Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing

Bin Li,Furong Lin,Yongqi Zheng,Ping Huang,Wenying Guo

doi:10.1186/s40659-020-00289-0

Abstract

BackgroundLiriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm.ResultsWe performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79.ConclusionsThe genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.

Highlights

Liriodendron chinense ranges widely in subtropical China and northern Vietnam; it inhabits several small, isolated populations and is an endangered species due to its limited seed production
Liriodendron chinense is a cross-pollinated plant; parthenogenesis exists, and gynoecium can develop without insemination, causing a low germination percentage in the natural environment
The development and utilization of L. chinense germplasm resources began in the 1960s when crossbreeding of Asia and American tulip trees was successfully accomplished

Summary

Introduction

Liriodendron chinense ranges widely in subtropical China and northern Vietnam; it inhabits several small, isolated populations and is an endangered species due to its limited seed production. Liriodendron chinense is a cross-pollinated plant; parthenogenesis exists, and gynoecium can develop without insemination, causing a low germination percentage in the natural environment. Seed reproduction of this species often requires artificial pollination, whereas seeds still have poor vitality [6]. The development and utilization of L. chinense germplasm resources began in the 1960s when crossbreeding of Asia and American tulip trees was successfully accomplished. The original genetic resources that breed all kinds of cultivars may be missing due to long cultivating history, multiple market circulation and careless management. Comprehensive lineage cataloguing and genetic diversity investigation are required to supervise and protect a healthy development of tulip tree resources [7]

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