Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane

Wang, Le; Yeo, Shadame; Lee, May; Endah, S.; Alhuda, N. A.; Yue, G. H.

doi:10.1007/s00438-023-02040-2

Cited by 2 publications

(3 citation statements)

References 78 publications

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“…The current methodologies available for handling polyploid species via linkage analysis do not adequately address the nuances of sugarcane genetics (Mollinari et al 2020). The construction of linkage maps in sugarcane typically yields numerous unsaturated linkage groups characterized by substantial intermarker distances (Costa et al 2016; Balsalobre et al 2017; Yang et al 2018; You et al 2019; Wang et al 2022b; Wang et al 2022b, 2023a). As a consequence, many markers are excluded from the analysis, thereby limiting the pool of SNPs available for QTL identification.…”

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“…CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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%

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Multiomic insights into sucrose accumulation in sugarcane

Aono,

Pimenta,

Diniz

et al. 2024

Preprint

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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.

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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

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show abstract

“…Yang et al identified 106 DNA markers and 107 genes associated with 10 fiber components. Other studies have also reported GWAS investigations on the identification of genetic loci for disease resistance, − leaf angle, and economic traits − in sugar cane. However, most of the current GWAS analyses in sugar cane have primarily been conducted on the species S.…”

Section: Introductionmentioning

confidence: 99%

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

Zhang,

Huang,

Zhang

et al. 2023

J. Agric. Food Chem.

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Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yieldrelated 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.

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Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane

Cited by 2 publications

References 78 publications

Multiomic insights into sucrose accumulation in sugarcane

Multiomic insights into sucrose accumulation in sugarcane

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

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