene so such BC1F1 plants are selected which phenotypically resemble A and have the resistance gene. This process if you repeat for up to 6 generations, you will have a genotype having >99% genome of A plus that particular resistant gene. Simply it can be said that A will be improved for resistance against a diesease or insect-pest. So the bottleneck of A will be overcome.
For fast and more precise results, now MABC (Marker Assisted Back-crossing) is in common use. Here plants having particular gene(s) are selected in early growth stages using available DNA markers.
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The CRISPR CAS9 technology has become popular for crop improvement and is considered to be better than the other biotechnology termed as genetic engineering. Can people from the field explain [in less technical terms] the basic differences in terms of human safety, environmental sustainability and cost? It is appreciated if the discussion(s) also includes the conventional genetic improvement using mutagenesis. Thanks.
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With GMO there is introduction of foreign genetic material from different organism hence referred to as transgenic or from same organism hence refere to as Cisgenic whereas with CRISPR/CAS9 involves changing/altering original base pair arrangements within the genome of an organism (in simple terms) hence there is no introductions.
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Effects of allelochemicals on beneficial microbial population for crop improvement
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A review on weeds as source of novel plant growth promoting microbes for crop improvement
January 2014
Project: PGPR in crop production
C. SarathambalC. SarathambalIlamurugu KrishnaswamyIlamurugu KrishnaswamySrimathi Priya LakshminarayananSrimathi Priya LakshminarayananK K Barman
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I need to calculate the genetic heritability of different yam species using different parameters. Which is a suitable study for crop improvement program.
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Here’s a thought exercise: suppose the Venezuelan HD pedigree has some consanguinity, which means that relatives often share more IBD than their nominal relations to each other would suggest.  Does that bias the heritability estimate?  I am still undecided on my answer.  At first I thought the answer was no, because if you think of heritability as (variance explained by genes) / (total variance), then both the numerator and denominator are affected by consanguinity.  Yes, first degree relatives share ‘extra’ IBD and so correlate better than they ‘should’, but so does everyone in that dataset.  However, Visscher 2006 presents formulas for controlling for parent inbreeding, implying consanguinity does matter.  Leave me a comment if you have the answer.
In talking about consanguinity, my concern is with excess IBD.  But you might also ask whether excess identity-by-state (IBS) matters for heritability calculations.  After all, even if you only look at SNPs that are polymorphic within my ethnic group, I’m still going to share plenty of alleles with any other random person just by chance. For a C/T SNP with minor allele frequency 50%, there are three possible genotypes CC, CT and TT, and so me and some random person will have a 50% chance (.25^2 + .5^2 + .25^2) of sharing a genotype and a 87.5% chance of sharing at least one allele (1-2*.25^2).  And most SNPs are relatively uncommon, with an average minor allele frequency around 10 – 15% in many studies, which makes those odds even higher.   Accordingly I’ll also share way more than half my alleles with my sibling just by chance.  So does that mess up the heritability calculations?  Again, since it affects both the numerator and denominator – you have extra IBS with your siblings and with random people in the population – I believe the answer should be no.
However, leaving consanguinity behind now, the fact is that different sibling pairs do share different amounts of IBD, and different unrelated individuals do share different amounts of IBS.  This variability has enabled a couple of very cool modern approaches to calculating heritability.
The first of these is sibling IBD regression. Visscher 2006 presents an excellent (and perhaps the first with any considerable sample size?) analysis of heritability of height using this approach.  Due to random segregation of parental alleles, siblings don’t always share exactly 50% of alleles IBD.  The mean is 50%, standard deviation ± 4% – a fair number of sibling pairs share as little as 40% of alleles or as many as 60%, as shown in Visscher’s histogram from Figure 1:
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Scientists are still not getting very much successful in designing stress tolerant crops even after applying conventional ,omics and transgenics approaches to stress tolerance . .What are the main reasons behind it .
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Shubham,
That is quite a complex question. While much work is being done on that topic, it is very challenging to make progress. One reason would be the Genotype X Environment interaction that is such a challenge for plant breeders. There may not always be consistency among cultivars that perform well in stress vs. non-stess environments.
Even with tools like omics, transgenics, etcs., it is still necessary to consider how a given cultivar will interact with the environment. Since many of the most productive regions are low stress due to fertile soil and inputs (i.e. fertilizer, irrigation, etc.), the best performing cultivars will be focused on these areas.
With more awareness on climate change and the limitation of resources like water and fertilizer, more breeding efforts are focusing on stressful environments.
Below are a few links to show some of the work that is ongoing on this important topic.
Best wishes for your research!
