Marcus's Dissertation

Genomic Analysis of Agroclimatic Traits In Sorghum


What are agroclimatic traits? 
TThese are traits that confer crop adaptation to different agroclimatic zones and often vary in morphological distribution across these zones. My research focuses on the use of both quantitative and population genomic tools for the dissection of the genetic architecture of these traits.

Study 1

 My first study focuses on the inflorescence morphology of sorghum. 

Phenotyping

Here, I phenotyped the sorghum Nested Association Mapping population across two locations (Humid Continental, Manhattan KS and Semi-Arid, Hays, KS) for two years (2014 and 2015). Site by year combination resulted in five environments.


Genotyping

We genotyped the NAM RILs and their parents following Elshire et al. 2011. TASSEL 5.0 was used for SNP calling as part of a bigger Sorghum GBS build composed of about 17,000 accessions. Imputation was done using BEAGLE 4.0 and FSFHap implemented in TASSEL 5.0. A total of 118,000 SNP markers were identified after filtering for 5% minor allele frequency and removing RILs with more than 10% heterozygosity. 


Genomic Dissection

Joint linkage mapping, Genome-wide association mapping (GWAS) and Linkage mapping were conducted using stepwise regression (TASSEL 5.0), multi-locus mixed model (Segura et al 2012) and composite interval mapping (Broman- RQTL).

Population Genomic Analysis

We also used a sorghum global germplasm comprising of 6500 geo-referenced accessions to understand the distribution of identified QTL across diverse agroclimatic regions.

Study 2

  

Phenotypic Data: 2014