Using 14 codominant microsatellite markers that amplify loci across 14 different Hydrangea L. species, we analyzed gene diversity and genetic similarity within Hydrangea. Samples also included Dichroa Lour., Platycrater Sieb. and Zucc., and Schizophragma Sieb. and Zucc. genera to establish their relatedness to Hydrangea species since previous work suggests they may be closely related. Our results support the close affiliation between Macrophyllae E.M. McClint. and Petalanthe (Maxim.) Rehder subsections and their separation from the other Hydrangea species. Most of the Hydrangea species analyzed cluster within their designated sections and subsections; however, genetic distance between species within each subsection varied considerably. Our data suggest that morphological analyses which labeled H. serrata (Thunb.) Ser. as a subspecies of H. macrophylla (Thunb. Ex J.A. Murr.) Ser. are probably more accurate than recent genome size data suggesting H. macrophylla ssp. macrophylla (Thunb.) Ser. and H. macrophylla ssp. serrata (Thunb.) Makino are separate species. Gene diversity estimates indicate that 64.7% of the total diversity is due to differences between species and 49.7% of the overall variation is due to differences between subsections. Low diversity suggests a lack of gene flow between species and subsections and underscores the difficulty in making wide hybrids. Since only 35.3% of the genetic variation is common to all species, unique alleles were used to develop a molecular key for unambiguous species identification and interspecific hybrid verification. Genetic similarity estimates for all 85 samples suggests a roadmap for introgressing horticulturally important traits from different Hydrangea species.
Timothy A. Rinehart, Brian E. Scheffler, and Sandra M. Reed
Anna L. Hale, J. Creighton Miller Jr., K. Renganayaki, Alan K. Fritz, J.J. Coombs, L.M. Frank, and D.S. Douches
The objective of this study was to differentiate six intraclonal variants of the potato (Solanum tuberosum L.) cultivar Russet Norkotah. One-hundred-twelve AFLP primer combinations producing 3755 bands and 79 microsatellite primers producing over 400 bands failed to identify any reproducible polymorphisms among the intraclonal variants and `Russet Norkotah'. The inability to detect differences between clones underscores the degree of genetic similarity between them, despite differences in phenotypic expression. This inability could be due to the tetraploid nature of the clones and/or to epigenetic differences not detected by the utilized procedures.
Riaz Ahmad, Darush Struss, and Stephen M. Southwick
We evaluated the potential of microsatellite markers for use in Citrus genome analysis. Microsatellite loci were identified by screening enriched and nonenriched libraries developed from `Washington Navel' Citrus. Microsatellite-containing clones were sequenced and 26 specific PCR primers were selected for cross-species amplification and identification of cultivars/clones in Citrus. After an enrichment procedure, on average 69.9% of clones contained dinucleotide repeats (CA)n and (CT)n, in contrast to <25% of the clones that were identified as positive in hybridization screening of a nonenriched library. A library enriched for trinucleotide (CTT)n contained <15% of the clones with (CTT)n repeats. Repeat length for most of the dinucleotide microsatellites was in the range of 10 to 30 units. We observed that enrichment procedure pulled out more of the (CA)n repeats than (CT)n repeats from the Citrus genome. All microsatellites were polymorphic except one. No correlation was observed between the number of alleles and the number of microsatellite repeats. In total, 118 putative alleles were detected using 26 primer pairs. The number of putative alleles per primer pair ranged from one to nine with an average of 4.5. Microsatellite markers discriminated sweet oranges [Citrus sinensis (L.) osb], mandarin (Citrus reticulata Blanco), grapefruit (Citrus paradisi Macf.), lemon [Citrus limon (L.) Burm.f.], and citrange (hybrids of trifoliate orange and sweet orange), at the species level, but individual cultivars/clones within sweet oranges, mandarins and grapefruit known to have evolved by somatic mutation remained undistinguishable. Since these microsatellite markers were conserved within different Citrus species, they could be used for linkage mapping, evolutionary and taxonomic study in Citrus.
Mobashwer Alam, Craig Hardner, Catherine Nock, Katie O’Connor, and Bruce Topp
The Hawaiian cultivars Keaau (HAES660) and Mauka (HAES741) were selected by the University of Hawaii—released in 1966 and 1977, respectively—and have been used extensively in macadamia orchards throughout the world. Recent molecular evidence suggests that these two cultivars are almost identical genetically; however, commercially they have been considered phenotypically different. This study reviews available molecular, historical, and phenotypic evidence to examine the hypothesis that these two cultivars are the same genotype. Phenotypic variability for morphological traits was observed in a replicated trial at Wolvi, QLD. Historical evidence suggests that both ‘HAES660’ and ‘HAES741’ were derived from the same orchard. We identified strong genetic and phenotypic similarities between these cultivars, with variability in some simple traits. This study provides evidence that these two cultivars are isogenic or near isogenic and may have been derived from the same plant source.
