Genome-wide association mapping of quantitative traits in a breeding population of sugarcane

Abstract

Background: Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. Previous sugarcane genome-wide association analyses (GWAS) have found few molecular markers associated with relevant traits at plant-cane stage. The aim of this study was to establish an appropriate GWAS to find molecular markers associated with yield related traits consistent across harvesting seasons in a breeding population. Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY) and sugar content (SC) at two locations during three successive crop cycles. GWAS mapping was applied within a novel mixed-model framework accounting for population structure with Principal Component Analysis scores as random component. Results: A total of 43 markers significantly associated with CY in plant-cane, 42 in first ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were associated with CY in 2 years. Additionally, 38 significant associations for SC were detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker-trait association was found significant for the 3 years of the study, while twelve markers presented association for 2 years. In the multi-QTL model several markers with large allelic substitution effect were found. Sequences of four DArT markers showed high similitude and e-value with coding sequences of Sorghum bicolor, confirming the high gene microlinearity between sorghum and sugarcane.

Population Structure and Genomewide Association Analysis of Resistance to Disease and Insensitivity to Ptr Toxins in Canadian Spring Wheat Using 90K SNP Array

“…The number of cultivars used in the present study was larger than the 70 winter wheat lines used for genomewide association mapping of resistance to both tan spot and Stagonospora nodorum blotch (Liu et al, 2015) and was comparable with the 80 inbred lines in maize (Zea mays L.), 80 RILs in barley (Hordeum vulgare L.) (Inostroza et al, 2009), and 88 clones in sugarcane (Saccharum spp.) (Racedo et al, 2016). Our population size was smaller than several other studies, which may have lowered the power of QTL detection (Yu et al, 2008).…”

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

“…Current studies had three major improvements compared with previous GWAS performed in sugarcane (Débibakas et al 2014; Gouy et al 2015; Racedo et al 2016; Wei et al, 2006, 2010). First, a representative diversity panel with a large number of accessions derived from WCSRG was assembled and used in sugarcane GWAS.…”

“…Hence in most cases, GWAS in polyploids treated molecular markers as diploids, which might not reflect the actual genetic effects. Since the first GWAS was conducted (Haines et al 2005), a few GWAS have been performed in sugarcane (Débibakas et al 2014; Gouy et al 2015; Racedo et al 2016; Wei et al 2006, 2010). However, all of them were challenged by the difficulties mentioned above.…”

Virus-Induced Flowering: An Application of Reproductive Biology to Benefit Plant Research and Breeding

“…Modern cultivars are highly polyploid, and this genetic complexity challenges standard and molecular breeding programs. The transition to flowering in sugarcane also has genotype-specific requirements for plant age and size, photoperiod, temperature, and humidity, such that the range for breeding under natural (Paterson et al, 2013;Racedo et al, 2016). Sorghum is naturally a short-day plant and is cultivated as grain, forage, sweet, and high biomass varieties (Kimber et al, 2013;Morris et al, 2013).…”