Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China

Abstract

Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

“…We also found an LD decay distance of ∼94.56 kb (Figure 3D), much smaller than that reported by Fricano et al (2012). STRUCTURE analysis identified two subpopulations in the panel (Figure 3B), and clustering results showed that the genetic background of 94 accessions is diverse and complex, consistent with most studies on tobacco (Fricano et al, 2012;Dadras et al, 2014;Wang et al, 2021). There are high genomewide SNP variations in the panel used in this study that are suitable for association mapping (Mackay and Powell, 2007;Wang et al, 2009;Ikram et al, 2020).…”

“…Thus, it is challenging to assemble a natural population with rich genetic diversity. However, based on the 126,602 SNPs, we found 24.46 kb/SNP in the whole genome ( Supplementary Table 3 and Figure 2C ) and higher coverage density than reported elsewhere ( Leng et al, 2010 ; Wang et al, 2021 ). We also found an LD decay distance of ∼94.56 kb ( Figure 3D ), much smaller than that reported by Fricano et al (2012) .…”

“…Tobacco cultivars exhibit low genetic diversity, and their existing alleles may not improve TBW resistance ( Qian et al, 2013 ; Wang et al, 2021 ). New alleles identified through germplasm screening will improve TBW resistance.…”

Population Genetics and Development of a Core Collection from Elite Germplasms of Xanthoceras sorbifolium Based on Genome-Wide SNPs

“…This is mainly because the elite germplasms used in this test were all selected and obtained from local seedlings; in the long-term selection process, germplasms from different provinces were introduced or exchanged. Wang et al (2021) reported similar results in a study conducted on 113 cigar tobacco accessions; the accessions were not completely classified based on their geographical origins [43].…”

GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratenseL.)

“…However, the method remains expensive and often requires a high number of replicates, so scalability is often not straightforward (Lohman et al, 2016). Genomic DNA fingerprinting (e.g., ddRadSeq; Hohenlohe et al 2011) or genotyping by sequencing (GBS; Elshire et al 2011)) is now widely used to perform association studies in many species, including those with complex genomes (Caballero et al 2021), for revealing genetic diversity and population structure (Müller et al 2019), for fingerprinting germplasm resources (Wang et al 2021), or for the detection of candidate genes by fine mapping, especially for improving plant breeding strategies (e.g. Purugganan & Jackson 2021).…”