Jianfeng Liu, Bowen Yang, Yuetong Ming, Yuchu Zhang, and Yunqing Cheng
desirable genetic attributes, including relative abundance, high polymorphism, codominant inheritance, transferability to related species and genera, and good genome coverage ( Guo et al., 2016 ). The expressed sequence tag (EST)-SSRs are widely used in the
Shuang Jiang, Haishan An, Xiaoqing Wang, Chunhui Shi, Jun Luo, and Yuanwen Teng
breeding technology, the breeding process can be accelerated by molecular maker-assisted selection ( Collard et al., 2005 ). SSRs, also known as microsatellites, are one of the most efficient genetic markers. An SSR refers to a DNA sequence 1 to 6 bp in
Xiaoying Li, Hongxia Xu, Jianjun Feng, and Junwei Chen
germplasm resources in genetic breeding, they must be evaluated and identified using efficient molecular methods. Microsatellites or SSR are 1- to 6-bp DNA regions repeated in tandem that are ubiquitous in both prokaryotes and eukaryotes ( Gao et al., 2013
Minou Hemmat, Susan K. Brown, and Norman F. Weeden
The genetic basis of resistance to apple scab [Venturia inaequalis (Cke.) Wint.] in the Russian apple seedling R12740-7A (Malus Mill. sp.) was investigated. Segregation ratios obtained in crosses with susceptible cultivars suggested that at least two genes were involved, and three foliar resistance reactions (chlorotic, stellate necrotic, and pit type) were observed after inoculation. DNA markers were identified for both the stellate necrotic (Vr) and pit type (no locus designation, Vx suggested) resistance phenotypes. Comparison of resistance phenotypes with marker segregation demonstrated that only two major dominant genes were present in R12740-7A, one producing the stellate necrotic lesion and the other the pit-type lesion. The chlorotic lesion could be attributed to either unclear expression of the resistance phenotype or to susceptible genotypes not contracting the disease. These markers along with a previously published marker for Vf were used to analyze inheritance of resistance in a Vr × Vf cross in advanced breeding material. The markers identified successfully all susceptible progeny, as well as apparent escapes and individuals possessing both Vf and Vr. Thus, the markers should be useful in future screening of segregating progeny and in the pyramiding of scab resistance genes in new cultivars.
Maria Susana Lopes, Duarte Mendonça, Kristina M. Sefc, Fabíola Sabino Gil, and Artur da Câmara Machado
A collection of 130 olive samples, originating from diverse areas in Europe and corresponding to 67 different cultivars denominations, was genotyped at 14 microsatellite loci. In total, 135 alleles with a mean number of 9.6 alleles per locus were detected. All but 30 accessions showed unique genotypes. Several cases of synonymy listed in the FAO database of olive germplasm could not be confirmed, as different allelic profiles were obtained from putatively synonymous cultivars. The existence of homonyms or mislabeled samples in olive germplasm collections was evidenced by allele differences of up to 60% between samples of the same denomination. An allele-sharing phenogram of the analyzed genotypes revealed several cultivars with high levels of intra-varietal polymorphism, as well as cultivar families consisting of closely related cultivars with similar denominations. Our work shows that the current designations of olive cultivars fall short of describing the genetic variability among economically important plant material. A thorough investigation of the existing variability will prove of major importance for both management and economic production of olive trees.
Summaira Riaz, Keith E. Garrison, Gerald S. Dangl, Jean-Michel Boursiquot, and Carole P. Meredith
In total, 25 clones of Vitis vinifera `Pinot noir' and 22 clones of `Chardonnay' were analyzed with 100 microsatellite markers, selected from an initial screening of 228 markers. Of the 100 markers, 17 detected polymorphism within one or both of the cultivars. In `Pinot noir', 15 polymorphic markers detected 15 different genotypes, uniquely distinguished 12 clones out of the 25 and separated the remaining 13 clones into 3 groups. In `Chardonnay', 9 polymorphic markers detected 9 genotypes and uniquely distinguished 6 clones out of the 22. The remaining 16 clones were separated into 3 groups. For markers that were polymorphic in `Pinot noir' and `Chardonnay', none of the variant alleles were common to both cultivars. It is inferred from this result that the natural cross that produced `Chardonnay' probably occurred when `Pinot' was still relatively young. Many of the variant genotypes were expressed as three alleles. Further analysis revealed the presence of chimeras in which the third allele was present in leaf but not root or wood tissues, confirming that the grape apical meristem is functionally two-layered. Some clones that share the same microsatellite genotype are documented to have originated in the same locality, suggesting that the origins of undocumented clones may be traced by comparing their microsatellite genotypes with those of well-documented clones. Because clones of `Pinot noir' and `Chardonnay' are often visually indistinguishable, microsatellite genotyping may also be useful to detect identification errors in collections and nurseries.