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

Siraree, Archana; Banerjee, Nandita; Khan, Mohammad Suhail; Singh, Pritpal; Kumar, Sanjeev; Sharma, Swati; Singh, Rameshwar; Singh, Jogendra

doi:10.1007/s12298-016-0403-x

Cited by 27 publications

(10 citation statements)

References 30 publications

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“…ESTA61_15 may be a unique allele that causes important phenotypic variation. Previous studies detected MTAs for the SW [37,39], SN [18,39,40,42], SH [18,39,40,42] and BRIX [18,40–42] traits, and the percentages of phenotypic variation found in the present study were similar for SW, SH and BRIX and higher for SN. Therefore, these MTAs may be validated as an initial approach to support breeding programs with introgression or selection processes [37,41,42].…”

Section: Discussionsupporting

confidence: 84%

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

et al. 2019

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Sugarcane ( Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection.

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Section: Discussionsupporting

confidence: 84%

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

et al. 2019

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“…As previously noted by Racedo et al 75 , assembling and phenotyping large sugarcane association panels is a challenging task. Thus, it is not uncommon for association studies of this crop to evaluate fewer than 100 genotypes 44 , 75 – 78 . Our study was particularly burdensome, as extremely laborious inoculation and quantification techniques were employed to generate highly reliable phenotypic data.…”

Section: Discussionmentioning

confidence: 99%

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

Pimenta

Aono

Burbano

et al. 2021

Sci Rep

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Sugarcane 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.

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“…Gouy et al [77] conducted genome wide association (GWA) mapping of 183 sugarcane accessions, genotyped with 3327 AFLP, DArT, and SSR markers and phenotypes for 13 traits related to morphology, yield, bagasse residue content, and resistance to disease. Siraree et al [67] used 1546 marker loci produced by 174 SSR primers and phenotypic characterization for 32 traits to complete a panel of 92 sugarcane varieties from sub-tropical areas in India. Edmé et al [58] developed a map of S. spontaneum/S.…”

Section: Genome Mappingmentioning

confidence: 99%

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

et al. 2018

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Recently-developed molecular markers are becoming powerful tools, with applications in crop genetics and improvement. Microsatellites, or simple sequence repeats (SSRs), are widely used in genetic fingerprinting, kinship analysis, and population genetics, because of the advantages of high variability from co-dominant and multi-allelic polymorphisms, and accurate and rapid detection. However, more recent evidence suggests they may play an important role in genome evolution and provide hotspots of recombination. This review describes the development of SSR markers through different techniques, and the detection of SSR markers and applications for sugarcane genetic research and breeding, such as cultivar identification, genetic diversity, genome mapping, quantitative trait loci (QTL) analysis, paternity analysis, cross-species transferability, segregation analysis, phylogenetic relationships, and identification of wild cross hybrids. We also discuss the advantages and disadvantages of SSR markers and highlight some future perspectives.

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

Cited by 27 publications

References 30 publications

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

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

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

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