Chris
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Implementation and evaluation of farmers variety
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Farmers should be involved in plant breeding and variety selection trough participatory plant or variety selection! They can select plant and variety they prefer from their own criteria! From selected plant or variety, they can be trained on seed production and marketing. They can be linked to seed producers or to be themselves seed producers and sellers!
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Precision farming has become popular to everyone associated with advancement in farming strategies. Similarly, in plant improvement what is the scope of precision breeding? I think, it possess great potential particularly for the improvement of the perennial tree crops. Please post your opinion on this aspect.
Thank you
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Precision breeding techniques are a broad set of technologies that provide additional tools to introduce genetic variation into the genome; these techniques should not be treated as a single class. These techniques drive new improvements to agriculture and a broad range of solutions to help farmers deliver better harvests. Within the context of conventional breeding, most of these techniques pose no unique safety issues
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I am working on Genetic analysis of tolerance to Low Phosphorus soils of Sub-Saharan Africa in Cowpea. I just finished phynotyping 120 cowpea lines under two levels of P in the Glass-house. I really need to make selection for the tolerant and susceptible varieties for my crosses. Hence the need to calculate PSI. 
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Thank you very much for this clarification. I will search for the literature but if you have it I will be glad to get a copy from you.
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What can be the factors affecting the economic performance of a crop?
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Dear Rao, 
Yields of maize and soya in my region range from 8 to 12 t / ha and 2.5 to 6 t / ha for both crops. In general, the costs per hectare to produce maize and soy do not vary considerably for a minimum and maximum yield. This cost variation is approximately 10-15% above or below the average cost. As for grain prices, it only has a high impact on economic performance when yields are below the minimum mentioned above. Otherwise, the economic performance of both crops is linearly related to yield. This assertion originates from the analysis of economic results of companies during 5 or 6 agricultural cycles.
I hope the clarification helps, any doubt we are in contact.
Regards
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The paper should deal with physiology of modern corn and sorghum cultivars. How it differs from physiology of traditional corn and sorghum? I am in need of few papers related to the above mentioned aspect.
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Ok, now I get it. Thanks for clarifying.
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seek information in context of the biofertilizer and improvement of yield
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According to ecological rules " there is no such thing as a free lunch". Plants spend energy to gain something.
For sure, there is a cost, but how much and how to quantify it, perhaps, it need to be studies thoroughly.
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Example : are (a)(P1*P2) x P3 and (b)(P2*P1) x P3 equals in term of seed quality ?
P1= parent of genitor hybrid taken as female for the (a) 3-way hybrid and male for the (b) one
P2 = parent of genitor hybrid taken as male for the (a) 3-way hybrid and female for the (b) one
P3 = male parent of the 3-way hybrid
I am thinking that cytoplasm donnor could play a role in seed quality. Do you have any references on this subject ?
Thx in advance
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Hello Mr.Cyprien,
Yes, the quality of the seed will differ depending on which parent you use as a seed parent in a commercial set-up e.g. biotic or a-biotic  stress tolerance of the seed parent will affect the seed quality.
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I am looking for some information on the effect of doubled haploids on inbreeding depression in crop plants. Attaining homozygosity through several cycles of selfing leads to inbreeding depression in many crops. What is the inbreeding depression observed in plant made homozygous through anther/microspore culture?  Haven't had much success in finding relevant literature through web search. Any help/guidance will be much appreciated.
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Dear Hafiz, I agree with what Luke said. Tracing the nature of inbreeding depression in DH lines is indeed difficult because those plants hardly survive the variations. We have been involved with the development of some rice DH lines and have observed that, while it responded well with some Japonica rice lines, microspore culture exhibit a very low frequency with the Indica genotypes. This is mostly because of recalcitrant effect of the existing variations within a group of genotypes.. 
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The strategy should produce similar results as transgenic strategy that involves fusing different protein modules or domains to get both auxin and GA responses when adding only auxin to rice.
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Hi Rahul,
maybe you have to specify your question. If you want to do what you plan, then you have also to use in vitro recombined DNA and then introduced it or the transcribed RNA into the cells/organisms you want to test it.
Possibly you are asking for transient transformation/ transfection as a short-term transgenic situation vs. the long-term establishment of (stable) transgenic lines.
Best wishes,
Tony Schaeffner, Munich, Germany
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hi dear researchers 
I have worked on cross between soybean cultivars since two years ago but many of crosses were not successful.
according to your experience, could you tell me what are optimum conditions for setting up soybean crosses?
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I applied 10 mg/l for every day spraying. 
