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Plant Breeding - Science topic

Plant breeding, Plant breeders, Crops, Crop Improvement, Genetics
Questions related to Plant Breeding
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Genetic engineering should be seen as one of the many tools available for use by plant breeders to improve crop varieties so that we increase food production, control pests, and improve farm profits.
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Dear @Sravani Ponnam
Plant breeding, in its broadest sense, is the art and science of changing the plants genetically in relation to their economic use. Whereas, genetic engineering is the genetic manipulation (bypassing sexual reproduction) such that individuals with a new combination of inherited properties are established. Plant breeding is essentially a technology, and it utilizes various techniques. To my opinion, genetic engineering is the well utilised technique of present day plant breeding. Of course, many hold different opinions! The details can be accessed at:
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plant breeding and genetics
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Dear nishit
Negetive variance is not possible due to square value but it may be due to lack of random mating while developing half sib, sampling error but must be report because of arise due to very dmall megnitude of respective component.
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I couldn't see much paper where plant breeders use biochemical such as proline content Malondialdehyde (MDA) and dyes such as NBT or DAB( for ROS detection) for screening stress-tolerant accession on a large scale (100-200 which I suppose is possible to do). Are not these methods better than phenotyping grain yield, biomass, plant height, NDVI, LAI, etc?
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The biochemical analysis are important, but if you have plant breeding programme should be more interesting and effective to make evaluation on the field. In those conditions you can evaluate and select the best plants for abiotic stress plants, and maybe to others topics like vigorous plants, also for production and quality. Then, you can select the most promissed material for your proposed objectivesz.
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Some domestic oilseed rape genotypes express extra long seed viability (>80% are germinated after 13 years of storage at room temperature). Is it a genetically controlled trait? I know that hybrid seeds have shortest length of life, does this correlate with homozygosity? There is no references exept of a few ones devoted more to seed dormancy: http://www.nrcresearchpress.com/doi/abs/10.1139/b83-405#.U2w-yIF_unM, and seed coat properties: http://link.springer.com/article/10.1007/BF02857926/
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This work supports that seed longevity in oilseed rape (Brassica napus L.) is genetically controlled.
So far, such feature was found in several more Brassica rapa and B. juncea genotypes, and frequency of viable seeds suggests a recessive gene control.
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Genotypes: 138
Replications: 3
Site: 1
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Thanks, Vikas Kumar Singh. I will do that and see how everything goes.
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Dear colleagues,
I used the R package for line*tester analysis (Agricolae library).
It calculated the GCA effects, SCA Effects, S.E. (gca for line), S.E. (gca for tester) and S.E. (sca effect).
The experimental material comprises eight genotypes. Five genotypes were used as females (line) and three genotypes were used as males (testers).
The 15 F1’s and their parents were evaluated in a randomized complete block design with three replications.
I want to know the degree of freedom (T-test table) for performing the significance test of General combining ability (gi) effects and Specific combining ability (sij) effects.
Regards
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For significance test of both GCA (of lines and testers) and SCA (of crosses) effects, you should consider error degree of freedom, that is, (r-1) x (tr-1) = 2 x 22 = 44.
For further detals, you may go through:
Sharma JR. 1998. Statistical and biometrical techniques in plant breeding. New Age International Publishers, New Delhi, Pp. 138-152.
Singh RK and Chaudhary BD. 1996. Biometrical methods in quantitative genetic analysis. Kalyani Publishers, New Delhi, Pp. 205-214.
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Dear all,
I want to analyze a factorial split-plot in time using SAS.
Factorial Experiment using Completely Randomized Design (CRD);
Factor A: treatments (a1-a4)
Factor B: harvest time, different days after treatment (b1-b5)
Replication: 3
Does anyone have SAS codes for this analysis?
Regards,
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What is the advantages of estimating BLUPs for GWAS studies
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Dear Gregor Steve , great question!
There are different ways of using BLUPs for and from GWAS. However, there are also limitations!
Generally speaking, we want to use phenotypic records in all statistical analyses. But, sometimes this is not possible (for several reasons) and we may use BLUPs instead. Here are three common reasons for using BLUPs instead of phenotypes:
Example 1: Complex models
- Some software have limitations in performing some type of analyses, such as, but not limited to: including random effects other than the residual, repeated records (related to the previous one), multivariate analysis (aka multiple-trait analysis), etc.
- In this case, one could use BLUPs that are already adjusted for these effects when performing GWAS
Example 2: Limited phenotypes
- Given a genetic relationship matrix (e.g., A matrix, Genomic Relationship Matrix) that measures the genetic similarities (i.e., covariance) among individuals, the Mixed Model Equations (MME; Henderson, 1963) allows every single individual in the relationship matrix to have a BLUP, regardless of the individual having or not phenotypic records.
- Hence, when the genotypic data include individuals with and WITHOUT phenotypic records, a larger dataset used for analysis could be obtained by using BLUPs instead of phenotypic records.
Example 3: Individuals with large progeny records
- In general terms, when an individual in the relationship matrix has lots (i.e., hundreds to thousands) of progeny records, the BLUP of this individual should be highly accurate.
