A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

Jianhua Zhao,Bo Zhang,Yuhui Xu,Wei An,Yue Yin,Haoxia Li,Yanlong Li,Yajun Wang,Youlong Cao,Ting Huang

doi:10.1186/s12870-021-03115-1

Jianhua Zhao, Bo Zhang + Show 8 more

Open Access

https://doi.org/10.1186/s12870-021-03115-1

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Abstract

BackgroundLycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers.ResultsIn this study, two parental strains, ‘Ningqi No. 1’ (Lycium barbarum L.) and ‘Yunnan Gouqi’ (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis.ConclusionsA chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.

Highlights

Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits
Next-generation sequencing (NGS) coupled with the growing number of reference genome sequences presents an opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis [7], which can result in ultra-high-density linkage map construction and localized quantitative trait loci (QTLs) for multiple traits [8, 9]
With the decreasing costs of sequencing technologies, wholegenome sequencing has been applied to an increasing number of plant species; in addition, the numerous single nucleotide polymorphism (SNP) markers developed by aligning resequencing data to the corresponding reference genome can provide a powerful approach for deciphering the genetic basis of complex traits and for large-scale gene discovery [13]

Summary

Introduction

Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. Many compounds from L. barbarum fruits and leaves, including flavonoids, carotenoids, and polysaccharides, have been reported to be closely associated with the health-enhancing effects of this species [5, 6]. With the decreasing costs of sequencing technologies, wholegenome sequencing has been applied to an increasing number of plant species; in addition, the numerous single nucleotide polymorphism (SNP) markers developed by aligning resequencing data to the corresponding reference genome can provide a powerful approach for deciphering the genetic basis of complex traits and for large-scale gene discovery [13]

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Conclusion