Development of Microsatellite Primers of Quercus championii with RAD-seq Data

doi:10.7525/j.issn.1673-5102.2020.04.018

Abstract

Abstract: Microsatellite(simple sequence repeat, SSR) is a co-dominant molecular marker commonly found in plant genome with high polymorphism. This genotyping method is widely used in the study of spatial genetic structure of populations. With the blooming of the new sequencing technologies, the development method of SSR is also more diverse. Quercus championii is a precious wood species in the evergreen broad-leaved forest of South China. The development of its molecular markers can promote the species breeding and germplasm conservation. We used the reads obtained from RAD-seq(restriction-site associated DNA sequence) of four individuals of Q.championii to developed SSR primers. The pyRAD analysis showed that:(1)the reads containings 46 000-84 000 repeats sequence in each individual; (2)within the individual ranged clustering, 5 500-24 000 loci were detected; (3)1 158 concordance loci were obtained after clustering between individuals. Finally, 186 loci with flanking sequences were not mutated and repeating base was in the middle were obtained. A total of 25 primers pairs were designed using premier 5.0 and validated in 36 individuals from 3 populations. The results showed that 17 primer sets were successfully amplified and 106 alleleswere obtained. The number of alleles per primer between 2-12, and the average number is 6.2. The expected heterozygosity and observed heterozygosity of the primers were 0.19-0.88 and 0.11-0.76, respectively. The rapid, effective, and low cost in this method can be applied to the development of molecular markers of population genetics.

Key words: Quercus championii, RAD-seq, SSR molecular marker, genetic diversity

CLC Number:

S792.16

NING Xin, JIANG Xiao-Long, DENG Min, XU Gang-Biao. Development of Microsatellite Primers of Quercus championii with RAD-seq Data[J]. Bulletin of Botanical Research, 2020, 40(4): 629-634.

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