Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd.

Ying Wang,Zhongfu Lu,Xiaohua Wu,Zishan Feng,Yanwei Li,Xinyi Wu,Guojing Li,Baogen Wang,Zihan Mu,Jiang Wang

doi:10.3389/fpls.2021.747940

Ying Wang, Zhongfu Lu + Show 8 more

Open Access

https://doi.org/10.3389/fpls.2021.747940

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Abstract

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

Highlights

Bottle gourd [Lagenaria siceraria (Mol.) Standl.] (2n = 2x = 22), known as calabash or long melon, is a cultivated vegetable, medicinal plant, decorative cucurbit, and grafting rootstock belonging to the Cucurbitaceae family, together with other major cucurbit crops, including cucumber (Cucumis sativus L.), melon (Cucumis melo L.), and watermelon (Citrullus lanatus L.) (Heiser, 1979; Beevy and Kuriachan, 1996; Erickson et al, 2005; Morimoto et al, 2005)
We further evaluated the discriminatory power of the core single-nucleotide polymorphism (SNP) set by analyzing the genetic structure of the 206 bottle gourd germplasm collections using the core SNP set and the aforementioned 93 high-quality SNPs
random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and InDel markers, which involve complex processes, would be superseded by the development of SNP molecular markers, which are suitable for large-scale high-throughput screening of multiple samples and sites, SNPs combined with Kompetitive allelespecific PCR (KASP) are yet to be utilized for large-scale germplasm characterization in bottle gourd

Summary

Introduction

Core SNP Marker Set Identification of 297 Mb was released for the Chinese landrace “Hangzhou Gourd” (Xu et al, 2021). An increasing number of homogeneous new bottle gourd varieties are being released onto the market, and intellectual property disputes could emerge in cases where different species have been assigned the same name or where different names have been assigned a single species. Traditional identification and registration of germplasm collections or varieties are primarily dependent on field planting, which is both time-consuming and inefficient. Plant traits are often influenced by environmental variation (Jamali et al, 2019). A precise, rapid, convenient, and cost-effective procedure, e.g., using molecular markers to predict traits (Jones and Mackay, 2015), is urgently needed to resolve intellectual property disputes and for cultivar improvement

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