Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

Abstract

Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

Genetic Diversity and Relationship of Mulberry Genotypes Revealed by RAPD and ISSR Markers

“…Moreover, the total number of polymorphic bands detected by ISSR primers (106) was higher than that detected by RAPD primers (67), which suggested that ISSR markers were superior to RAPD markers in generating informative bands in a single amplification. Similar results of better information generation ability of ISSR primers over RAPD primers have also been reported in other perennial crops such as Harpagophytum (Muzila et al 2014), Morinda species (Singh et al 2011), pecan (Jia et al 2011), and plumbago (Panda, Naik, and Kamble 2015). The high reproducibility of ISSR primers may be because this technique involves the use of a single microsatellite sequence along with a short arbitrary sequence, which targets a subset of microsatellites and amplifies the region between two closely spaced and oppositely oriented simple sequence repeats (Zeitkeiwicz, Rafalski, and Labuda 1994).…”

Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish

“…Based on their locations, SSRs can be classified into genomic SSRs (gSSRs) and Expressed Sequence Tag-SSRs (EST-SSRs) [9]. Because of high level of polymorphism, SSRs have wide applications in population genetics, such as parentage analysis [10], Quantitative Trait Locus (QTL) mapping [11], marker assisted selection (MAS) [12], and phylogenetic studies [13]. Traditional methods of developing gSSR markers require fragmented genomic DNA and are usually time-consuming and labor-intensive.…”

Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

“…To date, several molecular marker types have been used in pecan, such as amplified fragment length polymorphism (AFLP) [10], random amplified polymorphic DNA (RAPD) [11], inter-simple sequence repeat (ISSR) [12], simple sequence repeat (SSR) [13], and single nucleotide polymorphism (SNP) [14]. Compared to the dominant markers (AFLP, RAPD and ISSR), SSRs are superior in terms of their high informative content, high allelic variation, and good reproducibility [15].…”