- Hence, in a large number of genotyped individuals have a large number of (non-genotyped/limited-genotyped) progeny with phenotypic records, the use of BLUPs in place of its phenotypic records could provide with better/more accurate GWAS results.
However, as I mentioned, there are also limitations about this approach:
Example 4: BLUPs have different accuracies
- When talking about real data, we see a large variation on the number and degree of relationships among individuals, the number of phenotypic records, and more.
- Therefore, some BLUPs should be more accurate than others. HENCE, the statistical analysis using BLUPs should be properly weighted by the level of uncertainty of these BLUPs.
- Such weighing procedure could be complex or impossible to be implemented (depending on the software and dataset)
Example 5: BLUPs are only part of story
- BLUPs are estimates of the additive values of the individuals. Thus, if your goal in your GWAS is to identify non-additive effects, such as dominance and epistasis, it is not expected to identify associations for SNPs with non-additive estimates.
- Therefore, BLUPs, unless specifically calculated to include those effects*, should not provide you with these associations.
*By the way, if non-additive effects are included, we shouldn't call them BLUPs anymore.
There are additional thoughts about this, but I think this could give you some clarity.
Please let me know if you have any other questions. Thanks, Nick
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Typically exposing plant parts such as seeds, stems, pollen grains etc. to radioactive isotopes (e.g. gamma radiation and x-ray) and chemical mutagens (e.g. ethyl methanesulfonate [EMS]) induce vital mutations for plant breeding programs.
BUT Natural radiation and microgravity in space induce genetic mutations for selection. Below is a summary:
  • Grow plants in the space station to maturity for one or few cycles.
  • Space grown plants are exposed to natural stresses (reduced soil moisture, nutrients, and carbon dioxide during reproduction).
  • This stress is induced by natural cosmic radiation (cosmic rays and effluvia from the sun) and earth’s gravity both enhancing genetic mutations.
  • Seeds harvested from space-grown plants can be grown on Earth to select novel mutants under glasshouse and field conditions for various traits (e.g. tolerance to drought and heat stress, resistance to insect pests and diseases, early maturity, flower colour, plant architecture, reduced plant height, improved gas exchange, better root growth etc.).
  • The new mutant varieties can be bred further or the seed deployed to farmers for commercial production.
Satellite missions and subsequent selections have produced some 200 improved crop varieties in China.
StarLab Oasis, a private organisation, is set up to raise plants in space for this purpose.
It reads like science fiction, but it is a fascinating, optimistic and complementary tool to conventional breeding.
I hope this service will be available for major crops in the near future. I cannot wait to send my seeds to the International Space Station (ISS), and I hope you do too.
The above read is extracted from
Shimelis Hussein
Professor of Plant Breeding
University of KwaZulu-Natal
South Africa
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Dear @Hussein Shimelis Yes, there are several reports and reviews that have thrown lights on space breeding:
I don't know whether the space bred varieties of crop plants have been tested in other countries. I doubt varieties bred under microgravity (zero gravity) will perform similarly under the influence earth's gravity. Moreover, the basic philosophy remains the same, that is, radiation induced genetic alteration which leads mostly to recessive and deleterious mutations. Although application of artificial mutagenesis to crop improvements started as early as 1928 by Stadler in barley, it never gained much importance in practical crop improvement. Even through site directed mutagenesis, not much has been achieved so far. If China has achieved so much in a short span (just in 3 decades), I call it highly impressive achievements! Let China share its space bred varieties to other countries to assess their performance!
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Dear All
I am writing this concern to find out if any author (as a corresponding author) belongs to one of developing countries and tries to submit his work in the Crop Journal (The Crop Journal | ScienceDirect.com by Elsevier). I have submitted twice and got a rejection from the editor without convincing reasons (your paper doesn't meet the standards of the journal)
1- The first rejection, I have contacted the handling editor providing many similar articles published in the journal in the same year (2020) and with fewer analyses than I did in my paper. His reply was, "submit it again and select another editor"). The same manuscript was successfully published in BMC Plant Biology
2- second rejection was in 2021. Imagine I submitted a new article (two years data, with three locations) and after three hours I got a rejection from the handling editor telling me the same silly reason. I am quite sure that three hours for a manuscript including many figures and tables and more than 6-8 supplementary files were not enough to make a fair judge on the paper. I resulted from it again asking the chief in the editor to assign another editor. After one house, I got the rejection by the same handling editor.
So, it looks to me that the editor just read the affiliation and decide to reject the paper without reading it carefully. I officially complain to the Elsevier publisher about this situation.
Does any face the same situation?
Your feedback is extremely important.
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Dear Amira M.I. Mourad I have had an opportunity to publish one of my reviews "Integrated physiological and molecular approaches to improvement of abiotic stress tolerance in two pulse crops of the semi-arid tropics" in the Crop Journal (Vol 6, No. 2). Although the review process was highly rigorous, the handling editor seemed to be cooperative. However, at that time, the journal was devoid of "impact" factor. Soon after, it received an impressive impact factor, and thereafter, it began to charge publication fee. Because of high publication fee, I did not even think further to submit any paper to this Journal.
