Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. ×ananassa Duschene ex Rozier `Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5′UTR (80% polymorphic) or 3′UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.
K.S. Lewers, S.M.N. Styan, S.C. Hokanson, and N.V. Bassil
J. Steven Brown, R.J. Schnell, J.C. Motamayor, Uilson Lopes, David N. Kuhn, and James W. Borrone
A genetic linkage map was created from 146 cacao trees (Theobroma cacao), using an F2 population produced by selfing an F1 progeny of the cross Sca6 and ICS1. Simple sequence repeat (SSR) markers (170) were used principally for this map, with 12 candidate genes [eight resistance gene homologues (RGH) and four stress related WRKY genes], for a total of 182 markers. Joinmap software was used to create the map, and 10 linkage groups were clearly obtained, corresponding to the 10 known chromosomes of cacao. Our map encompassed 671.9 cM, approximately 100 cM less than most previously reported cacao maps, and 213.5 cM less than the one reported high-density map. Approximately 27% of the markers showed significant segregation distortion, mapping together in six genomic areas, four of which also showed distortion in other cacao maps. Two quantitative trait loci (QTL) for resistance to witches' broom disease were found, one producing a major effect and one a minor effect, both showing important dominance effects. One QTL for trunk diameter was found at a point 10.2 cM away from the stronger resistance gene. One RGH flanked the minor QTL for witches' broom resistance, implying possible association. QTLs mapped in F2 populations produce estimates of additive and dominance effects, not obtainable in F1 crosses. As dominance was clearly shown in the QTL found in this study, this population merits further study for evaluation of dominance effects for other traits. This F2 cacao population constitutes a useful link for genomic studies between cacao and cotton, its only widely grown agronomic relative.
Imen Rekik, Amelia Salimonti, Naziha Grati Kamoun, Innocenzo Muzzalupo, Oliver Lepais, Sophie Gerber, Enzo Perri, and Ahmed Rebai
markers ( Grati Kamoun et al., 2006 ; Taamalli et al., 2006 ) and simple sequence repeat (SSR) markers ( Taamalli et al., 2006 , 2007 ). However, there is still a need for better genetic diversity assessment and varietal identification using high
Hussam S.M. Khierallah, Saleh M. Bader, Michael Baum, and Alladin Hamwieh
have used SSR markers to genotype cultivars. Elshibli and Korpelainen (2008) investigated genetic diversity in Sudan germplasm representing 37 female and 23 male accessions using 16 SSR primers. In Qatar, Ahmed and Al-Qaradawi (2009) used 10 primers
Tim Rinehart, Cecil Pounders, and Brian Scheffler
Crapemyrtles (Lagerstroemia) are deciduous shrubs or trees with prolific summer flowers. Their popularity is due in large part to low maintenance requirements in sunny climates, wide range of growth habits, disease resistance, and bark characteristics, as well as having a long flowering period (up to 120 days). Once well-established, they are extremely tolerant to heat and drought. Lagerstroemia was first introduced to the southern U.S. from southeast Asia more than 150 years ago, and is comprised of at least 80 known species. Most modern cultivars are L. indica and L. fauriei hybrids. L. speciosa is a tropical crapemyrtle with very large flowers, but lacks cold hardiness. It is a vigorous plant, but only when grown in Hardiness zones 9 or 10. We recently established microsatellite markers for Lagerstroemia and evaluated their utility for verifying interspecific hybrids. Here we verify F1 hybrids between L. indica `Tonto', `Red River', and L. speciosa. We also genotyped two commercially available L. speciosa hybrids. Currently, we are using crapemyrtle SSRs for cultivar identification and germplasm conservation. Future research includes marker-assisted breeding to produce powdery mildew and flea beetle resistant cultivars, as well as improved growth habit and fall foliage color.
