Precise colocalization of sorghum’s major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy

Chilling tolerance in crops can increase resilience through longer growing seasons, drought escape, and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), breeding for chilling tolerance has been stymied by coinheritance of the largest-effect chilling tolerance locus, qSbCT04.62, with the major gene underlying undesirable grain proanthocyanidins, WD40 transcriptional regulator Tannin1. To test if this coinheritance is due to antagonistic pleiotropy of Tannin1, we developed and studied near-isogenic lines (NILs) carrying chilling tolerant haplotypes at qCT04.62. Whole-genome sequencing of the NILs revealed introgressions spanning part of the qCT04.62 confidence interval, including the Tannin1 gene and an ortholog of Arabidopsis cold regulator CBF/DREB1G. Segregation pattern of grain tannin in NILs confirmed the presence of wildtype Tannin1 and the reconstitution of a functional MYB-bHLH-WD40 regulatory complex. Low-temperature germination did not differ between NILs, sugg..., Genetic analyses and plant materials
Data on published QTL was downloaded from the Sorghum QTL Atlas (Mace et al. 2019). QTL were filtered for biparental and NAM mapping studies and plotted by genomic location using custom R v4.1.2 scripts (R Core Team 2021). Three RILs from the chilling tolerant NAM BTx623 × Hong Ke Zi (PI 567946) family were used as starting material to reduce subsequent backcrossing effort (Marla et al. 2019). The RILs were then crossed to BTx623. F1 progeny were selected on two criteria: heterozygosity at the QTL of interest using a KASP marker system and visually for resemblance to BTx623, the recurrent parent. Selected progeny were then backcrossed to BTx623. Selection and backcrossing were repeated four times. Four suitable BC4F1 lines were then selected and selfed. From the segregating progeny, homozygotes for both alleles of the QTL of interest were selected, making eight total BC4F2 lines. Those eight lines were then advanced to the BC4F5 generation through si..., , # **Data from: Precise colocalization of sorghum's major chilling tolerance locus with *Tannin1* due to tight linkage drag rather than antagonistic pleiotropy**

**[https://doi.org/10.5061/dryad.z34tmpgms](https://doi.org/10.5061/dryad.z34tmpgms)**

**Summary**

All data and scripts are provided in a single zipped folder. Folders are set so that scripts will run within the given folder

* Figure 1A:
*  Data as well as R script used for plotting analysis are included. Data for Figure 1A contains all known chilling tolerance QTL and was downloaded from the Sorghum QTL Atlas. An R script was used to filter for relevant experiments and plot locations.
* Figure 2: 
* Data as well as R script used for plotting and analysis are included. Data for figure 2 contains SNPs for chilling tolerance NIL lines (progeny) as well as Kaoliangs and BTx623 (parents) which were used for sliding window haplotype analysis
* Figure 3
* See figure 2
* Figure 5:
* Data as well as R script used f...