Characterization of Genomic Microsatellite Markers and Analysis of Pollen Donors Number for Single Cone of Chinese fir

Kui-Peng Li ,Kaiyong Huang,Leiming Dong,Daixi Chen,Shichang Chen,Jing Liang

doi:10.5376/tgmb.2020.10.0005

Abstract

Chinese fir [ Cunninghamia lanceolate (Lamb.) Hook] is one of the most important indigenous timber tree species in China. The aim of the present work is to characterize simple sequence repeat (SSR) loci derived from the specific length amplified fragment sequencing (SLAF) data of the genome and to investigate the number of pollen donors for per cone was with novel SSR markers of low-frequency null alleles. A total of 58855 SLAF-SSR with frequency of 42.04 SSR/Mbp were identified in about 1.40 Gb Chinese fir genome. Dinucleotide repeat SSR contributed to 66.4% of the total SSR from SLAF data. The AT/AT and ATG/CAT motifs were predominant in the category of din- and trinucleotide repeat SSR. Low frequencies of null alleles (<5%) were detected at the nine novel SSR markers with average expected heterozygosity of 0.513 and polymorphism information content score of 0.508. The number of tested progeny of a cone was from 4 to 13. It could be 67 pollinizers for 15 cones and the average number of pollen donors per cone was 4.5. The study points out, for the first time, that there are multiple pollen donors for single cone in gymnosperm.

Highlights

The aim of the present work is to characterize simple sequence repeat (SSR) loci derived from the specific length amplified fragment sequencing (SLAF) data of the genome and to investigate the number of pollen donors for per cone was with novel SSR markers of low-frequency null alleles
The number of di- and trinucleotide SLAF-SSR was declining accompanied by number increase of the motif repeat. 1.2 Validation of SLAF-SSR and EST-SSR A subset of 100 markers, which were successfully designed the primer, were randomly chosen respectively from SLAF-SSR and EST-SSR of Chinese fir. 12 individuals were employed to test the amplification validation
The AT/AT and AAG/CTT repeats were predominant in din- and trinucleotide repeats of EST-SSR of Chinese fir (Wen et al, 2015)

Summary

Introduction

The aim of the present work is to characterize simple sequence repeat (SSR) loci derived from the specific length amplified fragment sequencing (SLAF) data of the genome and to investigate the number of pollen donors for per cone was with novel SSR markers of low-frequency null alleles. A total of 58855 SLAF-SSR with frequency of 42.04 SSR/Mbp were identified in about 1.40 Gb Chinese fir genome. The basic characteristic of genomic SSR from Chinese fir is unknown and the research on the pollen donors number of offspring from a cone of gymnosperm has not been reported. In the present study we describe: (1) characterization of SSR derived from the specific length amplified fragment sequencing data(SLAF-SSR)of the Chinese fir genome. (4) analysis of the pollen donors number of a Chinese fir cone In the present study we describe: (1) characterization of SSR derived from the specific length amplified fragment sequencing data(SLAF-SSR)of the Chinese fir genome. (2) Evaluation of the primers validity and diversity information parameters of SLAF-SSR and expressed sequence tag (EST-SSR). (3) development of SSR markers with low-frequency null alleles (

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