High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

Gaur, Rashmi; Jeena, Ganga; Shah, Neelima; Gupta, Shefali; Pradhan, Seema; Tyagi, Akhilesh K.; Jain, Mukesh; Chattopadhyay, Debasis; Bhatia, Sabhyata

doi:10.1038/srep13387

Cited by 43 publications

(30 citation statements)

References 65 publications

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“…The most widespread variation was A/G (31.86%) while the least common variation was C/G, accounting for 6.53% of the total detected SNPs. We observed a transition:transversion (Ts/Tv) ratio of 1.78, which was similar to the observations for other plant species (Gaur et al 2015;Pootakham et al 2015). A set of bi-allelic SNPs were scored as lm x ll, nn x np and hk x hk.…”

Section: Genome-wide Identification Of Snpssupporting

confidence: 85%

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The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Koch

Coggeshall

et al. 2018

Preprint

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Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n=46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid invasion of emerald ash borer (EAB, Agrilus planipennis) from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few resources for genetic studies and improvement of green ash are available. In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic-and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al. 2015;Lane et al. 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1,201 markers in 23 linkage groups spanning 2008.87cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds (LOD) of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee. KeywordsGreen ash, linkage map, single nucleotide polymorphism (SNP), simple sequence repeats (SSRs), Genotyping-by-Sequencing (GBS), syntenyThe genetic and molecular mechanisms underlying diverse biological traits in green ash are unknown. Genetic linkage maps are powerful tools for genomics and genetics research. With a large number of DNA markers, fine mapping of quantitative trait loci (QTL) can support marker-assisted selection for breeding programs. Candidate genes can also be positioned within the quantitative trait locus (QTL) regions identified by association studies. Combined with transcriptome studies, differentially expressed genes can be mapped and localized so that genes related to specific traits of interest can be characterized. In addition, linkage maps can also be used to conduct comparative analyses with other species to detect genomic synteny and to improve and correct chromosome-scale genome assemblies. Linkage maps have been reported in many non-model species (Tian et al. 2015;Moumouni et al. 2015;Raman et al. 2014), but the resolution of genetic maps depends on the number of markers segregating in the mapping population.Recently, the innovation of NGS methods for genetic marker discovery combined with reduced costs has facilitated the genotyping of thousands of SNPs across hundreds of samples. New methods, such as reduced-representation libraries (RRLs) (Van Tassell et al. 2008), restriction-site associated sequencing (RAD-seq) (Davey and Blaxter 2010) and genotyping-bysequencing (GBS) (Elshire et al. 2011), utilize restriction enzyme digestion of target genomes to reduce the complex...

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Section: Genome-wide Identification Of Snpssupporting

confidence: 85%

“…The ratio between transition and transversion was 1.42 in sunflower (Celik et al 2016). In chickpea, a Ts/Tv ratio of 1.74 was reported from SNP discovery (Gaur et al 2015).…”

Section: Discussionmentioning

confidence: 96%

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Koch

Coggeshall

et al. 2018

Preprint

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“…ICC 4958 x C. reticulatum acc. PI 489777) 20 . The gaps of unknown sizes were joined with 100 N as per National Centre for Biotechnology Information (NCBI) guideline.…”

Section: Methodsmentioning

confidence: 99%

Draft genome sequence ofCicer reticulatumL., the wild progenitor of chickpea provides a resource for agronomic trait improvement

Gupta

Nawaz

Parween³

et al. 2016

DNA Res

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Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.

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“…However, CMD resistant loci have been described using eight molecular markers (Rabbi et al, 2014;Okogbenin et al, 2012;Lokko et al, 2005;Akano et al, 2002) that are sparsely distributed, making it impracticable to precisely associate flanking markers with CMD resistant status. High quality genome assembly and dense genetic maps are essential tools for mapping to allow identification of loci associated with traits (ICGMC, 2015;Gaur et al, 2015;Zhang et al, 2015). In soybean, for example, a high density genetic map saturated with 2500 molecular markers were developed to precisely map QTLs conferring resistance to Fusarium graminearum on 300 kb region of chromosome 8 (Acharya et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Identification and analysis of cassava genotype TME3 bacteria artificial chromosome libraries for characterization of the cassava mosaic disease

Kuria¹,

Ateka²,

Miano³

et al. 2016

Afr. J. Biotechnol.

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Cassava is an economically important crop in sub-Saharan Africa; however, its yield potential is constrained by cassava mosaic disease (CMD) infection. Classical genetics and biotechnology are being harnessed to overcome the disease and secure yields for farmers. The CMD2 resistance locus flanked by three simple sequence repeats (SSR) markers and one sequence characterized amplified region (SCAR) marker were mapped in West African genotypes and shown to impart qualitative resistant to all species of CMGs. However, gene(s) associated with the CMD2 locus and their mode of actions remains unknown. In an effort to discover gene(s) located in CMD2 locus region, TME3 BAC collections were screened for the presence of CMD2 flanking markers. CMD susceptible and resistant cassava genotypes were found to contain 100% of the markers flanking CMD2 locus. SNPs and nucleotide deletions were identified within the marker sequences but there was no evidence of trait and marker association. All the SSR markers flanking CMD2, and the more recently characterized CMD3 loci were to be located on chromosome 12. Through BAC pools library hybridization with marker probes, 130 BACs were identified, but only 23 BACs contained at least CMD2 specific two markers. Whole BAC sequencing identified five clones that mapped to the marker regions. BAC29 assembled into a 100 kb contig and encoded tandem repeats of three full length R genes (3.5 kb) and two partial repeats. These R genes were conserved and highly expressed in CMD susceptible and CMD resistant cassava genotypes. Promoter sequences derived from R genes showed similar transient expression of GUS as 35S promoter. On cassava genome V6.1 BAC29 sequences were mapped to chromosome 16, eliminating their potential role in CMD resistant.

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High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

Cited by 43 publications

References 65 publications

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Draft genome sequence ofCicer reticulatumL., the wild progenitor of chickpea provides a resource for agronomic trait improvement

Identification and analysis of cassava genotype TME3 bacteria artificial chromosome libraries for characterization of the cassava mosaic disease

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