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Development and characterization of SSR markers for Sanguinaria canadensis based on genome skimming.

ABSTRACT: Premise:Polymorphic nuclear simple sequence repeat (nSSR) markers were developed for Sanguinaria canadensis (Papaveraceae), a spring ephemeral native to eastern North America. Methods and Results:Based on the genome skimming data of S. canadensis, a total of 240 nSSR primer pairs were designed for 80 loci from the assembled nuclear contigs. Of these primer pairs, 19 were selected for initial validation in four populations (80 individuals). All 19 loci produced heterologous amplification. The numbers of alleles per locus ranged from one to 21; the levels of observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.000 to 0.847, respectively. Transferability of the loci was tested in the related species Eomecon chionantha. Conclusions:The developed nSSR markers revealed polymorphism in the four studied populations and may contribute to investigations of the genetic diversity of S. canadensis and E. chionantha.

SUBMITTER: Liao R

PROVIDER: S-EPMC6764431 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Development and characterization of SSR markers for <i>Sanguinaria canadensis</i> based on genome skimming.

Liao Renyu R Luo Yuxin Y Yisilam Gulbar G Lu Ruisen R Wang Yuguo Y Li Pan P

Applications in plant sciences 20190924 9

<h4>Premise</h4>Polymorphic nuclear simple sequence repeat (nSSR) markers were developed for <i>Sanguinaria canadensis</i> (Papaveraceae), a spring ephemeral native to eastern North America.<h4>Methods and results</h4>Based on the genome skimming data of <i>S. canadensis</i>, a total of 240 nSSR primer pairs were designed for 80 loci from the assembled nuclear contigs. Of these primer pairs, 19 were selected for initial validation in four populations (80 individuals). All 19 loci produced hetero ...[more]

PMID: 31572630

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Project description:Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01035-w.

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Development and characterization of SSR markers for Sanguinaria canadensis based on genome skimming.

Publications

Development and characterization of SSR markers for <i>Sanguinaria canadensis</i> based on genome skimming.

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