That what you have narrated happens sometimes with most authors. Sometimes, even for simple reasons (such as language, grammatical mistakes, etc), the editor decides to reject the submission. For authors, these may be simple reasons, but for the editor these may become the major ones. Moreover, the number of submissions and acceptance rate also account for such rejections. To my knowledge, the journal is an official publication of the Chinese Academy of Agricultural Sciences; I don't think the handling editor can practice any bias towards authors belonging to developing nations.
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Dear colleagues,
I used the R package for line*tester analysis (Agricolae library).
It calculated the General combining ability effects (GCA) of parents, but I don't know how to calculate the significance of the results.
In addition, I want to Estimate Narrow sense heritability and Heterosis (Better Parent (BP) and Mid-Parent (MP)) for hybrids by R.
Does anyone have a solution?
Regards
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Dear @Mostafa Modarresi Please go through below mentioned books:
1. Biometrical methods in quantitative genetic analysis by Singh, R. K. and Chaudhary, B. D., Kalyani Publishers, New Delhi
2. Quantitative Genetics in Maize Breeding by Arnel R. Hallauer, J. B. Miranda Filho, and Marcelo J. Carena, Springer
In addition, you can also access a paper of your interest. Hopefully, you can find solution to your problem.
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What open-source softwares are available to generate a heat map of the Jaccard similarity coefficient for SSR diversity from the available data set?
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```r
nc <- ncol(dat)
out <- matrix(0, nrow = nc, ncol = nc, dimnames = list(colnames(dat), colnames(dat)))
Jaccard <- function(x, y) {
i_len <- length(intersect(x, y))
u_len <- length(union(x, y))
return(i_len/u_len)
}
for (i in seq_len(nc)) {
for (j in i:nc) {
out[i, j] <- Jaccard(dat[, i], dat[, j])
}
}
pheatmap::pheatmap(out)
```
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Hi,
I'm new here so sorry If I'm in the wrong place.
I've been working in UK Agriculture for around 10 years now and I've decided to pursue a career in R&D and plant breeding after working for a seed production company with a local breeding site. I found it all fascinating so I've started a biology degree at Open University and I'm hoping to get a job as a technician or something similar soon.
I know I'm still a fair way from my ultimate goals but in the mean time I'm looking for any good books that go into detail on agricultural plant breeding methods, plant biology, genetics and modern techniques such as Marker Assisted Selection, Doubled Haploid and tissue culture.
I'm looking for something that covers these subjects in detail but on a suitable level for a student (I like diagrams and pictures haha). One of the best looking ones I've found so far is "Plant Biotechnology and Genetics: Principles, Techniques, and Applications" by C. Neal Stewart Jr. But i could do with some advice from anyone who's read any books like this in the past.
Thanks
Stuart
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Greeting to all researchers,
As we all know that YVMV in okra is not yet all seed transmitted viral disease, so, what happens if we go for harvesting of those infected plants. because, breeding for viral disease resistance is not only concerned trait.. so, the question arises can we go for harvesting of YVMV infected plants for generation proceeding?
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To me, big no, viral diseases are systemic so harvesting already infected pods could be a source of contamination for the new progenies.
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CMS lines are important in breeding programs. Crossing CMS with maintainer line maintains CMS lines.
But How lines with heritable Male sterility Characteristics are produced initially?
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Dear Radhakrishna Bhandari Cytoplasmic male sterility is controlled by the cytoplasm (called sterile cytoplasm), but may be influenced by nuclear genes. It may result when a plant with recessive nuclear genes has defective mitochondria due to mutation. The sterile cytoplasm often results from the introduction of nuclear chromosomes into a foreign cytoplasm. In past, CMS lines in sorghum were produced by placing "kafir" genome into "milo" cytoplasm by pollinating a milo plant with kafir pollen, and successively pollinating the progeny as the female back to kafir as the male, until the entire kafir chromosomes was recovered. The same procedures were followed to obtain CMS lines in wheat, rice and pigeonpea. The details can be found by accessing books by John Milton Poehlman, and RW Allard.
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Is there anyone empirically investigating agrobiodiversity loss? Specifically I'm asking about Crop Genetic Diversity and thus not the loss of cultivars by itself or the variety of cultivated crops. Accordingly, the loss of genes (or traits) can be prevented by Ex-Situ conservation.
I found only one source empirically investigating crop genetic diversity loss and this was stating that on the gene level, there is no loss for the 8 crops investigated (Van de Wouw et al. 2010).
Then there is this famous FAO-Statement: «Since the 1900s, some 75 percent of plant genetic diversity has been lost as farmers worldwide have left their multiple local varieties and landraces for genetically uniform, high-yielding varieties.» However, I couldn't find any empirical support for this statement. And this document links to a paper about women's role for agrobiodiversity, but nothing about agro biodiversity loss.
Can anyone help?
References:
FAO (n.d.): What is happening to agrobiodiversity? Online available under: http://www.fao.org/docrep/007/y5609e/y5609e02.htm [Accessed July 5, 2013].
FAO. 1999b. Women: users, preservers and managers of agrobiodiversity. http://www.fao.org/sd/nrm/Women%20-%20Users.pdf
Van de Wouw M., Van Hintum T., Kik C., Van Treuren R., & Visser B. (2010): Genetic diversity trends in twentieth century crop cultivars: a meta analysis. In: Theoretical and applied genetics., vol. 120:6, 1241–52.