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I am looking for advise on environmental conditions for successful crossing of soybean grown in winter under controlled environmental conditions.
We have good experience and success rate in crossing soybean lines in field conditions in summer, but we want to be able to perform crosses also out-of-the-season in a greenhouse with regulated temperature, humidity and light conditions.
Any tips or ideas would be highly appreciated.
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Success for crossing under protected structures is less for soyabean. Under open conditions soyabean performs better for pod setting. But you need to find out off season locations with in your country or in a different country under open conditions to save a season. In India sowing is done from June to 15 August. I think it is one of off season location for you. You need to check.
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In cotton, fruit shedding is a big problem. Any suggestion to improve it.
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In my opinion, the elevated temperature is causing sever shedding in cotton growing areas of pakistan. Follow better crop production and protection practices so that the crop may compensate later on......
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It has been widely reported that the Biochar application can increase crop production through addition of plant nutrients,retention and release of nutrients and water,adsorption of heavy metals and green house gases etc.The biochars of diverse origin, nature and properties can hold different amounts of water in their macro and micro-pores. The application rates of biochars varied widely from 5 to around 200 tonnes/ha.The long term benefits of application of biochars are also not known.So the main questions are, what type of biochars hold more water ?,whether the water held by the biochars is available to plants(especially that held in micropore)? ,what are the reasonable rates of biochar application to different soils to get benefit of its application?,Once applied ,how long the biochar benefits the soil by holding more water?
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The water holding capacity of biochars depends very much on the feedstock and the pyrolysis process. Herby it is not only the physical pore structure and the degree of tars that clog pores which are decisive but also the biochar surface chemistry which determines how the water penetrates into the pore structure. However, it is easy to measure the WHC (see EBC analytical methods: http://www.european-biochar.org/en/analytical%20methods). There are biochars that can hold up to 7 times its own weight in water, others can hardly hold one times its own weight. At an application rate of 10 t ha-1 this is not more than 1 to 7 liters per m2. If this is superficially labored into a given soil this may reduce the water stress for one or two hot days only. However, if you apply the biochar concentrated into the root zone of your cultivated plants, this water stored close to the roots and far from the hot soil surface may make a much longer difference for the plant and its microbiom (see also here: http://www.mdpi.com/2077-0472/5/3/723).    
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Among different management practices like tillage, no tillage, plowing, residue retention, residue burning, manure application, What kind of practices are adopted by farmers for improving soil fertility in different countries. Is there any distinctive traditional soil management practice adopted by the locals, which is only unique to that particular place?
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Basically the soil texture, soil organic matter and the occurrence of natural lime in the soil (acid soils and alkaline soils).
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A question asked in competitive examination how do you break male sterility
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Cytoplasmic male sterility is used to develop hybrids in many crop species. The system depends on a maintainer stock to maintain the female parental line and a restorer male line to produce a fertile offspring.
Major seed companies have experimented with a transgenic Avidin gene from Streptomyces bacteria. The avidin protein sequesters the biotin vitamin resulting in male sterility. The addition of biotin via timely sprays can recover the male infertility and the sprayed plants can be used as male stock while the unsprayed can function as females in a crop like maize.
In sorghum a plastic bag can prevent pollen from forming based on high humidity and temperature. These plastic bagged plants can be used as females and paper bagged plants are used to collect viable pollen which is used as the male. The female plants are dwarf colorless and the male can be pigmented so with germination only pigmented plants represent the hybrids.
There are various chemicals that can induce male sterility while maintaining female function and a literature review is recommended for greater information and engagement.
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can you provide me available  methods for crop improvement through Biofortification?
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See www.harvestplus.org for numerous publications regarding biofortification breeding (for Zn, Fe and provitamin A).
Some key publications:
- 2007: HarvestPlus: Breeding Crops for Better Nutrition: http://bit.ly/22FvBq6
- 2007: Biofortification: Breeding Micronutrient‐Dense Crops: http://bit.ly/1Mm6swA
- 2011: Biofortification: A new tool to reduce micronutrient malnutrition: http://bit.ly/1Rl5T2S
- 2013:  Biofortification: Progress toward a more nourishing future: http://bit.ly/1MCmVaO
- 2016: Biofortification Techniques to Improve Food Security: http://bit.ly/1LGZeTL
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 Our major staple crops: bread wheat, potato, oilseed rape, etc. are polyploids and/or alloploids. They still have smaller genome than plant with largest one  - Paris japonica with 150 billion bp. Can we expect to see in future a new alloploid crop that will be a major source of food in the World affected by the Global Climate changes?
