Chapter 2 Data
Here, we will look at phenotype data collected during the 2019 and 2020 field season. We have three hybrid lineages of interest and 2 related controls. The first is a continuation of backcrossing the sW22 hybrid to W22 (referred to as sW22. We also backcross the sW22 hybrid to both the B73 and Mo17 maize lines (referred to as sW22_B73 and sW22_Mo17), and we create controls for these lines by backcrossing W22 to both these lines as well (referred to as W22_B73 and W22_Mo17). For all of our lineages, we create crosses where either the sick lineage is always the maternal parent, always the paternal parent, or a mix of both. This is denoted at the end of the genotype with either a 'm', 'p', or 'mix'. The table below highlights which rows in the field correspond to each lineage for each season.
| Lineage | 2019 Rows | 2020 Rows |
|---|---|---|
| sW22 | SA688 - SA690, SA692 - SA693, SA736 - SA738, SA740 - SA741, SA784 - SA786, SA788 - SA789 | HD001 - HD004, HD011 - HD020, HD247 - HD260 |
| W22 | SA691, SA694, SA739, SA742, SA787, SA790 | HD005 - HD010, HD245 - HD246, HD334 - HD335 |
| sW22_B73 | SA649 - SA652, SA654 - SA657, SA697 - SA700, SA702 - SA705,SA745 - SA748, SA750 - SA753 | HD021 - HD029, HD038 - HD047, HD261-279 |
| W22_B73 | SA659 - SA661, SA663 - SA665, SA707 - SA709, SA711 - SA713, SA755 - SA757, SA759 - SA761 | HD048 - HD055, HD062 - HD071, HD280 - 297 |
| B73 | SA653, SA658, SA662, SA666, SA701, SA706, SA710, SA714, SA749, SA754, SA758, SA762 | HD030 -HD037, HD056 - HD061, HD241, HD242, HD330, HD331 |
| sW22_Mo17 | SA670 - SA673, SA675 - SA678, SA718 - SA721, SA723 - SA726, SA766 - SA769, SA771 - SA774 | HD072 - HD079, HD088 - HD095, HD248 - HD313 |
| W22_Mo17 | SA680 - SA682, SA684, SA728 - SA730, SA732, SA776 - SA778, SA780 | HD096 - HD105, HD113 - HD118, HD314 - HD329 |
| Mo17 | SA674, SA679, SA683, SA685, SA722, SA727, SA731, SA733, SA770, SA775, SA779, SA781 | HD080 - HD087, HD106 - HD112, HD243, HD244, HD332, HD333 |
For each plant, we know the segregating genotype, the sex of the sick parent, and which field it was planted in. We consider 3 distinct comparisons: (1) sW22 backcrossed to W22, (2) sW22 and W22 backcrossed to B73, and (3) sW22 and W22 backcrossed to Mo17. We start by first just examining the distribution of each measured trait in these categories, paying attention to how this differs between the segregating genotypes. We can evaluate whether the mean of specific genotypes differs using a t-test to compare genotypes to the backcross line (W22, B73, or Mo17) and between sW22 and W22 with the same number of genotypes. We end up by using an ANOVA to specifically assess whether there is a significant influence of the segregating genotype, the sex of the sick parent, or an interaction between these two.
We will go through our results for the following phenotypes: (1) Plant Height, (2) Ear Height, (3) Ear Length, (4) Seed Weight, and (5) Cobb Weight. Plant height is the only phenotype that we have data from both 2019 and 2020, while the remaining phenotypes have data collected during the 2019 field season.
A few notes, I use a blue color palette for sW22 genotypes and a green color palette for W22 genotypes. The gradient of the color palette represents the number of backcross generations, with darker colors indicating more generations of backcrossing (i.e sW22_BC1 is a light blue while sW22_BC4 is a dark blue). However, do be cognizant of the genotype labels as the maternal vs paternal sick lineage is colored differently (usually the paternal line is slightly darker than the maternal one).