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Dear colleagues, I’m thrilled to get to announce that we have finally published a major review of crop genetic erosion, which is open access here: https://doi.org/10.1111/nph.17733. Thank you for this thread, which was useful toward this effort. Regarding the mysterious origins of the “75% of crop diversity lost in the past century”, please see Box 1 in the article. This represents our ongoing work to clarify the origin of this narrative. Spoiler – we still aren’t sure of the origin, but we have some good ideas about where it may have come from. Thank you again. Please pass this paper around.
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Several stability statistics can be used for evaluating the mean performance and stability of genotypes across a set of environments. Aiming at improving the R package 'metan' <https://tiagoolivoto.github.io/metan/> I would appreciate know from the community which are the most used stability methods, and if someone knows or use a method not yet implemented in open-source software. If you use R to compute stability statistics, what is the main difficulty you face? Which would you expect from an R package for multi-environment trial analysis?
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Our study has just been published in volume 113 of the Agronomy Journal, part of the American Society of Agronomy. Another practical contribution to multivariate selection for mean performance and stability in plant breeding trials. Full-text is available at https://bit.ly/2ZaAsZG and supplementary material with example codes at https://bit.ly/2Za3c4N. Thanks to Maicon Nardino, Daniela Meira, Carine Meier, Diego Follmann, and Velci Queiroz de Souza for the collaboration!
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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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good morning
Through this scientific initiative, I would like to present an initiative to form an international scientific team among us to develop joint ideas and research from the brothers who are sick and working in the field of cotton. From the field of plant breeding, genetics, physiology and agricultural transactions.
Waiting for your responses
The approver puts the name, institute, university, country, and email
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This is loudable idea, I am not currenting work on cotton but I have a friend who is working on it. I will recommend this to him in order to get in touch with you. Hope my suggestion help. All the best
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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.
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You could use SNP, PCR, molecular markers, and other molecular methods to differentiate the DUS Characteristics in large germplasm lines.
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Turmeric is a polyploid. Mostly sterile. However, it sets seed occassionally. I have collected seed and kept in poretrays filled with cocopeat. I have not observed any germination even after 15 days. Yesterday I have kept some seed on germination paper spread in a petridish. Can any one tell me what is the viability and time taken for germination of turmeric seed. Seed was collectd from inflorescences fifteen days ago, the flowering was complete about five months ago. Seeds were within the inflorecences for about five to six months before collection and sowing.
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Seed set is observed in turmeric (Curcuma longa L.). Both triploids and tetraploids are available in cultivated turmeric. The turmeric seeds are arillate which have two seed coats, the outer thick and the inner thin. Staggered germination is observed, usually commences after 20 days after sowing and continued for several months. The percentage of seed germination varied with cultivars, and even plant to plant.
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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?
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The polymorphism at DNA level depends on several factors of which genetic divergence of the parents or the genotypes under study is one of the most important one. Secondly, as very rightly mentioned by Ricardo Julian Licea-Moreno sir, it requires detailed information about the genotypes and the markers you are using because it is possible that many of those markers may belong to the same region of a specific chromosome.
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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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Hii, please give me a complete guide or any material to analyse the Experimental data of RBD, CRD etc. to a find Genetic diversity, Character association, Path analysis & other Plant Breeding related experiments by using IBM SPSS
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Dear @Rajasekhar Chowdary Duddukur As suggested by @Suyash Bhimgonda Patil, I also suggest you to access online portal of OP Stat for analysis of genetic diversity, character association, path coefficient analysis and other plant breeding experimental data. It is useful, and I have used it several times.
Best wishes, AKC
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I am from Nepal and we lack adequate resources/ infrastructures for advanced researches in this field. Also, I do not have sufficient knowledge at present to pursue these researches independently. I am willing to devote a lot of time if given the opportunity to collaborate.
I hope to get some updates regarding the ongoing researches in Nepal (in Plant breeding/ genetics.)
Thank you!
Happy learning!
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Dear Amrit Sharma, although the scientific bases of plant breeding are the same, doesn't matter the species, the objectives respond to local particularities and necessities. Focus your attention on regional and/or national bottlenecks and problems. Depending of what are you pursuing, in some cases you wouldn't need too much resources. Observation is an important part of research, and selection is likely the "stronger" allied for plant breeders. Of course, in other cases you would need potent scientific infrastructures to deep in your research field, and for to obtain faster advances. However, your capacity to adapt to your conditions as well as to optimize the use of your resources might give you many satisfactions and advances to reach your goals.
Good luck!!!!
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Which one software is best for agricultural data analysis?
Experimental design
Plant Breeding Trials
Quantitative Genetics
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R is free and has high flexibility in most genetic and statistical analyses.
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I use the R package agricolae a lot in my work but it doesnt offer the option to design an Alpha-Lattice experiment. There are a few packages on how to calculate means from experiments like this but I can't find packages to set up trials like this. Any suggestions
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can anybody help me to brief about how to do stability analysis in plant breeding, based on wheat rust data how can i do the stability analysis for wheat rust resistance and how much time it take to do that
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AMMI and GGE biplot analysis can be used
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In your opinion, what plant breeding plant can be important and useful in the future?