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I feel each crop will have its own problems so not sure finding a new crop is the answer. My opinion is to improve the crops we have on hand rather than look for new. We developed Triticale and it remained a minor crop even in spite of the advantages. 
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Plants need 16 nutrients  as their basic feed. but , different forms of nutrients are used to feed a plant. Of them , a comprehensive feed called substrate is supposedly anticipated to take care of both plant as well as soil health in a most befitting manner.  In this background, i propose following questions to our learned colleagues for their valuable responses :
* What is the logic of substrate?
* What is the logic of adding dynamics to a substrate?
* What could be the possible components of  an effective substrate  for achieving better plant  health  ?
*  How could dynamics of a substrate be traced across different growth stages of a crop ?
* What are the developments so far,   have taken place in  the field of substrate dynamics ?
*  How can we tailor the dynamics of a substrate as per requirements of  crop ?
Thanks and regards 
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Dear Anoop Kumar and All
If I understand your question my answer is this:
Soil starts as soon as the plant and animal life comes to live in the debris of the decomposition of a rock. On the death of these creatures, their material is incorporated into the soil, mixing with mineral substances. They then represent Soltner as "organic ingredients" or "organics"
Given the different types of organic matter (live, fresh, humic matter) that have multiple functions: processing, energy substrate, physical fertility. It follows a physicochemical fertility (mineral intake, therefore soil structure a long-term stability)
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Webworld of microbes in soil fertility transformation is distinctly visible on various kinds of crop responses. But , responsiveness of such microbial inoculation is often claimed to be bit time consuming . And annual crops are often debarred from such benefits compared to perennial crops. Very often , we keep talking of source specific microbes, crop specific microbes, native microbes and so on ...In this background, i have few very pertinent quarries to be responded by my learned colleagues . These are as follows:
* How far soil microbes compare with plant endophytic microbes?
*Is there any crop specific study to establish the superiority of soil microbes over plant endophytic microbes and vice-versa?
* Is there any tissue specific microbes more accountable to crop response?
* What kind of microbes are more favored in studies on plant endophytic microbes?
* What kind of inoculation procedures should be adopted for plant endophytic microbes?
* Is there any possibility of having plant endophytic microbial consortium for elevated crop response?
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Dr Deka , so  far researches accrued on this issue , it is claimed bacteria of endophytic origin are more efficient compared to rhizophere origin , they are supposed to be metabolically more like a part of plant functioning . But , I wonder how to inoculate them ?. Shall we adopt soil inoculation or seed inoculation , very often seed inoculation finds difficulty in generating good plant response.
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Even if crop models have N or NPK interaction, pH greatly influence nutrients' availability, in particular micro-nutrients, which may reduce the yield even under adequate NPK supply, we need to identify the attainable yield under problem soil and thereafter predict the effects of stresses arising due to N, P and K, water and insects/pests. 
None of the models handled this way to address problem soils. 
Crop Nutrition experts need to be consulted and simple models on this aspects to be developed
regards
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Dr Subba Rao, I too all the time think about this question raised by you, that how to take care about these interactions within a model, some of the approaches in model says that take the stress effect of the individual nutrient contributing the most stress, but that somehow is not convincing, for example if Zn is deficient even uptake efficiency of N is reduced, so many examples raised by you, we have to think together and bring some solution thanks for your valuable comments
regards
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The consumption of legumes/pulses and other whole foods is so minimal in developing countries. What are the factors behind? I know consumption of foods from these categories of foods has got numerous health benefits, particularly in preventing lifestyle complications like cancer, obesity and heart disease.
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Inter alia, cheap meat price in the western countries offsets the consumption of pulses and wholegrains as a source of protein. Developed world also has high per capita income which puts the 'pulses and wholegrains' under inferior commodities resulting in less consumption.
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It is said that this fungus provide better growth of plants. I m willing to carry an experiment about it on maize seedlings
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Hi Sylvain,
yes, there is already some work with P. indica in maize under different plant growth conditions (see the file attached). I´m sure you will get very good colonization in maize seelings but the most important thing for your research is to have a new and interesting question to carry out experiments with this endo-system.
Best,
Diana
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Could anyone help me with SAS script for line x tester analysis in crop breeding?
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How many lines and tester? I have an excel sheet with formulas.
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I am looking for technical data and methodology to study old Setaria sphacelata cv. Narok pasture rejuvenating, mainly focusing on soil fertility and perennial weeds. The research is undergoing in a 10 years old setaria pasture, over a clayey soil with a low phosphorus level and a few natural species (Paspalum urvilley, Schizachirium paniculatum, Sporobolus indicus) and weeds like Eringium spp and Vernonia chamaedrys  which pose strong competition to pasture.
