Association Mapping for Sugarcane Quality Traits at Three Harvest Times

Coutinho, Alisson Esdras; Silva, Marcel Fernando da; Pérecin, Dilermando; Carvalheiro, Roberto; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade; Pinto, Luciana Rossini

doi:10.1007/s12355-021-01056-5

Cited by 2 publications

(4 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of the 30 primers, 25 were amplified, and all these primers were tested for association studies. EST-SSR markers are a tool for association studies ( Ukoskit et al., 2019 ; Coutinho et al., 2022 ). The EST-SSR markers related to sucrose content could be more effective than markers that focus on the varied functions of the gene.…”

Section: Resultsmentioning

confidence: 99%

“…A mapping population obtained from a cross between commercial cultivars indulges in the introduction of EST-SSR markers into sugarcane linkage mapping ( Oliveira et al., 2007 ; Palhares et al., 2012 ). There are some published reports of association mapping in sugarcane for traits such as biotic stress, cane yield, and sugar content ( Wei et al., 2006 ; Wei et al., 2010 ; Débibakas et al., 2014 ; Banerjee et al., 2015 ; Gouy et al., 2015 ; Singh et al., 2016 ; Barreto et al., 2019 ; Fickett et al., 2019 ; Ukoskit et al., 2019 ; Coutinho et al., 2022 ). There are only a few studies that have investigated the identification of markers or genes for sugar yield traits using interspecific crosses ( Reffay et al., 2005 ; Ukoskit et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Divakar,

Jha,

Kamat

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Divakar,

Jha,

Kamat

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…In Pop2, the plants were planted in 2 m rows with a spacing of 1.5 m between the plants. Additionally, the Pop1 experiment was replicated three times, corresponding to harvest times in May, July, and September (Coutinho et al 2022).…”

Section: Methodsmentioning

confidence: 99%

“…Additionally, the Pop1 experiment was replicated three times, corresponding to harvest times in May, July, and September (Coutinho et al 2022).…”

Section: Plant Materialsmentioning

confidence: 99%

Multiomic insights into sucrose accumulation in sugarcane

Aono,

Pimenta,

Diniz

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Sugarcane (Saccharumspp.) holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits, such as sucrose content, remains challenging due to the complex genomic landscape of the crop. In this study, we conducted a multiomic investigation to elucidate the genetic architecture and molecular mechanisms governing sucrose accumulation in sugarcane. Using a biparental cross (IACSP95-3018 × IACSP93-3046) and a genetically diverse collection of sugarcane genotypes, we evaluated the soluble solids (Brix) and sucrose content (POL) across various years and environments. Both populations were genotyped using a genotyping-by-sequencing (GBS) approach, with single nucleotide polymorphisms (SNPs) identified via bioinformatics pipelines. Genotype‒phenotype associations were established using a combination of traditional linear mixed-effect models and machine learning algorithms. Furthermore, we conducted an RNA sequencing (RNA-Seq) experiment on genotypes exhibiting distinct Brix and POL profiles across different developmental stages. Differentially expressed genes (DEGs) potentially associated with variations in sucrose accumulation were identified. All findings were integrated through a comprehensive gene coexpression network analysis. Strong correlations among the evaluated characteristics were observed, with estimates of modest to high heritabilities. By leveraging a broad set of SNPs identified for both populations, we identified several SNPs potentially linked to phenotypic variance. Our examination of genes close to these markers facilitated the association of such SNPs with DEGs in genotypes with contrasting sucrose levels. Through the integration of these results with a gene coexpression network, we delineated a set of genes potentially involved in the regulatory mechanisms of sucrose accumulation in sugarcane, collectively contributing to the definition of this critical phenotype. Our findings constitute a significant resource for biotechnology and plant breeding initiatives. Furthermore, our genotype‒phenotype association models hold promise for application in genomic selection, offering valuable insights into the molecular underpinnings governing sucrose accumulation in sugarcane.

show abstract

Association Mapping for Sugarcane Quality Traits at Three Harvest Times

Cited by 2 publications

References 49 publications

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Multiomic insights into sucrose accumulation in sugarcane

Contact Info

Product

Resources

About