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Have a look at our publication on edible plants, where we recommend a number of promising plant species to improve people's diet and livelihoods:
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Considering the present situation of the world for a safer future, In which direction plant breeding research mostly require to focus? Quantity(higher productivity) or quality (more nutritious)
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T.R. Das Should be focus on both. For example, China is developing super hybrid rice to increase yield. But they also need to use some disease resist elite lines to do that. So, the final product can be disease resistance and high yield production.
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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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Dear all
I am wondering what is the advantage of multi response models of the form
trait1,trait2 = Genotype + Environment + GenotypexEnvironment
Where trait1 and trait2 are traits that are measured at the same experimental unit, e.g. yield and protein content of a certain plot in a cultivar trial.
The GNU R package sommer offers in its function mmer() the possibility to specify such a model.
What I had expected, is that the residuals (for trait 1 and trait 2) after such an analysis are uncorrelated since the information of the covariance is used to have a more precise estimate for the effects in the model (BLUPs, variance components).
However, for simulated data with correlated experimental error, I see no difference/advantage of such multi-response models.
So what are the advantages? Does anyone have an idea?
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This answer is not referring to my question.
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Dear all, Please suggest the plagiarism checker software which is 100% free and also don't have the restriction of word limits.
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Pankaj Sharma: Do you believe that there is a completely free one?
Since there is no guarantee that the original content of your manuscript might not be copied and sold to others before it is published by you, I discourage using any free-software-checkers for plagiarism; some of them are betrayers.
If I were you, I prefer using my own words instead.
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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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I have a population of a dioecious species with significant phenotypic variation and want to select individuals from this population. What statistical methods can I use to perform multi-trait selection or dissimilarity studies with data of individual plants? If have a R package is better yet.
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Dear Hugo Gabriel Peres Your question is highly interesting. To my opinion, before performing multi-trait selection you will have to pay attention on whether the traits in question are uncorrelated or correlated, and whether your population consists of equal number of male and female individuals. If traits are genetically uncorrelated, for practicing 5% selection intensity you will have to select 37% best individuals for each trait (if you are concentrating on 3 genetically uncorrelated traits). If your population consists of equal number of male and female individuals, it's well and good. However, if there is significantly unequal number of male and female individuals, then your effective population size will drastically come down! Keeping these facts into consideration, you may proceed further as suggested by Maurice Ekpenyong
Thanks!
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Please recommend some simple software that is available in free for analysis of different conventional breeding experiments
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Dear Punam Bhattacharjee,
You can use R software for any kind of breeding analysis.
Kindly visit the CIMMYT website, you will find several free and easy software for analyzing phenotypic and molecular data.
I recommend META-R for multi-environment trials and Rindsel for disease data.
With best regards.
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Scientific community is now facing a new threat of unethical publications in predatory journals.
How someone can identify the predatory journal?
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Pankaj - it is not too difficult to recognise predatory journals. One just has to know the 'classic' and common signs of a predatory journal. They don't necessarily expect to exists for long - so they often use 'minimal effort for maximum financial gain' - and therefore there are often many errors and of poor quality - at least in parts.
There are certain factors then that make it reasonably easy to identify predatory journals - or at least ‘cause doubt’ so further investigation is required. Essentially, rule number one with predatory journals is always be very wary when any journal approaches you directly. If you are not sure - then the Directory of Open Access Journals (DOAJ) is a good site to check first. It lists the 'good' journals. If the journal targeting you is not on their list - it's another warning sign. Then there are many other warning signs - such as:
· Poor quality online interface.
· Minimal and/or very broad journal scope i.e. we publish almost anything related to a whole discipline.
· Poor English quality and grammatical errors.
· Check the country of origin. Many predatory journals are based in certain countries (usually sub-continent). Some, however, will try to give the impression that they are based elsewhere i.e. US, Europe.
· Unknown editors.
· Unknown or no editorial board and/or all based in the country of origin
· Unsophisticated online manuscript submission processes i.e. send a word document by email
· Upfront publishing charges
· Not registered or associated with any reputable professional bodies and/or citation agencies - nor are credible Impact Factor sources stated. Articles may not have been assigned a Digital Object Identifier (DOI) number.
· Check the quality of existing articles in the journal. They are usually a very mixed and poor quality.
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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?
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Borrowing from researcher César Jiménez-Yanez:
Regularly predatory journals have the following characteristics:
Send emails regularly inviting to publish
They offer impact factor and show medals and high indicators
Offer to publish in a very short time (days or weeks)
They are multidisciplinary, that is, they accept jobs from all areas and disciplines.
Charge to be published (high costs)
They do not detail the arbitration process (sometimes they do not even mention it)
Present the DOI or Crossref logo as something "important"
The name of the magazine regularly looks like a serious academic journal
They are not affiliated with COPE (https://publicationethics.org/)
You can check the ISSN of the magazine in the MIAR database http://miar.ub.edu/
You can check the ISSN of the magazine in the SCIMAGO database https://www.scimagojr.com/
You can check the ISSN of the magazine in the Clarivate Analytics database http://mjl.clarivate.com/
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how can linkage disequilibrium used in plant breeding
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In 2016 I have developed a set of mutants in two varieties of turmeric-Mydukur and Prathibha. Now, in M1V4 evaluation, have identified a few are performing better than the parents. I am going to analyze quality parameters in these selected lines. I have sown M1V5 (selected mutants) along with parents this 2020-21 season. From here, I want some of these to be developed and released as varieties. Whate are the steps to be taken from here. Please help me.
