Transferability of Cucumber Microsatellite Markers Used for Phylogenetic Analysis and Population Structure Study in Bottle Gourd (Lagenaria siceraria (Mol.) Standl.)

Abstract

Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

Genetic Diversity of South African Bottle Gourd [Lagenaria siceraria (Molina) Standl.] Landraces Revealed by Simple Sequence Repeat Markers

“…These values are comparatively higher than those reported by Sarao et al (2013) with 0.23 to 0.73 and Xu et al (2011) with 0.11 to 0.72 (mean = 0.4). Yildiz et al (2015) reported PIC values of 0.12 to 0.52 (mean = 0.15) in bottle gourd, whereas Bhawna et al (2015b) found PIC values of 0.05 to 0.54 (average = 0.33) using 19 SSR markers. The PIC defines a relative measure of the informativeness of a marker or discriminatory power of a polymorphic marker, which depends on the number of alleles and relative frequency of an allele in the population (Bhawna et al, 2015b;Gaikward et al, 2008).…”

“…Yildiz et al (2015) reported PIC values of 0.12 to 0.52 (mean = 0.15) in bottle gourd, whereas Bhawna et al (2015b) found PIC values of 0.05 to 0.54 (average = 0.33) using 19 SSR markers. The PIC defines a relative measure of the informativeness of a marker or discriminatory power of a polymorphic marker, which depends on the number of alleles and relative frequency of an allele in the population (Bhawna et al, 2015b;Gaikward et al, 2008). In the present study, the highest PIC value was detected using marker LSR015 (0.84), closely followed by LSR020 (0.83).…”

“…Koffi et al (2009) reported the number of alleles per locus varying from 1.0 to 1.4 with a mean of 1.2 suggesting a low allelic richness. Yildiz et al (2015) and Bhawna et al (2015b) reported the number of alleles ranging from 1 to 5 (mean = 1.64) and 2 to 4 alleles (mean = 2.84) in bottle gourd, respectively. In the current study, the number of effective alleles ranged from 1.58 to 6.14 with a mean of 3.1.…”

Genetic diversity and population structure of Castanopsis eyrei based on simple sequence repeat markers

“…SSRs are used because of their codominant inheritance, multiallelic nature, abundance in the genome, and high reproducibility, but SSR marker development is time-consuming and costly. In this study, polymorphic SSRs were screened from the literature, indicating the transferability of SSRs from closely related species, which has also been found in other studies (Cui et al, 2008;Bhawna et al, 2015). Therefore, screening SSR markers from closely related species is a time-and money-saving method.…”

Development of novel gene-based microsatellite markers for robust genotyping purposes in Lagenaria siceraria

“…Numerous health benefits are reported in bottle gourd including its anti-cancerous (Saha et al, 2011), Cardio for detecting genetic diversity, genetic linkage mapping, association mapping and evolution analysis (Jiao et al, 2012). Despite bottle gourd being an important tropical vegetable crop, having abundant health benefits and proven for climate change adaptation strategies (Chimonyo and Modi, 2013), very limited molecular marker studies have been reported to study its genotyping, such as ISSR, SNP, SSR, RAPD (Bhawna et al, 2014;Xu et al, 2011;Bhawna et al, 2015;Sarao et al, 2014;Srivastava et al, 2014;Decker-Walters et al, 2001 respectively), but no study has been reported to characterize bottle gourd populations by constructing enriched SSR genomic library. To preserve the genetic richness of this crop, efforts must be directed towards the achievement of reliable collection and conservation strategies.…”