Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids

Abstract

In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques.

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

“…However, no information is available on the number and structural variability of WRKY TFs in Solanaceae wild species, which represent an important reservoir of genetic variation for breeding. This study was set up with the aim to profile WRKY encoding genes in S. commersonii and S. chacoense, two noteworthy tuber-bearing potato species used in potato breeding programs 20,[43][44][45] .…”

“…2a) and SchWRKYs (Fig. 2b) revealed their dynamic and differential expression in various tissues and that the range of expression 67, 81, 84_like, 85, 86, 88 and 89) showed very low or undetectable expression (FPKM values from 0 to 0.5) in all studied tissues, while 16 (20.2%) genes (18,23,03,48,87,08,11,47,79,10,51,45, 05, 06, 12 and 49) were highly expressed (FPKM > 5) in all tissues. Some of the remaining genes showed tissue specificities.…”

“…These results indicate that, compared to the cultivated potato 22 , S. commersonii possesses a lower number and S. chacoense a higher number of WRKY genes. Both species displayed a number of WRKYs greater than that of barley (45) 46 , castor bean (58) 47 , cucumber (55) 48 , rapeseed (43) 49 and grapevine (59) 50 , and lower than that of cotton (120) 51 , maize (136) 52 , soybean (131) 53 and rice (100) 25 . From this comparison, it appears that the number of WRKY encoding genes is not proportional to the genome size of the respective plant species, as also reported by Waqas et al 54 .…”

Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing Solanum commersonii

“…It is particularly attractive for its freezing tolerance and capacity to cold acclimate [23]. Furthermore, it is the first wild potato whose genome sequence has been released [23], paving the way to different studies aimed to gain insights into genomic evolution at the sequence level from the wild to the cultivated form [24,25]. S. commersonii possesses a diverse mixture of glycoalkaloids, such as dehydrotomatine, dehydrodemissine and dehydrocommersonine, which are among the most poisonous compounds against different potato pests [26].…”

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

“…Several methods were reported in the detection of SNP markers, including SSCP (Kozlowski and Krzyzosiak, 2001), DGGE (Guldberg et al 1993), CAPS (Li et al 2012), DNA-chip (Singh et al 2015), DHPLC (Wolford et al 2000;Colasuonno et al 2016), mass spectrometric detection (Park et al 2017), and HRM (high-resolution melting) (Villano et al 2016;Kim et al 2016). The recently developed HRM analysis method provided us a novel, quick, and close-tube PCR approach to analyze SNPs (Nguyen et al 2012).…”