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Dear Eduardo
You need to start with a thorough soil testing regime. This will reveal the needs related to liming, micro and macronutrients. The testing should include analysis of any plow pan or constricted soil layers.
Under your condition it might be best to figure a optimal mixture and establish your pasture mix under a nurse crop of a winter cereal.
To improve the quality of your forage it would be important to stress a mixture of legumes and grasses adapted to your area. To remove all the limitation you might need to do some tillage to incorporate lime and or control perennial weeds.
If you provide a complete analysis of your soil and ideas on the position and adaptation I would gladly take a look and make my suggestions as a sounding board.
Sincerely, Paul Reed Hepperly
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I've done a canola hybrid trial to evaluate the mid- and high- parent heterosis in field. The design was: 4 major heterotic groups as the main plots, each plot contained "male parent row-hybrid row -female parent row" unit. Group I size= 29 units, Group II = 20 units, Group III = 14 units. Randomization was done within every group (e.g. Goup I, 29 units were randomly assigned). Experiment had two replications at one location. Field layout was attached below.
I need to compare the means of each group over different traits (e.g. yield), so is it an alpha lattice design or incomplete Block design? what's the SAS code to calculate lsmeans of the traits, comparison of means of different heterotic groups? Thanks.
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I completely understand the desire of researchers to see their parents and progeny planted closely for visual comparison. That does not excuse the use of an experimental design that will not answer the question being asked.
You can certainly analyze your data very simply using the code Salvador provided. I would caution that you should interpret your results with a very large "grain of salt", acknowledging that your design is not appropriate for answering the question of whether or not there are differences among groups for heterosis.
I strongly recommend that you visit your stats department (linked below), which offers statistical consulting to graduate students. They can help you analyze your data in the most effective way possible, so you can get your work published and move on to the next project where you can apply what you have learned to ensure that your next design is solid. Best of luck in your research!
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I need to know how can I identify new restorer loci for hybrid breeding and which cytoplasm provides male sterility in wheat.
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Thank you Pierre
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If wheat is relayed (by broadcasting) in cotton cultivars of different architecture,
1) Can wheat yield vary?
2) Can there be any residual effect of cotton on wheat performance?
3) What factors can effect on wheat performance?
In a study, Zhang et al. (2010) reported factor such light interception that influence yield but i want to know what can be other factors that can influence.
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Dear Ehab A. Ibrahim Ibrahim Draz, and Agha Mushtaq:
Cotton-wheat cropping system is one of the major cropping systems of Pakistan. However, major constraint in cotton-wheat cropping system is reported to be associated with late sowing of wheat. Generally, farmers sow wheat late because of late harvesting of cotton crop and in greed of earning more net return from cotton, they allow cotton to stand in field even up to December. Late sown wheat crop resultantly exhibited poor stand establishment and subsequently with less yield. This is the problem.
Here comes relay cropping or inter cropping (both names are available in literature). Relay cropping is advanced form of intercropping and involves the sowing of second crop in first crop at time when it is at or near to harvest maturity. Further benefits of relay cropping include timely sowing, attainment of more net income per unit area, ecological and biological pest control, yield compensation and increased soil productivity (Wallace et al. 1992; Slosser et al. 2000)
Nasrullah et al. (2010) found that yield was reduced by 1.0–1.5% per day delay in sowing beyond 20th of November. However, preliminary research regarding relay intercropping revealed that wheat showed substantially higher grain yield and biomass when it was surface seeded in standing cotton than delayed sowing after cotton harvest (AARI, 1992).
A review on the detailed benefits of relay cropping has been submitted for publication, hope this review will further explicit the role of relay cropping or inter cropping in arable cropping system.
Now my question:
Obviously we have different cotton cultivars with different yield potential and architectures. Can there be any kind of residual effect or may be shade effect on wheat if relay intercropped in standing cotton varieties or cultivars of different architectures.
Hope now the question is clear.
Reference:
AARI, 1992. Annual Report, Ayub Agricultural Research Institute, Faisalabad, Pakistan.
Wallace, S.U., T. Whitwell, J.H. Palmer, C.E. Hood and S.A. Hull. 1992. Growth of relay intercropped soybean. Agron. J. 84: 968-973.
Slosser, J.E., M.N. Parajulee and D.G. Bordovsky. 2000. Aphis gossypii and their natural enemies on aphid-resistant and aphid-susceptible wheat varieties in wheat- cotton relay intercropping system. Entomol. Exp. Appl. 121: 235-241.
