Doctor of Philosophy (PhD)


Plant, Environment and Soil Sciences

Document Type



Sugarcane, being a complex aneu-polyploid, poses unique challenges to fine mapping of quantitative trait loci (QTL) controlling agronomic traits of interest. Genome-wide association studies (GWAS) could be a better alternative to identify molecular markers associated with specific traits due to high linkage disequilibrium in sugarcane. In the first study, marker-trait associations (MTAs) were evaluated for three sucrose traits, Brix, total recoverable sugar (TRS), and percent sucrose on 48 elite and historic Louisiana breeding clones using 1,062 alleles. These sucrose traits were highly correlated (P-value < 0.0001) at >0.96. TASSEL 5.1 and JMP Genomics 8.0 were compared with eight models run in each program. Two identity by state (IBS) K-matrices were paired with four different Q-matrices: a Q-matrix from STRUCTURE 2.3.4, a principal component analysis each from TASSEL and JMP Genomics, and a maximum distance separable matrix from JMP Genomics. The Q-matrix contributed the majority of variation in the results, with minor differences between the software. Additionally, three markers were identified to be associated with sucrose traits. The second study was the first study to use genotyping by sequencing for MTA in sugarcane. It used JMP Genomics to evaluate MTAs on a Louisiana core collection for 10 cane yield-component (CYC) and sucrose traits: stalk count, stalk height, stalk diameter, stalk weight, TRS, Brix, percent sucrose, fiber, Pol, and purity using 6,299 single nucleotide polymorphisms (SNPs) and 235 insertions-deletions (InDels). There were some significant (P-value < 0.05) and highly significant (P-value < 0.0001) correlations among CYC traits, and between fiber and CYC traits. All sucrose traits except fiber were highly correlated. A total of 154 and 209 MTAs were identified for CYC and sucrose traits, respectively. These associations were from 238 distinct markers with 56 markers associated with more than one trait. The third study assessed the genetic diversity among 1,236 clones from the World Collection of Sugarcane and Related Grasses (WCSRG) and 249 clones from the Louisiana breeding programs using 423 alleles. A 309-clone sugarcane diversity panel (SDP1) was developed for GWAS to identify markers associated with agronomic trait(s) of interest for their use in marker-assisted breeding in Louisiana and elsewhere.



Committee Chair

Baisakh, Niranjan