Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study

Abstract

Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane are always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed genome-wide association studies (GWAS) with a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes with +2, +3, and +4 leaf at the seedling, elongation, and mature stages. A total of 288 significantly associated loci of sugarcane leaf angle at different developmental stages (eight phenotypes) were identified by GWAS with 4,027,298 high-quality SNP markers. Among them, one key locus and 11 loci were identified in all three stages and two stages, respectively. An InDel marker (SNP Ss6A_102766953) linked to narrow leaf angle was obtained. Overall, 4,089 genes were located in the confidence interval of significant loci, among which 3,892 genes were functionally annotated. Finally, 13 core parents and their derivatives tagged with SNPs were selected for marker-assisted selection (MAS). These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine protein kinases, etc. They are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.

A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane

“…Thus, GWAS has been successfully utilized in many plants for identifying significant marker–trait associations and putative candidate genes, such as cotton ( Islam et al., 2016 ; Thyssen et al., 2018 ; Wubben et al., 2019 ), maize ( Pace et al., 2015 ), barley ( Matthies et al., 2014 ), wheat ( Tadesse et al., 2015 ), sorghum ( Morris et al., 2013 ), and soybean ( Vuong et al., 2015 ). However, many genetic studies using GWAS have been reported in sugarcane ( Debibakas et al., 2014 ; Racedo et al., 2016 ; Singh et al., 2016 ; Barreto et al., 2019 ; Yang et al., 2019a ; Yang et al., 2019b ; Yang et al., 2020 ; Pimenta et al., 2021 ; Chen et al., 2022 ). To the best of our knowledge, there have been no QTL and/or GWASs related to the RA trait in sugarcane reported so far.…”

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

“…27 Yang et al 28 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, 29−31 leaf angle, 32 and economic traits 33−41 in sugar cane. However, most of the current GWAS analyses in sugar cane have primarily been conducted on the species S. officinarum and S. spontaneum, as well as modern varieties/genotypes that encompass the genomes of these two previous Saccharum species, 42 and only a limited number of studies have focused on hybrid progeny derived from Saccharum-related genera that possess potential in sugar cane breeding programs, such as Miscanthus 43 and Erianthus.…”

“…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.…”