Simplified Genome SSR Information and Development of SSR Primers of Halenia ellipitica(Gentianaceae)

doi:10.7525/j.issn.1673-5102.2018.02.018

Bulletin of Botanical Research ›› 2018, Vol. 38 ›› Issue (2): 292-297.doi: 10.7525/j.issn.1673-5102.2018.02.018

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Simplified Genome SSR Information and Development of SSR Primers of Halenia ellipitica(Gentianaceae)

WANG Jiu-Li^1,2, CHEN Shi-Long¹, XING Rui¹, SONG Xiang-Jie³, ZHU Ming-Xing³, ZHANG Fa-Qi^1,4

1. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008;
2. University of the Chinese Academy of Sciences, Beijing 100039;
3. College of Ecology-Environment Engineering, Qinghai University, Xining 810016;
4. Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008

Received:2017-09-21 Online:2018-03-15 Published:2018-03-23
Supported by:
National Natural Science Foundation of China(31400322); Applied Basic Research Programs of Qinghai Province(2016-ZJ-761); The Natural Science Foundation of Qinghai Province(2015-ZJ-925Q);Qinghai Provincial Key Laboratory of Crop Molecular Breeding (2017-ZJ-Y14)

Abstract

Abstract: The restriction-site associated DNA sequencing(RAD-seq) technology was used to analyze simple sequence repeats(SSR) information of Halenia ellipitica D. Don; SSR markers for this species were developed based on RAD-seq data. We identified 6 201 SSR loci with at least 100 bp at two ends, including five types(di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide, and hexa-nucleotide). Primers of 3 865 loci were designed successfully. Among which, amount of tri-nucleotide SSR loci is the most. Repeat motif type number is 316, and type number of penta-nucleotide motif is the most(91). Afterward, 65 designed primers were randomly selected to represent the five SSR types, and tested using annealing temperature gradient PCR. Subsequently, 32 individuals from four natural populations of H. elliptica were employed to estimate the SSR primers that can be amplified. One monomorphic and 13 polymorphic SSR loci were developed according to the result of PCR and Polyacrylamide gel electrophoresis. The number of alleles of the 13 polymorphic SSR loci is high(mean 5.462), and no linkage relation was found(P<0.01); ten loci deviate from HWE(P<0.01) and have many homozygotes(observed heterozygosity mean of 0.226); the range of inbreeding coefficient is in -0.443-1(mean of 0.656); the gene flow N_m is 0.474.

Key words: Halenia ellipitica, RAD-seq, SSR molecular marker, simplified genome sequencing

CLC Number:

Q949.776.4

WANG Jiu-Li, CHEN Shi-Long, XING Rui, SONG Xiang-Jie, ZHU Ming-Xing, ZHANG Fa-Qi. Simplified Genome SSR Information and Development of SSR Primers of Halenia ellipitica(Gentianaceae)[J]. Bulletin of Botanical Research, 2018, 38(2): 292-297.

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Simplified Genome SSR Information and Development of SSR Primers of Halenia ellipitica(Gentianaceae)

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