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Hello Kalidas,
You can take these selected mutants and grown under different environmental conditions with different locations to test their performances and selected the best variety that has not change its performance.
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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.
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You should check the availability of Cas9 structure also. If the Cas9 still in your homozygous plant (consider the target gene), you can have other heterozygous progenies.
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Can anyone help to confirm whether I am using correct stages for Chickpea crossing? I am using hooded bud for crossing and half open flower to collect pollen (please find attached pictures for stage). 
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R1
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I feel, highly focused conventional breeding methods give better target results than a MAS exercise with all the cost:benefit worked out. Maybe, there would be a time loss in conventional breeding, but we end up in a highly adapted concrete product, even though this point may be debatable. In that, MAS can give better results. But looking at an average plant breeder's lack of laboratory, money, skill etc type of resources, will it not be prudent to slog rather than be protocol driven? The practical learning that conventional breeding gives is unparalleled. Of late, there has been a significant shift of even conventional breeders to some molecular breeding aspects. Good, if the target is well defined and the work plan gives a better result. But again, look at the voluminous data being produced and published in the molecular breeding field as against conventional breeding, and it now longer has remained a level playing field. Journals are also attracted towards molecular breeding papers. Where are we heading?
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My suggestion is never to compare. Try to do best what resources available with you. Only thing is that you fix your target and dedicate for it. However, If you have both facilities then use both because both have their own value.
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In Jamun there is no phenotypic differences in the growth of both nucellar and zygotic seedling also the point of initiation of these seedling are also same.
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I think , this is the easiest method followed in all polyembryonic crops . Use of molecular markers is really difficult , where such mass scale production is required....
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Software should be able to phenotypic as well as marker genotypic data analysis. Kindly suggest probable price and the authentic source from where it can be purchased.
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STAR, PBTools and CropStat are free available and very user friendly softwares for various types of field data analysis. These softwares require minimum data formatting and IRRI also provides user manuals. Easy to learn and work. Try them.
This is the link
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Different chemical mutagens are available with different modes of action.
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EMS
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What is the best statistical analysis software for agricultural sciences especially for plant breeding & agronomic research?
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I prefer minitab as i am working a lot with this program and used to it every month there is updates regarding parameters: variabilities/means/normalities/ANOVAs etc there is also SPS : equivalent to SAS and it is also very good in performing statistics estimations regarding variations, and clusterings in Agriculture fields greenhouse trials, lab tests, control and treatment tests etc ...
for R I use it one time in genomic modeling (wheat crossing estimations) :D it was HORRIBLE trying it I have just understand that minitab can do what R do (almost) esecially when you want to compare big data (more than 10 ... variables/factors) and you deal with cofficeint and componenets ''multivariable"" and minitab or SPS/SAS can do it too
NEVER try Phyton though
best of luck
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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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Any free software for the design of experiments for agronomic and plant breeding data??
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Manuel, RStudio tiene un conjunto de paquetes estadisticos que te pueden ayudar dependiendo de los que quieras analizar ... Yo lo uso para interacción genotipo por ambiente y permite un análisis adecuado...
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Rice is the seed of the grass species Oryza sativa (Asian rice) or Oryza glaberrima (African rice). As a cereal grain, it is the most widely consumed staple food for a large part of the world's human population, especially in Asia. It is the agricultural commodity with the third-highest worldwide production (rice, 741.5 million tonnes in 2014), after sugarcane (1.9 billion tonnes) and maize (1.0 billion tonnes).
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Hey Mohammed Shaker Hossain; After conducting all the necessary trials which involve Stage I, Stage II, Preliminary Yield, advanced Yield Trials, Multi-location trials for the target traits of interests, You need data on DUS which is Distinctness, Uniformity and Stability for this variety and it is supposed to be different from the existing varieties that have been released before. You can even go further to genotype it to develop it's fingerprint for reference in case you want to do a QC/QA.
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Dear research scholars, I am working at the area of Plant Breeding since 2011. At present I want to learn gene editing technology specially CRISPR/Cas9 Genome editing. So I need all of your kind consideration.
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Dear Pak Haksong,
Yes, I know this, but for me this is totally new area. I have not enough knowledge from where and how I need to start. I read few article about this topic. Really it is so much applied and beneficial for plant improvement.
So, my request to you, if possible please give little space in your lab, so that I learn the whole process.
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hello,
I got data on 25 germplasm lines for flowering time. I want to plot box plots of best linear unbiased predictors with error bars (either by taking SE or SD) by taking flowering time on X axis and germplasm lines on Y-axis. The three replication data for the germplasm lines and check variety for flowering time was recorded and i want to show the variability present in the flowering time.
Kindly suggest the  best software to do this.
ashok
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I have enrolled for a Ph.D in Genetics and Plant Breeding in the University of Nigeria. I am looking for a research grant to fund my research work, I'll be pleased if anyone can give me useful information on research grant opportunities for Nigerian Students. Thanks.
