Repository of paper Identification of Genetic Markers Linked to Alfalfa Yield, Height and Fall Dormancy
Phenotypic data of 1_MSC, 2_DM, 3_Height, 4_Yield, and 5_FD were collected in three locations: WA, OR and ID in 2018, 2019 and 2020. The same accessions were genotyped using genotyping-by-sequencing followed by SNP calling and filtering. Genome-wide association studies were performed to identify genetic markers associated with alfalfa yield, height and fall dormancy.
There are three locations, three years (multiple cuts), and five traits:
Table 1. Harvest interval by year and location. Three-cut system was applied in 2018 in all locations. Four-cut system was applied in ID 2019 and in OR 2019 and 2020. Five-cut system was applied in WA in 2019 and 2020.
| Year | ID | OR | WA |
|---|---|---|---|
| 2018 | 1,2,3,− | 1,2,3,− | 1,2,3,−,− |
| 2019 | 1,2,3,4 | 1,2,3,4 | 1,2,3,4,5 |
| 2020 | − | 1,2,3,4 | 1,2,3,4,5 |
Table 2. Traits collected in three locations; Idaho (ID), Oregon (OR), and Washington (WA) from 2018 to 2020, multiple times by year. Traits tested were maturity measured as mean stage by count (MSC), dry matter (DM), plant height (PH), yield (Yi), and fall dormancy (FD).
| Dataset | MSC | DM | PH | FD | Yi | Total |
|---|---|---|---|---|---|---|
| Total_ID | 2 | 2 | 1 | 1 | 9 | 15 |
| Total_OR | 3 | 3 | 6 | 3 | 14 | 29 |
| Total_WA | 8 | 3 | 12 | 2 | 16 | 41 |
| Total | 13 | 8 | 19 | 6 | 39 | 85 |
It is possible to generate an analysis to obtain BLUP values (ST0 and ST1) to run GWAS:
- Forage yield Stage BLUEs Measures.
- Single cut 1_stage 22.
- Single year 2_stage 6.
- Single loc 3_stage 3.
- All 4_stage 1.
It is important to accurately evaluate the developmental stage of forage crops in order to precisely establish the appropriate harvest time and to optimize their yield, nutritive value and persistence. This guide illustrates and explains the developmental stages of timothy and alfalfa, the two main forage species cultivated in Quebec. It also describes two methods used to determine the mean stage of such forage: the Mean Stage by Count (MSC) and the Mean Stage by Weight (MSW).
There are some problematic env with yield:
- Yi_ID_2018_1
- Yi_ID_2018_2
- Yi_OR_2018_1
- Yi_OR_2018_2
- Yi_OR_2019_1
- Yi_OR_2020_1
- Yi_WA_2018_1
Check correlation matrices in /home/hawkins/Documents/git/Norberg_2020/BLUE_values/cor1.
Generation of files 3_ST1_Yi.R and save.image("~/Documents/git/big_files/tidy_Norberg_Yi.RData") with yield corrected for outliers and re-analysis with GWASpoly.
Most of the markers associations detected in this work were specific to particular harvests. Forage yield needs to be consistent in order to interpreting phenotypical relevance of traits in perrenial forage crops. This is the evaluation of the same trait across developmental time and also across multiple environments.
The final goal of genetic mapping os to identify markers that are either the true causative polymorphism or tghtly linked to the trait. This is one of the most complete sets of markers generated by GBS including allele dosage.
How many candidate genes were detected bases on gene function?
The most important trait in alfalfa is forage yield. The SNPs associated with the trait suggest that the genes needed in a perenial forage crop that is harvested multple times have different locations and some of them may mot be present in this population.
There are different approached to improve Norberg paper:
- Reduce (refine) number of markers to only effective markers.
- Check Pearson cor matrix to check problematic hervest. Done for yield.
- Geenrate an index for highly correlated traits e.g., Yi and PH before to run GWAS.
- Check descritptive statistics in order to find and remove ourliers. Done with metaN.
- How to fix error in m.eff GWASpoly R pakage.
- Generate a variance covariance matrix to Yi.
This is confusing. Talk about total yield from all cuttings. Then talk about each individual cuttings. WA should have the highest total yield.
The average total yield is 20-35 tons per hectare (or 8-14 tons per acre) per year (distributed in 5-6 cuts). Top yields (intensive farming) can exceed 40 tons per hectare (16 tons per acre) per year.