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

Zhang, Baoqing; Huang, Yuxin; Zhang, Lijun; Zhou, Zhongfeng; Zhou, Shan; Duan, Weixing; Yang, Cuifang; Gao, Yijing; Li, Sicheng; Chen, Meiyan; Li, Yangrui; Yang, Xiping; Zhang, Gemin; Huang, Dongliang

doi:10.1021/acs.jafc.3c02935

Cited by 4 publications

(2 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous GWASs have elucidated the association of sucrose accumulation with polymorphisms located near different genes. These genes encompass annotations mostly related to plant growth, development (Racedo et al 2016; Fickett et al 2019; Wang et al 2023b), and responses to both biotic and abiotic stresses (Wang et al 2023b; Zhang et al 2023). In our GWAS analysis, although we found noteworthy similarities with previous studies, particularly regarding the involvement of phosphatases, kinases, and ubiquitin-like proteins (Fickett et al 2019; Wang et al 2023b; Zhang et al 2023), we were able to expand upon these findings.…”

Section: Discussionmentioning

confidence: 99%

“…CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is Traditionally, addressing such complexity has involved either simplifying SNP markers by assuming fixed ploidy (Fickett et al 2019;Yang et al 2020;Pimenta et al 2021;Wang et al 2023a;Zhang et al 2023) or estimating specific ploidy levels for individual markers (Balsalobre et al 2017;Batista et al 2022). However, in our study, rather than disregarding allele variations, we opted to represent SNPs not as dosages but as allele proportions.…”

Section: Strategies For Dealing With Sugarcane Genetic Complexitymentioning

confidence: 99%

See 1 more Smart Citation

Multiomic insights into sucrose accumulation in sugarcane

Aono,

Pimenta,

Diniz

et al. 2024

Preprint

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

Section: Discussionmentioning

confidence: 99%

Section: Strategies For Dealing With Sugarcane Genetic Complexitymentioning

confidence: 99%

Multiomic insights into sucrose accumulation in sugarcane

Aono,

Pimenta,

Diniz

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Evaluation of sugarcane genotypes (Saccharum sp. hybrid) for multi-trait stability analysis across diverse environments

Appunu,

Hemaprabha,

Sreenivasa

et al. 2024

Industrial Crops and Products

View full text Add to dashboard Cite

Identification of candidate single-nucleotide polymorphisms (SNPs) and genes associated with sugarcane leaf scald disease

Li,

Lin,

You

et al. 2024

Sci Rep

View full text Add to dashboard Cite

Leaf scald, caused by Xanthomonas albilineans, is a severe disease affecting sugarcane worldwide. One of the most practical ways to control it is by developing resistant sugarcane cultivars. It is essential to identify genes associated with the response to leaf scald. A panel of 170 sugarcane genotypes was evaluated for resistance to leaf scald in field conditions for 2 years, followed by a 1-year greenhouse experiment. The phenotypic evaluation data showed a wide continuous distribution, with heritability values ranging from 0.58 to 0.84. Thirteen single nucleotide polymorphisms (SNPs) were identified, significantly associated with leaf scald resistance. Among these, eight were stable across multiple environments and association models. The candidate genes identified and validated based on RNA-seq and qRT-PCR included two genes that encode NB-ARC leucine-rich repeat (LRR)-containing domain disease-resistance protein. These findings provide a basis for developing marker-assisted selection strategies in sugarcane breeding programs.

show abstract

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

Cited by 4 publications

References 84 publications

Multiomic insights into sucrose accumulation in sugarcane

Multiomic insights into sucrose accumulation in sugarcane

Evaluation of sugarcane genotypes (Saccharum sp. hybrid) for multi-trait stability analysis across diverse environments

Identification of candidate single-nucleotide polymorphisms (SNPs) and genes associated with sugarcane leaf scald disease

Contact Info

Product

Resources

About