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European Research Council (ERC) supporting top researchers from anywhere in the world:
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I want to find up-to-date information on the current state of conventional (traditional) plant breeding in the world. Is the conventional breeding approach applied in the small breeding companies or crop giants like Monsanto and Syngenta now? For example in order to produce lines for subsequent marker-assisted selection (MAS) or genetic modification (GM). Or the traditional breeding approaches are currently totally substituted by the MAS and GM approaches?
If you know reviews and/or book chapters on this topic please suggest.
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i think the breeder must be create variation first and he evaluate this variability and select the good new recombination to produce a new strains or new varieties
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Due to the development and spread of mobile applications ones that can replace the old-fashioned paper filed books has emerged. Such applications could facilitate the work of agronomists, plant breeders and increase the data accuracy for researchers worldwide. Currently, there are at least three applications freely available for android OS: Field Book, PhenoBook, PhenomeApp.
Do you know some other and maybe better applications?
Do you already use such applications?
Has it facilitated your research already?
Please share your experience.
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High throughout phenotyping is the need of the day, scientists should consider it as a priority.
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Root exudates
Dear All:
Have you ever measured root exudates to soil?
Would you please mention some techniques?
Thanks in advance, with the best regards,
José
Dr. José Carlos Lorenzo Feijoo
Head, Lab for Plant Breeding and Conservation of Genetic Resources,
Bioplant Centre, University of Ciego de Avila, 69450, Cuba.
Tel. 53 33 225768/212719 www.bioplantas.cu
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Yes I have measured root exudates. In solution culture, but the roots did exude phytosiderophores and we could measure them by HPLC after derivatizing them. https://www.researchgate.net/publication/11538514_Reversed-phase_liquid_chromatographic_determination_of_phytometallophores_from_Strategy_II_Fe-uptake_species_by_9-fluorenylmethyl_chloroformate_fluorescence
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Plant Breeding
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It is a cross where female parent is known.
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Does it make sense to breed plants for better NUE if we take in an account just certain gene existence or we should select plants based on what genes they express? Which approach to take?
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Hello Oteyami,
You may also follow our recently published article which would adds in the information regarding breeding for NUE,
Thank You
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I know about agricolae, gge plot etc. but to workout different plant breeding & genetics trials which packages should I include to my packages repository?
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You should first install packages like:
  • GGEBiplotGUI
  • ggplot2
  • reshape2
  • stability and may be others to analize stability and others
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Due to narrow range of variability existing in this crop mutation breeding might be proved an efficient tool for crop improvement.
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yes
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I retired from Iwate University as you know. Now I started hop breeding to make a new variety of hop. The history of my research is so long (about 40 years). Until now I worked many things, for example hop stunt viroid, gene sequence, gene transfer, soil analysis, plant breeding, and so on. I am now 62 years old. So I want to concentrate on breeding to make a variety of hop. Maybe it takes about 20 years from now. Because I don't know if I could repeat on this whether they are good or not. I hope I would get a good variety of hop while I am living. Best regards. Dr. Takayuki Momma
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I am continuing on hop research after retiring from Iwate University. In the near future I could get a new variety of hop. I have now some varieties of them. Best regards. Dr. Takayuki Momma
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Dear Scientist,
I kindly plead for any one who has an idea on this to clarify me. I ran a two way ANOVA with data collected from two locations and got no location X genotype interaction, then a reviewer is requesting me to present represent replication within location effect and triplicate within sample effect.
Please, can any one give an idea on this? I use XLSTAT to run the analysis.
Thank you
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The attached image is of model parameters. Presenting this may also be helpful but this is not what the reviewer is asking. The reviewer is asking for differences between pairs of species within location A and differences between pairs of species within location B.
You have not done anything wrong. All you need to do is to provide the output of pair-wise comparisons from XLSTAT.
For example: At cite A. The species differences are:
Specie 1 - Specie 2 = 10.24 - 16.29 = -6. If you get this from XLSTAT, it will also give you standard error, confidence intervals and z-values and p-values.
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As we know after Green Revolution there are several new technology were introduced in the field of Genetics and Plant Breeding for the modification of various crops and that also played a major role for mankind. But at the same time now we have reached such a great peak and there is no more increase in the productivity at the same time quality also.Using of pesticides, genetic modified crop and so more new other things that are creating more problems for the mankind. And it is again emphasizing us towards the traditional farming.Why, what are the actual drawbacks that we haven't look for it and also what's our role for come out from this critical situation ?
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Problem is that, if the seeds of the F1 hybrids are used for growing the next crops, the resulting plants do not perform as well as the F1 material ; resulting in inferior yields and vigor. As a consequence, the farmer has to purchase new F1 seeds from the plant breeder each year. The farmer is, however, compensated by higher yields and better quality of the crop.....
Also, creating F1 hybrids involves many years of preparation to create pure lines that have to be constantly maintained so that F1 seeds can be harvested each year, the seeds then become more expensive. The problem is compounded because to ensure that no self-pollination takes place, all the hybridization of the two pure lines, sometimes, has to be done by hand....
