Genetic analysis of agronomic traits in elite sugarcane (Saccharum spp.) germplasm

Abstract

Sugarcane (Saccharum spp.) is an important economic crop, supplying up to 80% of the table sugar and~60% of bio-ethanol worldwide. Due to population growth and dwindling fossil-fuel reserves, the demand for sugar and bio-ethanol requires significant improvement in sugarcane production. Breeding sugarcane cultivars with high-performance agronomic traits is undoubtedly the most efficient way to achieve this goal. Therefore, evaluating agronomic traits and dissecting underlying loci are critically important for this aim steps in providing genetic resources and molecular markers for selection. In this study, we assembled a diversity panel of 236 elite sugarcane germplasms originally collected from 12 countries. We evaluated 28 agronomic traits in the diversity panel with three replicates. The diversity panel was genotyped using amplified fragment length polymorphism markers, and a total of 1,359 markers were generated. Through the genome-wide association study, we identified three markers significantly associated with three traits evaluated at a stringent threshold (P < 0.05 after Bonferroni correction). The genotypes of the three associated markers grouped respective trait values into two distinct groups, supporting the reliability of these markers for breeding selection. Our study provides putative molecular markers linked to agronomic traits for breeding robust sugarcane cultivars. Additionally, this study emphasized the importance of sugarcane germplasm introduced from other countries and suggested that the use of these germplasms in breeding programs depends on local industrial needs.

Morphological, agronomical, physiological and molecular characterization of a high sugar mutant of sugarcane in comparison to mother variety

“…Hence, expanded genetic base for sugarcane cultivars would advance cane yield and decrease seriously upsetting disease eruptions because of planting varieties with diverse background in big areas. Introducing and using exclusive sugarcane clones from other countries or areas can meaningfully accelerate the attainment of sugarcane breeding goal for two important reasons, first is the top sugarcane clones, resulting from diverse breeding programs expectedly have unlike genetic backgrounds, while second is that these top sugarcane clones have high yield, high sugar and improved vital agronomic characters [ 23 ].…”

Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species

“…Phylogenetic trees for the 196 accessions were drawn using MEGA 7 [44] based on the Maximum Likelihood tree method using seven allele sets, namely, (1) all species-associated alleles (1), Saccharum spp. hybrids (2), S. barberi (3), S. officinarum (4), S. robustum (5), S. sinense (6), and S. spontaneum (7), respectively.…”

“…Genetic diversity research at the molecular level has natural advantages over traditional morphological markers. Since the late 1980s, the molecular markers including amplified fragment length polymorphisms (AFLP) [7][8][9], restriction fragment length polymorphisms (RFLP) [10], random amplification of polymorphic DNAs (RAPD) [11], single nucleotide polymorphism (SNP) [12], simple sequence repeats (SSRs) [13,14], inter simple sequence repeat (ISSRs) [15], and expressed sequence tag-simple sequence repeat (EST-SSRs) [16][17][18] were being developed by breeders and geneticists and applied in many sugarcane studies. Due to its co-dominant, multi-allelic characteristics, relative abundance, and high genome coverage, SSR primers are one of the most effective markers in plant genetics and breeding [19,20] and have been widely used to study sugarcane genetic diversity, genetic mapping, cross-transferability, paternity analysis, segregation analysis, and marker-assisted selection [21].…”

Applications of Quantitative Genetics and Statistical Analyses in Sugarcane Breeding

“…Many GWAS have been conducted on quantitative agronomic traits related to cane yield and cane quality, either among panels of elite and/or historic sugarcane clones (Wei et al 2010;Banerjee et al 2015;Racedo et al 2016;Barreto et al 2019;Fickett et al 2019;Zan et al 2020) or among panels mainly containing representatives of ancestral species (Yang et al 2019a, b). Results obtained are all the more directly useful for genomic breeding applications, as GWAS effectively control the risks of false-positive MTAs and that allele effects are found in large populations experimented in robust experiments.…”