Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

Abstract

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses showed a Jaccard's index from 0.3 to 1.0, indicating high genetic and intravarietal diversity. Accessions from all 19 communities were not spatially structured (r = 0.15, p < 0.054), with AMOVA indicating that most of the variability (58.2%) was distributed within households and only 18.1% of the variability was distributed between households within communities. The outcrossing mating system of sweet potato, and anthropic factors such as selection of different varieties and their maintenance within household small plots and home gardens, as well as an extensive exchange system between agriculturists, may all be contributing to these results.

Genetic differentiation of Slovenian sweet potato varieties (Ipomoea batatas) and effect of different growing media on their agronomic and nutritional traits

“…Dilutions of 1 ng µL -1 of DNA were used for PCR amplification. Eight primer pairs: Ib-316, Ib-318, Ib-242, Ib-248, Ib-255F1, Ib-255, Ib-286 and Ib-297 (Buteler et al, 1999;Veasey et al, 2008) were applied for SSR assessment. PCR reactions were performed in a final volume of 11 μL, containing 1 ng of genomic DNA and following reagents with starting concentrations of: 10 × PCR buffer (Biotools, Madrid, Spain), 10 mM of each dNTP's, 50 mM MgCl2 (Biotools), 10 µM of each primer, 10 µM 5' fluorescently labelled universal primer (6-FAM, NED, HEX) and 0.5 U of Taq DNA polymerase (Biotools).…”

“…Application of short sequence repeats (SSR markers) in genetic diversity studies of different agro-economically important species represents informative, effective and reliable marker system (Rusjan et al, 2012(Rusjan et al, , 2015Pipan et al, 2011Pipan et al, , 2013Pipan et al, , 2016Maras et al, 2015;Derlink et al, 2014) for distinguishing among different genetic resources. For sweet potato, which is a hexaploid (2n=6x=90) plant species with an out-crossing mating system (Veasey et al, 2008), SSR marker system is highly applicable due its codominant nature (Pipan et al, 2016).…”

“…For sweet potato, which is a hexaploid (2n=6x=90) plant species with an out-crossing mating system (Veasey et al, 2008), SSR marker system is highly applicable due its codominant nature (Pipan et al, 2016).…”

Distribution, management and diversity of the endangered Amerindian yam (Dioscorea trifida L.)

“…It was also observed that 56% of the farmers cultivate only one variety of D. trifida, unlike other species of vegetative propagation, such as cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas) (Brush et al, 1981;Salick et al, 1997;Sambatti et al, 2001;Emperaire and Peroni, 2007;Amorozo, 2008;Veasey et al, 2008), where it is customary to keep two or more varieties in the same farm. This decrease in the number of yam varieties maintained by farmers is worrisome because it is directly related to the loss of genetic resources and the process of genetic erosion.…”

Genetic analysis of yield and flesh colour in sweetpotato

“…Although over 1600 EST-based SSR markers have been identified for sweetpotato (Schafleitner et al, 2010), only a limited number of SSR markers have been tested and used in diversity analysis of sweetpotato by various authors (Zhang et al, 1999;Hwang et al, 2002;Gichuru et al, 2005;Elameen et al, 2008;Veasey et al, 2008;Karuri et al, 2010;Tumwegamire et al, 2011;Gwandu et al, 2012).…”