Genetic Diversity and Pedigree Analysis of Muscadine Grape Using SSR Markers

Abstract

<jats:p>Muscadine grape (<jats:italic>Vitis rotundifolia</jats:italic>) is the first native North American grape to be domesticated. During the past century, breeding programs have created a large collection of muscadine cultivars. Muscadine cultivars are usually identified by evaluating morphological traits and checking breeding records, which can be ambiguous and unauthentic. During this study, simple sequence repeat (SSR) markers were used to generate DNA fingerprinting profiles to identify muscadine cultivars and verify their reported pedigrees. Eighty-nine <jats:italic>Vitis</jats:italic> accessions were genotyped using 20 SSRs from 13 linkage groups. From these, 81 unique subgenus <jats:italic>Muscadinia</jats:italic> accessions were identified, and a core set of five SSR markers was able to distinguish all of them. Eighteen misidentifications were found, and five previously unknown accessions were matched with cultivars in the dataset. The profiles of 12 cultivars were not consistent with their reported parentage–progeny relationships. Genetic diversity was analyzed at four levels: all <jats:italic>V. rotundifolia</jats:italic> cultivars (N = 67); current cultivars (N = 39); historical cultivars (N = 28); and wild <jats:italic>V. rotundifolia</jats:italic> accessions (N = 9). There was substantial genetic diversity in both wild and historically cultivated muscadines. The principle coordinate analysis (PCoA) showed clear separation among subgenus <jats:italic>Vitis</jats:italic> cultivars, wild muscadine accessions, and cultivated muscadines, with PCoA1 and PCoA2 explaining 11.0% and 9.3% of the total variation, respectively.</jats:p>

Genetic Diversity of Wild and Cultivated Muscadine Grapes (Vitis rotundifolia Michx.)

“…One comparative study found that bunch grapes had significantly more genetic variation than muscadines, although those results are difficult to interpret due to the low number of accessions compared and the interspecific background of the bunch grape accessions included in the study ( Qu et al, 1996 ). Past studies using simple sequence repeat (SSR) markers to quantify genetic diversity in cultivated muscadines have found that observed heterozygosity was higher than expected ( Riaz et al, 2008 ; Cao et al, 2020 ). However, pedigree analysis has found that recently released varieties have higher inbreeding levels than historical varieties ( Williams et al, 2021 ).…”

“…It has been used sparingly in breeding efforts, most importantly in the pedigree of the cultivar “Southern Home” ( Mortensen et al, 1994 ). The USDA National Clonal Germplasm Repository (NCGR) maintains a single accession of V. popenoei (DVIT 2970) collected from Veracruz, Mexico, affording the species a minor presence in previous molecular studies (e.g., Wan et al, 2013 ; Cao et al, 2020 ).…”

“…However, pedigree analysis has found that recently released varieties have higher inbreeding levels than historical varieties ( Williams et al, 2021 ). Marker data also show that allelic richness appears to decline between historical cultivars and cultivars released after 1970 ( Cao et al, 2020 ). Despite the limited genetic base available to muscadine breeders and a loss of genetic diversity over time, inbreeding depression does not yet appear to be a significant issue in cultivated muscadines ( Goldy and Onokpise, 2001 ), although low vine vigor has been cited as a potential effect of inbreeding already present in some breeding material ( Williams et al, 2021 ).…”

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

“…Bassil et al (2018) also used SSRs to identify four accessions of previously undescribed hybrid origin during an analysis of the genetic diversity of wild Vaccinium species. Cao et al (2020) reported that five previously unknown grape accessions were matched by SSRs.…”

“…Klein et al (2018) also used high-throughput sequencing to clarify evolutionary relationships among North American Vitis species. Because SSR markers show high levels of polymorphisms, reproducibility, and codominant inheritance (Aradhya et al, 2013;Li et al, 2017), they have been widely used to study the genetic diversity of grapes (Cao et al, 2020;Guo et al, 2010), sugarcane [Saccharum officinarum (Ali et al, 2019)], wheat [Triticum aestivum (Abbasov et al, 2018)], cabbage [Brassica oleracea (El-Esawi et al, 2016)], and hazelnuts [Corylus heterophylla (Zhao et al, 2020)].…”