Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

Sugarcane, a major
sugar
and energy crop worldwide faces an increasing demand for higher yields.
Identifying yield-related markers and candidate genes is valuable
for breeding high-yield varieties using molecular techniques. In this
work, seven yield-related traits were evaluated in a diversity panel
of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern
sugarcane genotypes. All traits exhibited significant genetic variance
with high heritability and high correlations. Genetic diversity analysis
reveals a genomic decay of 23 kb and an average single nucleotide
polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes
were divided into 4 subgroups. Genome-wide association analysis identified
47 SNPs associated with brix, spanning 36 quantitative trait loci
(QTLs), and 138 SNPs for other traits across 104 QTLs, covering all
32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related
traits were identified, which contained 35 candidate genes. This work
provides markers and candidate genes for marker-assisted breeding
to improve sugarcane yields.