Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Çelik, İbrahim; Bodur, Sabahattin; Frary, Anne; Doğanlar, Sami

doi:10.1007/s11032-016-0558-8

Cited by 23 publications

(19 citation statements)

References 27 publications

(51 reference statements)

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“…The linkage map was constructed using 175 SNP markers, which comprised only 1.73% of the SNPs from the parent call due to the exclusion of SNPs with missing data and segregation distortion. This percentage was similar to the amounts used in other GBS-based linkage mapping studies in apple (0.9% of identified SNPs) and sunflower (1.7% of unfiltered SNPs) ( Gardner et al, 2014 ; Celik et al, 2016 ). The SNP linkage map spanned 1,383 cM, which is longer than the RFLP and AFLP maps of 1,064, 947, and 886 cM obtained previously ( King et al, 1998 ; Ohara et al, 2005 ; Galván et al, 2011 ).…”

Section: Discussionsupporting

confidence: 84%

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Purushotham

Han

et al. 2017

Front. Plant Sci.

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Single nucleotide polymorphisms (SNPs) play important roles as molecular markers in plant genomics and breeding studies. Although onion (Allium cepa L.) is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity. Genotyping-by-sequencing (GBS) offers a greater degree of complexity reduction followed by concurrent SNP discovery and genotyping for species with complex genomes. In this study, GBS was employed for SNP mining in onion, which currently lacks a reference genome. A segregating F2 population, derived from a cross between ‘NW-001’ and ‘NW-002,’ as well as multiple parental lines were used for GBS analysis. A total of 56.15 Gbp of raw sequence data were generated and 1,851,428 SNPs were identified from the de novo assembled contigs. Stringent filtering resulted in 10,091 high-fidelity SNP markers. Robust SNPs that satisfied the segregation ratio criteria and with even distribution in the mapping population were used to construct an onion genetic map. The final map contained eight linkage groups and spanned a genetic length of 1,383 centiMorgans (cM), with an average marker interval of 8.08 cM. These robust SNPs were further analyzed using the high-throughput Fluidigm platform for marker validation. This is the first study in onion to develop genome-wide SNPs using GBS. The resulting SNP markers and developed linkage map will be valuable tools for genetic mapping of important agronomic traits and marker-assisted selection in onion breeding programs.

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Section: Discussionsupporting

confidence: 84%

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Purushotham

Han

et al. 2017

Front. Plant Sci.

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“…Reduced representation sequencing methods, as genotyping by sequencing (GBS) and double digest RAD seq (ddRADseq) provide a high number of polymorphic loci at a relatively low cost. A few GBS approaches were reported recently for sunflower [39][40][41][42], with all of them being based on the Elshire et al [43] GBS protocol. Here, we present the first application of a ddRADseq approach for this crop, which involves the digestion of the genome using two different enzymes.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

Filippi

Merino

Montecchia

et al. 2020

Genes

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Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.

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“…Single nucleotide polymorphisms are the molecular markers most used either to map traits or to characterize the diversity of sunflower germplasm. Many genotyping methods are available but the most used for high-throughput genotyping are genotyping by sequencing (Elshire et al, 2011;Narum et al, 2013;Baute et al, 2016, Celik et al, 2016Badouin et al, 2017;Todesco et al, 2019) or genotyping arrays such as the two AXIOM ® arrays developed and used in sunflower for either mapping traits (Louarn et al, 2016;Duriez et al, 2019) or to describe the diversity of germplasms (Mangin et al, 2017) or the Illumina ® Infinium iSelect used for diversity analysis and genomic prediction (Livaja et al, 2016).…”

Section: From One Cultivated Sunflower Reference Genome To Reference mentioning

confidence: 99%

Gene banks for wild and cultivated sunflower genetic resources

Terzić¹,

Boniface

Marek³

et al. 2020

OCL

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Modern breeding of sunflower (Helianthus annuus L.), which started 100 years ago, increased the number and the diversity of cultivated forms. In addition, for more than 50 years, wild sunflower and other Helianthus species have been collected in North America where they all originated. Collections of both cultivated and wild forms are maintained in gene banks in many countries where sunflower is an important crop, with some specificity according to the availability of germplasm and to local research and breeding programmes. Cultivated material includes land races, open pollinated varieties, synthetics and inbred lines. The majority of wild accessions are ecotypes of wild Helianthus annuus, but also 52 other species of Helianthus and a few related genera. The activities of three gene banks, in USA, France and Serbia, are described in detail, supplemented by data from seven other countries. Past and future uses of the genetic resources for environmental adaptation and breeding are discussed in relation to genomic and improved phenotypic knowledge of the cultivated and wild accessions available in the gene banks.

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Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Cited by 23 publications

References 27 publications

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

Gene banks for wild and cultivated sunflower genetic resources

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