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I made crosses in different types of peanuts, and I was studding the F 1 and F 2 populations. In your opinion, the best way of conventional plant breeding to study the progeny in peanuts was according to the growth conditions of this plant, (vegetative, reproductive) should be considered?
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Hello Dr Paul
Thanks for the great comments and suggestions.
Best regards
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hi. I want to know how many hectare are cultivated by Camelina sativa in the world? thank you in advance
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Please check the following PDF attachment.
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I'm very interested in the field of plant science, especially about crops. Today, i'm prepared a research proposal for applying a scholarship from Indonesian government and M.Sc. program.
In my country (Indonesia), many rice cultivar are widely cultivated by local people. Many study was conducted for rice breeding and genetic improvement. And researcher who are studying wild rice still limited. So, i'm very interested to explore the germplasm of wild rice in Indonesia especially from swampland in Kalimantan island. I have some question:
Why studying about wild rice germplasm very important?
How to identify wild rice in their habitat based on morphological character?
Can anyone share a publication about wild rice?
Thanks for your response!
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You can contact Dr. Maria Celeste Banaticla-Hilario of the International Rice Research Institute (IRRI). She is a taxonomist in charge of wild rice , her email is m.banaticla@irri.org. She can provide you detailed information.
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Suppose I have scored 6 allele for an SSR marker in 50 population with major allele frequency of 0.2448. Now how can I determine the required PIC for the marker?
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Well, I had a similar query a few months ago and finally calculated my PIC with MolKin software version 3.0 (Gutiérrez et al. 2005).
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When farming in arid regions, the lack of soil moisture can be dealt in the following ways: either by enhancing the resistance to drought via plant breeding, or through an employment of irrigation. What are the advantages and/or disadvantages of each approach?
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Interesting discussion!
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How can we describe these two terms? Thanks
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Thank you so much. Your description is very helpful for me to understand plant breeding and genetics.
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Tree breeding; Genetics; plant breeding; Tree Improvement;
In trees after crossing done in diallel mating design pods obtained and its characters can be analysed as F1. It is confusing with agriculture crops like wheat and Maize as yield characters are evaluated in progeny raised after controlled crossing.
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After you crossed two plants, the seeds are hybrid, i.e. F1. However, pods (or other fruits) are derived from maternal tissues and are therefore of parental (maternal) genotype.
Seeds (their embryos and plants which will grow after you sow these seeds) are hybrid. But seed coat and fruits belong to the maternal plant.
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I m PhD in Biotechnology and Environment.
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Good Luck
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Can it cause problem if i collect rosemary leaves in winter(no snowy but cold(-3˚C)) for extraction?
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Thanks! If your aim is to study meatbolism, and make some quantification, condistions of plant growth must be standard.
Changes in conditions will led to chnage in substances.
with what extract you want to compare current one?
Even leaf collecetd at different day time (morning and evening) may have different metabolites.
My best wishes!
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I cant find any material which provides the procedure to calculate the contribution of each character to the total divergence. If anybody have materials, please share me...
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You can use PCA on XLStat, R and and so many.
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LOD helps in determining the QTL...
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Dear Dinesh
Greetings and thank you for your question
For LOD score and according to my previous work in the genome mapping in wheat we have classified the QTLs into strong and weak one or minor and major depend on the LOD score for example less than 2 minor QTLs and above 2 is major ones
with best regards
khaled
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I am working on cryopreservation of 'Echinacea purpurea' hairy roots , but my hairy roots all die. the medium of hairy roots (liquid WPM) has dregs and the color of the medium is conescent. Recently I have noticed that after I adjust PH to 5.8 (using KOH or NAOH and sometimes HCL) these dregs appear, but without adjusting PH there is no dregs and the medium is clear like water.
Can anyone let me know the scientific reason and advice for solving this problem, please?
Many thanks 
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It's interesting that after adjusting the pH, appear dregs. In some cases I have observed dregs after autoclaving, drastic changes in pH and/or after several days of culture. By now, I only can recommend to check the caducity of dry powder and/or water quality.
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I had 15 genotypes of sorghum planted in 6 replications. There was pre-harvest grain yield loss by birds that made it difficult to compare these genotypes based on yield performance. Is there any statistical approach to quantify this loss?
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Please try to get this publucation for free online which is "Estimating Bird Damage to Sorghum and Millet in Chad"
Stanislaw Manikowski and Michèle Da Camara-Smeets
The Journal of Wildlife Management
Vol. 43, No. 2 (Apr., 1979), pp. 540-544
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Dear Sir/ Ma'am
Can any researcher share/provide the reprint of following articles (Avdulov 1928, 1931) on grass cyto-systematics...
1. Avdulov, N. P. (1928). Systematicheskaya kariologiya semeestva Gramineae. Drievnik vsesojuznogo Sezda Bot. Leningrade 1928: 65-66.
2. Avdulov, N. P. (1931). Karyo-systematische Untersuchungen der Familie Gramineen. Bull. Appl. Bot., Genet. & Plant Breeding Suppl. 43: 1-438.
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I can only provide you with Avdulov (1931) in Russian version (>270 pp), German version is not available.
The file is attached. You will need DJVU player software in order to open the file (free download available from https://www.cuminas.jp/en/downloads/download/?pid=1 )