CGIAR BARLEY BREEDING TOOLBOX: A diversity panel to facilitate breeding and genomic research in the Developing World
Bibliographic record
Abstract
Abstract Despite the reduced cost of the new genotyping technologies, many public and private breeding programs, mostly in developing countries, still cannot afford them, hindering their research. The objective of the present study was to identify and assemble an Association Mapping panel of widely diverse barley genotypes to serve as a barley breeding toolbox, especially for the Developing World. The main criteria were: i) to be representative of the germplasm grown in the Developing World; ii) to cover a wide range of genetic variability and iii) to be of public domain. For it, we assembled and genotyped a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environmental conditions. The GBP accessions were genotyped using the barley Infinium iSelect 50K chip. A total of 40,342 SNP markers were polymorphic and displayed an average polymorphism information content (PIC) of 0.35, with 66% of them exceeding PIC=0.25. The analysis of the population structure identified 8 sub-populations mostly linked to the geographical origin of the lines (Europe, Australia, USA, Canada, Africa, Latin-America, ICARDA and others), four of them of significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines studied. Among origins, ICARDA material (n= 257) showed wide diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and Nei’s gene diversity and the fact that ICARDA lines were present in all 8 sub-populations and carried all 16 allelic combinations at phenology genes. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, 312 ICARDA lines and cultivated landraces were pre-selected to form the CGIAR Barley Breeding Toolbox (CBBT). Using the genotypic data and the Mean of Transformed Kinships method, we assembled the CBBT, an Association Mapping panel of 250 accessions capturing most of the allelic diversity in the global panel. The CBBT preserves a good balance between row types as well as a good representation of both allelic combinations identified at most important phenological loci and sub-populations of the GBP. The CBBT lines together with their genotypic data will be made available to breeders and researchers worldwide to serve as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.007 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".