Genome-Wide Association Mapping of Sugarcane Yellow Leaf Virus Resistance

AbstractThe breeding of sugarcane, a leading sugar and energy crop, is complicated by the extremely complex sugarcane genome, which burdens research in the area and delays the development of new cultivars. One of the main viral diseases that affect this crop is sugarcane yellow leaf (SCYL), which is caused by the sugarcane yellow leaf virus (SCYLV). The most common symptom of SCYL is the yellowing of leaf midribs and blades, but asymptomatic cases are frequent. Regardless of the manifestation of SCYL, infection by SCYLV can lead to substantial yield losses, making resistance to this virus highly relevant to sugarcane breeding. However, the genetic basis of this trait has not been widely explored or explained. In this context, genome-wide association studies (GWASs) have arisen as promising tools for the identification of molecular markers associated with SCYLV resistance that can be employed in marker-assisted selection. In the present work, we performed a GWAS on sugarcane using codominant markers and genotypes of interest for breeding. A panel of 97 sugarcane genotypes inoculated with SCYLV was analyzed for SCYL symptom severity, and viral titer was estimated by reverse transcription quantitative PCR (RT-qPCR). A genotyping-by-sequencing (GBS) library was constructed for 94 individuals of this population, enabling the identification of 38,710 SNPs and 32,178 indels with information on allele proportion (AP) and position on the Saccharum spontaneum genome. For association analyses, several combinations of population structure and kinship were tested to reduce model inflation, and diverse marker-trait association mixed models were employed. We identified 35 markers significantly associated with SCYL symptom severity and 22 markers strongly associated with SCYLV titer that can be applied in breeding programs upon validation. By aligning the sequences flanking these markers with their coding sequences in several plant species, we annotated the functions of 7 genes. The possible involvement of these candidates in the response to SCYLV infection is discussed.

Download Full-text

Genome-Wide Association Studies Identified Resistance Loci to Orange Rust and Yellow Leaf Virus Diseases in Sugarcane (Saccharum spp.)

Phytopathology ◽

10.1094/phyto-08-18-0282-r ◽

2019 ◽

Vol 109 (4) ◽

pp. 623-631 ◽

Cited By ~ 9

Author(s):

Xiping Yang ◽

Sushma Sood ◽

Ziliang Luo ◽

James Todd ◽

Jianping Wang

Keyword(s):

Disease Resistance ◽

Association Studies ◽

Germplasm Collection ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Yellow Leaf ◽

Saccharum Spp ◽

Genome Wide ◽

A Genome ◽

Leaf Virus

Sugarcane (Saccharum spp.) supplies globally ∼80% of table sugar and 60% of bioethanol. Sugarcane orange rust and Sugarcane yellow leaf virus (SCYLV) are major sugarcane diseases, causing up to 50 and 40% yield losses, respectively. Sugarcane cultivars resistant to these diseases are needed to sustain sugarcane production in several regions. Dissecting DNA sequence variants controlling disease resistance provides a valuable tool for fulfilling a breeding strategy to develop resistant cultivars. In this study, we evaluated disease reactions to orange rust and SCYLV of a sugarcane diversity panel in repeated trials. We conducted a genome-wide association study between high-density markers and disease resistance reactions. We identified 91 putative DNA markers and 82 candidate genes significantly associated with resistance to one of the two diseases. These provide an important genetic resource for finding genes and molecular markers for disease resistance. Our results emphasized the importance of utilizing a wide germplasm collection for breeding resistant sugarcane cultivars.

Download Full-text

Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance

Scientific Reports ◽

10.1038/s41598-021-95116-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ricardo José Gonzaga Pimenta ◽

Alexandre Hild Aono ◽

Roberto Carlos Villavicencio Burbano ◽

Alisson Esdras Coutinho ◽

Carla Cristina da Silva ◽

...

Keyword(s):

Virus Resistance ◽

Machine Learning Algorithms ◽

Energy Crop ◽

Yellow Leaf ◽

Sugarcane Yellow Leaf Virus ◽

Association Analyses ◽

Sugarcane Breeding ◽

Genetic Base ◽

Genome Wide ◽

Leaf Virus

AbstractSugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

Download Full-text