ASRB NET - Agricultural Statistics (and Computer Application / Bioinformatics) · India · Agricultural Scientists Recruitment Board (ICAR)
Original practice questions written to the published syllabus · not past papersStatistics for molecular-breeding data: genetic map construction, interval mapping of QTL, genome-wide association with mixed models, multiple-testing control, genomic prediction (GBLUP, ridge and Bayesian alphabet), and the analysis of high-throughput expression data.
In the exams: AICE-JRF Bioinformatics Unit 5 'Statistical Genomics' (heavy); AICE-JRF Ag Stat Unit 3 (present); AICE-JRF Genetics & Plant Breeding molecular units (present)
How our questions for ASRB NET spread across the units of Statistical Genomics: QTL Mapping, GWAS & Genomic Selection. Difficulty: 0 easy, 67 medium, 20 hard.
| Genomic relationship matrices and GBLUP | 11 | |
| Genomic selection: ridge regression BLUP and Bayesian methods (BayesA, BayesB) | 11 | |
| Linkage map construction and map functions | 9 | |
| QTL mapping: single-marker, interval and composite interval mapping | 9 | |
| Genome-wide association studies with mixed models | 9 | |
| Statistical genomics descriptive and inferential basics | 9 | |
| Molecular markers and genotype data quality | 8 | |
| Linkage disequilibrium and population structure | 8 | |
| Gene expression and RNA-seq differential analysis | 7 | |
| Multiple testing in genomics: Bonferroni and FDR | 6 |
Choose an answer, then open the working. Each explanation says why the right answer is right and why the others are not.
An SSR locus has three alleles at frequencies 0.5, 0.3 and 0.2. What is its expected heterozygosity?
D. 0.62
Hₑ = 1 − Σpᵢ² = 1 − (0.25 + 0.09 + 0.04) = 0.62. 0.38 is Σpᵢ² itself; 0.55 is close to the PIC, which subtracts a further term.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
Which LD measure most directly determines the power to detect a causal variant through a nearby marker?
B. r²
The sample size needed through a marker is roughly 1/r² times that needed with the causal variant itself. D′ can be 1 even when r² is small.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
How does a biparental population avoid the confounding by structure seen in diversity panels?
B. All individuals share the same two parents
Designed crosses have no structure by construction, but they sample only two alleles and have extended LD, so resolution is coarser.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
What does G capture that the pedigree relationship matrix A does not?
D. Realised, not expected, DNA sharing
A gives expectations (full sibs 0.5); G measures actual sharing, which varies around 0.5, and captures unrecorded relationships.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
Using r = √[Nh²/(Nh² + M_e)], what is the expected accuracy of genomic prediction with a reference of 1,000 animals, h² = 0.5 and M_e = 1,000?
A. 0.58
r = √(500/1,500) = √0.333 = 0.58. 0.33 forgets the square root.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
Using r = √[Nh²/(Nh² + M_e)], what is the expected accuracy of genomic prediction with a reference of 1,000 animals, h² = 0.5 and M_e = 1,000?
A. 0.58
r = √(500/1,500) = √0.333 = 0.58. 0.33 forgets the square root.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
A dairy programme has i = 2.0 and σ_A = 10 units. Progeny testing gives accuracy 0.85 and generation interval 6 years; genomic selection gives accuracy 0.70 and interval 2.5 years. What is the annual genetic gain under each?
A. Progeny testing 2.83; genomic 5.60 units per year
ΔG = i r σ_A/L: progeny testing 2 × 0.85 × 10/6 = 2.83; genomic 2 × 0.70 × 10/2.5 = 5.60. Despite lower accuracy, GS nearly doubles gain through the shorter interval. Ignoring L gives 17 and 14.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
A dairy programme has i = 2.0 and σ_A = 10 units. Progeny testing gives accuracy 0.85 and generation interval 6 years; genomic selection gives accuracy 0.70 and interval 2.5 years. What is the annual genetic gain under each?
A. Progeny testing 2.83; genomic 5.60 units per year
ΔG = i r σ_A/L: progeny testing 2 × 0.85 × 10/6 = 2.83; genomic 2 × 0.70 × 10/2.5 = 5.60. Despite lower accuracy, GS nearly doubles gain through the shorter interval. Ignoring L gives 17 and 14.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
Why can random k-fold cross-validation overstate the accuracy of genomic prediction for new breeding families?
B. Relatives span training and validation folds
Predictions of close relatives are easy; new families are less related to the training set. Forward or leave-family-out validation mimics actual use.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
What is the purpose of the bootstrap in QTL mapping?
C. Confidence intervals for QTL position
Resampling individuals with replacement and re-scanning gives an empirical distribution of the peak position. Permutation, not bootstrap, gives thresholds.
Further reading: Lynch and Walsh, Genetics and Analysis of Quantitative Traits; Isik, Holland and Maltecca, Genetic Data Analysis for Plant and Animal Breeding; original papers cited in the manual
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