Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping

Abstract

Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum that has a colossal damage potential. The fungus, prevalent mainly in the Indian sub-continent, keeps on producing new pathogenic strains leading to breakdown of resistance in newly released varieties and hence the deployment of linked markers for marker-assisted selection for resistance to this disease can fine tune the breeding programme. This study based on a panel of 119 sugarcane genotypes fingerprinted for 944 SSR alleles was undertaken with an aim to identify marker-trait associations (MTAs) for resistance to red rot. Mixed linear model containing population structure and kinship as co-factor detected four MTAs that were able to explain 10-16 % of the trait variation, individually. Among the four MTAs, EST sequences diagnostic of three could be BLAST searched to the sorghum genome with significant sequence homology. Several genes encoding important plant defence related proteins, viz., cytochrome P450, Glycerol-3-phosphate transporter-1, MAP Kinase-4, Serine/threonine-protein kinase, Ring finger domain protein and others were localized to the vicinity of these MTAs. These positional candidate genes are worth of further investigation and possibly these could contribute directly to red rot resistance, and may find a potential application in marker-assisted sugarcane breeding.

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…These maps were created for species using full-sib (F 1 ) individuals (i.e., the pseudo-test cross strategy) [88][89][90][91]. Yet, existing studies are limited by the complex genome, and describe only the most observable, primarily quantitative agronomic traits, resulting in identification of typically small effect markers [84,92].…”

Identification of marker-trait associations for morphological descriptors and yield component traits in sugarcane

“…In most crops, either family-based or linkage mapping has been used to tag the segregating trait(s) of interest and a number of examples of linkage mapping are available but in the past few decades, only a limited number of QTLs have been identified. Linkage disequilibrium (LD)-based mapping popularly called association mapping (AM) was initially adopted in human genetic studies but now it is being increasingly applied in crop plants including sugarcane mainly for identification of marker-trait associations (Wei et al 2006(Wei et al , 2010Debibakas et al 2014;Guoy et al 2015;Banerjee et al 2015;Singh et al 2016). In AM, the QTLs are identified by analyzing the degree of marker-trait associations that have been able to withstand segregation and reshuffling of the genetic elements in a diverse gene pool down the line of evolutionary recombination within the species (Gupta et al 2005).…”

“…In recent times, in sugarcane genomewide association mapping studies have been carried out for a number of traits (Wei et al 2006(Wei et al , 2010Debibakas et al 2014;Guoy et al 2015;Banerjee et al 2015;Singh et al 2016). However, such studies refer to a limited number of the most obvious agronomic traits that are predominantly quantitative, that resulted in identification of a multitude of small effect markers predominantly due to the complications of polyaneuploid genome.…”

Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene

“…falcatum infection [41, 42], these did not result in detection of functional candidate gene(s) for red rot resistance, as the analysis was carried out on a single sugarcane genotype without studying the segregation pattern and epistatic interactions. Singh et al [43] identified putative candidate genes for red rot resistance following linkage disequilibrium based association mapping; however, their involvement in imparting disease resistance has not been validated, thus restricting their use as molecular markers for identifying resistant genotypes and marker-aided selection in sugarcane.…”