Thank you
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With increasing population in several countries in Asia and Africa,they have to double their crop yields in coming decades.However crop yields have been stagnating in different parts of the world . Several possible reasons could be  limiting yield potential crops,in sufficient or imbalanced nutrition,limiting soil physical and biological conditions etc. Then how to improve the crop yield in future and meet the food and nutritional needs of  growing population?
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Dear Doctor Rao
In terms of the Phosphorus questions the synergism of legumes through Rhizobia stimulate the mycorrhizal system the stimulated to mycorrhizal fungi  promote Rhizosphere communities of fungi and bacteria that have Phosphorus mobilizing capacity the plant, bacteria and fungi work together synergistically when the system is optimized for them.
These synergistic symbiotic approach required distinctive nutritional support  aimed at supporting the symbionts for the synergism to be most effective. They are especially dependent of micronutrients such as Mo Co and Zn to be most effective and need to evaluated much more thorough.
Symbiotic synergistic is a way of getting more for less and changing negative environmental and energy footprints into positive ones. These solution are systematic in their nature and need interdisciplinary collaborative focus and coordination.
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The acid soils may constitute around 30% of world area especially large areas in the South America,Africa,Southeast Asia,and Australia .In India 90 million ha of geographical area has pH <6.5 and 25 million ha has pH<5.5.Soil acidity affects plant growth, nutrient availability to crop , causes elemental toxicity to plant ,affects soil biological activity and biodiversity.Many poor people live in acid soil regions.How to mange acid soils for higher productivity with cost -effective and easy to follow interventions?
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Dear Rao, I am glad to hear your question according to my expertise. Even I haven't did work during my PhD, but my friends/labmates did this types of work. And involve in same group during field and lab study. So if you interested to work using biochar technology. I suggest you to observe under lab condition first and see the bonding capability of Fe and Al with biochar and measure the soil pH. 
1. Soil ph 5.5 to 6.5 you need at least 5-10% rice husk biochar 
You can conduct a moro experiment under lab condition and incubate the soil for 40 days at least with 20% moisture conditions. Open the soil in mid and remix again and incubate for remaining time. and measure the properties.
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7 parental lines were crossed using diallel mating technique, I now have 21 F1 and 21F1 reciprocals and 21 F2 and 21F2 reciprocals. The objectives of the study are, to investigate the morphological and molecular traits associated with seed yield in the soybean genotypes, to evaluate QTLs conditioning seed yield and its components in the soybean genotypes and to investigate the consistency of the QTLs associated with seed yield and its components across the soybean genotypes.
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Agricultre Microbiologists, Soil scientist and Agronomicst
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This piece could be of help. Culled from "Microbial reclamation of saline and sodic soil" published online.......The method to reclaim sodic soils provides the use of consortium of alkalitolerant, halotolerant and acid producing microbial composition of bacteria and fungi that lowers down the soil alkalinity towards normality, and also enhances soil fertility. The microbial composition reduces sodium absorption ration, displays exchange of the sodium ions from the exchange complex of the soil and the subsequent leaching from clay particles, improving soil aggregation, thereby improving water holding capacity and texture of soil.
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for Mutation Breading purpose
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Each batch of EMS is slightly different than the one before, therefore a titration of kill curves should be performed to achieve an appropriate LD50 concentration for your particular wheat accession/cultivar/line.  Not only will each EMS batch potency be different, but the response from different genotypes will also vary.  Good luck  =)
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I'm writing a term paper about stay-green phenotype. Such suggestions will be a big help. Thank you!
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What are the traits to considered for development of drought tolerant sugarcane?
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In broad sense root and shoot traits should be considered. Root traits including root architecture, depth of growth, volume, number of root branches and angel of branching are some of the phynotypic traits that should be considered. Shoot traits including branching, leaf area, shoot dry weight or aboveground biomass, formation of cuticles on leaf surface, stomatal count (as this relates with transpiration) etc are some of the important parameters you should look after.
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Zinc deficient (low zinc content) rice is a cause of serious health problem for many rice eater people. Zinc deficiency is also a main reason of low productivity of rice. By changing rice cultivation management we can improve zinc availability for rice crop and crop yield. Better management and availability of zinc may improve zinc content in rice. So any individual and institution who have zinc analysis facility and interested for this study we can work together. I will take all responsibility of field work but I need partner for laboratory analysis of final product.     
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You can contact a scientist from Directorate of Rice Research, Hyderabad. I hope they have this facility and you can have a collaboration with DRR scientists.
You can find a related article here
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CRISPR/Cas9 Technology for Crop Improvement
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For CRISPR/Cas9 research, one the most important parts is the 'plasmids'. You can just purchase the plasmids you want and then do some simple work (place in your own short sequence) on it later. Then you are ready to go.