Paolo Boccacci, Roberto Botta, and Mercè Rovira
cultivars due to their high discriminating power at a relatively low cost. Among the available DNA markers, microsatellite or simple sequence repeat (SSR) markers appear to be best-suited to cultivar fingerprinting. They are generally codominant, highly
Njung’e Vincent Michael, Pamela Moon, Yuqing Fu, and Geoffrey Meru
al., 2003 ; Formisano et al., 2012 ; Gong et al., 2012 ; Paris et al., 2003 , 2015 ). Among these, SSR markers are preferred because of their abundance in the genome, reproducibility, high level of polymorphism and codominance ( Hodel et al., 2016
Pilar Soengas, Pablo Velasco, Guillermo Padilla, Amando Ordás, and Maria Elena Cartea
Brassica napus includes economically important crops such as oilseed rape, rutabaga, and leaf rape. Other vegetable forms of Brassica napus, namely nabicol and couve-nabiça, are grown in northwestern Spain and north of Portugal, respectively, and their leaves are used for human consumption and fodder. The relationship of nabicol with other Brassica napus leafy crops was studied before, but its origin remained unclear. The aims of this work were to study the genetic relationships among nabicol landraces and other B. napus crops based on microsatellites and to relate the genotypic differences with the use of the crop. The relationship among 35 Brassica napus populations representing different crops was studied based on 16 microsatellite markers. An analysis of molecular variance was performed partitioning the total variance into three components. The source of variation resulting from groups was defined considering the main use of the crop and accounted for a smaller percentage of variation than other sources of variation, proving that this division is not real. Populations clustered into seven different clusters using a similarity coefficient of 0.82. No clear association was evident between clusters and the main use of populations, suggesting genetic differences among populations could reflect differences in their origin/breeding or domestication. Spanish nabicol could have originated from a sample of couve-nabiças, and couve-nabiças could be used to improve nabicol landraces, because they have a narrow genetic basis that limits their potential for breeding.
Kim S. Lewers*, Eric T. Stafne, John R. Clark, Courtney A. Weber, and Julie Graham
Some raspberry and blackberry breeders are interested in using molecular markers to assist with selection. Simple Sequence Repeat markers (SSRs) have many advantages, and SSRs developed from one species can sometimes be used with related species. Six SSRs derived from the weed R. alceifolius, and 74 SSRs from R. idaeus red raspberry `Glen Moy' were tested on R. idaeus red raspberry selection NY322 from Cornell Univ., R. occidentalis `Jewel' black raspberry, Rubus spp. blackberry `Arapaho', and blackberry selection APF-12 from the Univ. of Arkansas. The two raspberry genotypes are parents of an interspecific mapping population segregating for primocane fruiting and other traits. The two blackberry genotypes are parents of a population segregating for primocane fruiting and thornlessness. Of the six R. alceifolius SSRs, two amplified a product from all genotypes. Of the 74 red raspberry SSRs, 56 (74%) amplified a product from NY322, 39 (53%) amplified a product from `Jewel', and 24 (32%) amplified a product from blackberry. Of the 56 SSRs that amplified a product from NY322, 17 failed to amplify a product from `Jewel' and, therefore, detected polymorphisms between the parents of this mapping population. Twice as many detected polymorphisms of this type between blackberry and red raspberry, since 33 SSRs amplified a product from NY322, but neither of the blackberry genotypes. Differences in PCR product sizes from these genotypes reveal additional polymorphisms. Rubus is among the most diverse genera in the plant kingdom, so it is not surprising that only 19 of the 74 raspberry-derived SSRs amplified a product from all four of the genotypes tested. These SSRs will be useful in interspecific mapping and cultivar development.
Timothy Rinehart, Sandra Reed, and Brian Scheffler
Hydrangea popularity and use in the landscape has expanded rapidly in recent years with the addition of remontant varieties. Relatively little is known about the genetic background or combinability of these plants. We recently established microsatellite markers for hydrangea and evaluated their utility for estimating species diversity and identifying cultivars. We also verified an interspecific cross using these markers. Future research includes marker assisted breeding, particularly with respect to remontant flowering traits.