Addgene (a non-profit organization) has continuously collected CRISPR-related plasmids around the world from different labs and different research fields, including mammalian, plant, yeast, bacteria,.......etc. [ https://www.addgene.org/CRISPR/?gclid=CjwKEAjw7MuqBRC2nNacqJmIpT0SJABQXAOt3LhgfBuP8g7h50DAOAWFMKnF4pcV98FdQWpRaS7EKBoC85Hw_wcB ]. 
You can look through their collection and choose those plant plasmids you want. They ship them internationally too. For ordering 1-5 plasmids, each is $65 (USD) + shipping fee ($45 internationally). See their price list at: https://www.addgene.org/ordering/#pricing
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Hello everyone, I was wondering if there is an published article about mitigation of cold stress in vegetable crops or tomato?
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you are welcome. Please, do not hesitate to contact if you need some information about  S.A.
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is there any body having some useful artical on comparative performance of single cross top cross and population cross hybrid in maize?
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Dear Imran,
Russell and Sandall are researchers from Nebraska University, USA.
Sincerely yours. Liliana
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a colleague is interested in assessing yield penalty for groundnut cultivars having multi resistance to diseases such as leaf miner, rosette, leaf spot, and tolerant to drought
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thank you very
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I am breeding lettuce for increased levels of iron and calcium. It is too time consuming to take extracts of every plant and test for Fe and Ca concentrations. Is there any faster way to screen thousands of lettuce plants to select the ones with high levels of Fe and Ca?
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I just responded to your other question on this topic before seeing this question.
Hani Antoun's answer is a partial solution, but as there are several elements that contribute to the colour of chlorophyll, so you cannot be sure that low chlorophyll = low Fe, as it could also be low Mg or low Cu. N and S deficiency can also cause chlorosis (decreasing the "greenness" that the chlorphyll meter measures).
Will growing plants in low Fe conditions achieve what you want? It may identify lines that acquire Fe more efficiently at low Fe availability, rather than high levels of Fe at normal Fe availability (your original question), but it might reduce some of your workload if you grow the efficient lines and then grow them in normal conditions and test them destructively by ICP. (NB You will miss the ones that are inefficient at Low Fe but acquire more Fe when adequately supplied).
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Hi to all. Can anybody help and provide a detailed procedure for the question above.
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I would also like to know if any scientist in the world has a protocol for producing haploidy in soybean including through anther culture and wide hybridization.
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I have observed in several experiments in acid, phosphorus fixing soils in western Kenya that application of urea to provide the recommended N rate of 60 kg/ha for maize when not accompanied by phosphorus application or with very low rates of P application e.g. 6 kg/ha often depresses yields when compared to the control treatment with no fertilizer application. What could be the reason for this?
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Hi Peter,
Phosphorus is likely to be a limiting nutrient in many acidic soils.  When urea is applied to soil it is converted to Ammonium and then undergoes nitrification.  As nitrification is an acidifying process, this may lead to further decline in soil pH (particularly in soils with low organic matter), thus exacerbating the problem, unless P fertilizer is applied along with Urea. I guess this may be one of the contributing factors.
-SJ 
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Hi, what is considered the ideal ratio of farmer:extension officer in the subtropics, especially the semi arid subtropics?
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Dearest Gloria,
the recommended farmer - extension officer ratio ranges from 10-50 farmers to one extension officers and, this depends on farm sizes and distance this agents have travel to the farmer's farm. However these extension agents are faced with challenges beyond their control for effective performance of the sector. These challenges include; lack of mobility (motor bikes/cars) and logistics (field aprons, field note books, vehicles) and irregular transport fare to travel and do farm visits; no access roads to farmers farm; no risk allowance; lack of demonstration farms; no maintenance allowance for already acquired vehicles; farmers inability to form lasting/viable farmer groups; farmer inability to adopt technology; no one structured stakeholder forum; lack of research-extension farmer linkages; long distance to farming land as a result of urbanization; extension farmer ratio in Ghana now is poor 1: 3000. Veterinary farmer ratio is also very poor 1: 5000. As demonstrated , these challenges have put more pressure on extension or veterinary agents to deliver quality services. Extension services provision and information delivery to crop and livestock producers has declined in the last decade.
for more information, you can read this paper: Systemic intervention to tackle the constraints and challenges facing stakeholders and the performance of the agricultural sector in Ghana
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Does any colleague have pTOK233 or pSB134 and want to share?
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Dearest Dr. Gaber, I was wondering what pTOK233 was and got his information at Google. Perhaps, you could make contact with this group if they will share their information with you.
To: Multiple recipients of list PLANT-TC <plant-tc@tc.umn.edu>
Subject: pTok233
From: "Vania L. Muniz de Padua" <vanpadua@CHAGAS.BIOF.UFRJ.BR>
Date: Tue, 22 Apr 1997 08:53:25 EST
Reply-To: Plant Tissue Culture <plant-tc@tc.umn.edu>
Sender: Plant Tissue Culture <plant-tc@tc.umn.edu>
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I want to know about the Mother Tiller Supremacy in crops, having tillering ability. If it is a desirable character, then what is its role? If there is any reference, it would be better.
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I was wondering if anyone has tried (and been successful) at generating  pathogen-resistant plants using CRISPR interference (CRISPRi).  The pathogen in question is an ascomycete fungus.
Does anyone know if the CRISPRi complex can make it to a pathogen's nuclei and stop transcription?
Thanks!
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Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. nature biotechnology,2014,doi:10.1038/nbt.2969
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Genetics of stay green in Sunflower and molecular markers linked or QTLs
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You have to try some of your list and see which one work better with your cultivar under your lab conditions. See attached article to see the a table of different ISSR primers
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For farmers working greater than 500 acres. 
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Thank you for your responses. 
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Prilled urea (0.8-3.8 mm) has become as easy to get as granular urea in the last 1o years. It spreads very well, and weight-for-weight supplies 10 times as many particles as granular urea. This is an important issue on pastures at low application rates. For example, at 30kg N/ha, granular supplies about 45 granules/m2, prilled urea 400-500! In a typical dairy pasture in NZ, there are over 400 plants/m2.
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Thanks for your comments Johann. Yes, we have found plant adhesion and foliar uptake to be an important part of the improvement in efficiency compared to granular urea. We will be presenting data on this next month, and hope to have the conference presentation up on ResearchGate soon after.
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The cooking quality parameters of aerobically grown rice are poor and keeping quality is also not good, please tell me the reasons.
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Dear Dr. Sunil,
I am not sure how much help I can provide but this is certainly an interesting observation. Do you have some literature on this observation? I have not seen the literature yet but my guess is that it might have to do with the following general reasons:
1. Relative grain-filling efficiencies; environmental factors are known to influence grain filling genes related to eating quality. For instance, ambient temperature is know to influence key eating quality traits like amylose content as well as amylopectin chain length distribution in rice grains. So your observation is a possibility.
2. Difference in fertility levels; lowland (submerged) soils are generally more fertile than upland (aerobic) soils, especially in the tropics. If you live in the tropics you might want to compare soil properties of the growth media or repeat your experiment under more controlled conditions.
3. Genetic background; If your observation was made with rice from different backgrounds then there is no basis for this. Otherwise you might need to compare the same variety (a lowland-upland or plastic variety wil be very useful in this case)
Hope I could help.
Sherman.
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I went through my first harvest of the rice and although I got some seeds from the WT plants, most of them were initiated (i.e. the pollen made it in etc.), but then they were aborted and the seeds were empty and brown, dried.
Is there anything I can do to help the plants to fill the seeds?
The rice is ecotypes Hwanyoung, grown in greenhouse. Shall I stop watering them and let them dry? If so, at what point?
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Dear thomas
Most important reasons for what called is sterility.
1. This is mainly due to insufficiency of nitrogen and potassium.
2. It is common in case of late emerged tillers as a result of intra competition
3. If panicle initiation, panicle emergence coincides with coldness and cloudiness
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What are the most important characteristics to consider when trying to identify legumes to use in pastures?
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Dear Francouis,
Many years ago my country had a program for establishing new and renewing existing pastures. In areas where there were possibilities to irrigate, alfalfa was the main crop. While in areas where such conditions did not exist two possibilities were to choose. The first one, mixture of 5-6 grass types (mostly Lolium and several other, for which I can't recall, as this was more than 20 years ago). The second choice, was to use Onybrychis sativa Lam.
The latter was especially appreciated as it has deep roots and is drought-resistant. It was especially appreciated by honey-bee keepers as well since it is very much loved by the bees.
Finally, first and utmost factor to determine what to seed/plant is the kind of animals that will graze (if using free-grazing system of exploitation). Remember that different animals use the grass differently i.e. cows just "cut" the grass, while sheep & goats tend to pull it off. So, depending on this you choose if you will use grass type with deep or shallow roots. Of course, do not neglect water availability, as grasses are huge water users.
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Methods related to weeding, fertilizers etc will be appreciated.
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