The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.
Gennaro Fazio, Yizhen Wan, Dariusz Kviklys, Leticia Romero, Richard Adams, David Strickland, and Terence Robinson
Jack E. Staub, Gennaro Fazio, Thomas Horejsi, Yael Danin-Poleg, Noa Reis, and Nurit Katzir
Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to characterize genetic relationships among 46 accessions in two C. melo L. subsp. melo (Cantalupensis, Inodorus) and subsp. agrestis (Conomon and Flexuosus) groups. Genetic distance (GD) estimates were made among and between accessions in four melon market classes [Galia, Ogen, Charentais, and Shipper (European and U.S. types)] of Cantalupensis, one market class of Inodorus (Cassaba and Honey Dew), one accession of Conomon, and one accession of Flexuosus by employing three GD estimators; simple matching coefficient, Jaccard's coefficient, and Nei's distance-D. Differences detected among 135 RAPD bands and 54 SSR bands (products of 17 SSR primers) were used to calculate GD. Band polymorphisms observed with 21 RAPD primers and 7 SSR primers was important in the detection of genetic differences. Estimators of GD were highly correlated (P > 0.0001; rs = 0.64 to 0.99) when comparisons were made between estimation methods within a particular marker system. Lower correlations (P > 0.001; rs = 0.17 to 0.40) were detected between marker systems using any one estimator. The GD of the Conomon and Flexuosus accessions was significantly different from the mean GD of all the market classes examined, and market classes were distinguishable from each other. Although lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs, the genetic relationships identified using these markers were generally similar. Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined.
Jack E. Staub, Fenny Dane, Kathleen Reitsma, Gennaro Fazio, and Anabel López-Sesé
Genetic relationships among 970 cucumber (Cucumis sativus L.) plant introductions (PIs) in the U.S. National Plant Germplasm System (NPGS) were assessed by observing variation at 15 isozyme loci. Allozyme frequency data for these PIs were compared to allozyme variation in heirloom and modern (H&M) cultivars released from 1846-1985 (H&M cultivars; 178 accessions), and experimental commercial (EC) germplasm (EC germplasm; 82 accessions) in use after 1985. Multivariate analysis defined four distinct groups of accessions (Groups A-D), where Group A consisted of PIs received by the NPGS before 1992, Group B contained PIs from India and China obtained by NPGS after 1992, Group C consisted of EC germplasm, and Group D contained H&M cultivars. Morphological, abiotic stress (water and heat stress tolerance) and disease resistance evaluation data from the Germplasm Resources Information Network (GRIN) for the PIs examined were used in conjunction with estimates of population variation and genetic distance estimates to construct test arrays and a core collection for cucumber. Disease resistance data included the evaluation of angular leafspot [Pseudomonas lachrymans (E.F. Smith) Holland], anthracnose [Colletotrichum lagenarium (Ross.) Ellis & Halst], downy mildew [Pseudoperonospora cubensis (Berk. & Curt) Rostow], rhizoctonia fruit rot (Rhizoctonia solani Kuhn), and target leafspot [Corynespora cassiicola (Berk. & Curt) Wei] pathogenicity. The test arrays for resistance-tolerance to angular leafspot, anthracnose, downy mildew, rhizoctonia fruit rot, target leafspot, and water and heat stress consisted of 17, 16, 17, 16, 17, 16, and 16 accessions, respectively. The core collection consisted of accessions in these test arrays (115) and additional 32 accessions that helped circumscribe the genetic diversity of the NPGS collection. The core collection of 147 accessions (115 + 32) represents ≈11% of the total collection's size (1352). Given estimates of genetic diversity and theoretical retention of diversity after sampling, this core collection could increase curatorial effectiveness and the efficiency of end-users as they attempt to identify potentially useful germplasm.
Renae E. Moran, Youping Sun, Fang Geng, Donglin Zhang, and Gennaro Fazio
Winter injury to the root systems of fruit trees can cause significant tree losses and yield reductions in the northern regions of the United States and Canada. To compare the root and trunk cold temperature tolerance, a series of experiments were conducted using ungrafted apple rootstocks. ‘Geneva® 11’ (G.11), ‘Geneva® 30’ (G.30), ‘Geneva® 41’ (G.41), ‘P.2’, and ‘Budagovsky 9’ (B.9) apple (Malus ×domestica Borkh.) rootstocks had root tissue hardiness similar to ‘M.26’, but ‘Geneva® 935’ (G.935) had greater cold-hardiness than M.26 when based on shoot regrowth in ungrafted trees. The LT50 of M.26 and P.2 roots ranged from –12 to –14 °C. The LT50 was –13 °C for B.9, –13.4 to –14.6 °C for G.30, and –12 °C for G.11. The LT50 of G.41 was one of the highest in one experiment, –8 °C, and one of the lowest in another, colder than –15.0 °C. The LT50 of G.935 roots was the lowest and ranged from –16 to –19 °C. Compared with M.26, trunk cold-hardiness in December was greater in B.9 and P.2 and was similar in G.30. Cold-hardiness of G.11 in December was mixed with less injury in the xylem but more injury in the phloem compared with M.26. In October, M.26 and G.935 trunks had little injury after exposure to –24 °C.
Briana L. Gross, Gayle M. Volk, Christopher M. Richards, Philip L. Forsline, Gennaro Fazio, and C. Thomas Chao
The U.S. Department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS), Plant Genetic Resources Unit apple (Malus) collection in Geneva, NY, conserves over 2500 trees as grafted clones. We have compared the genotypes of 1131 diploid Malus ×domestica cultivars with a total of 1910 wild and domesticated samples representing 41 taxonomic designations in the NPGS collection to identify those that are genetically identical based on nine simple sequence repeat (SSR) loci. We calculated the probability of identity for samples in the data set based on allelic diversity and, where possible, use fruit images to qualitatively confirm similarities. A total of 237 alleles were amplified and the nine SSRs were deemed adequate to assess duplication within the collection with the caveat that “sport families” likely would not be differentiated. A total of 238 M. ×domestica and 10 samples of other taxonomic groups shared a genotype with at least one other M. ×domestica individual. In several cases, genotypes for cultivars matched genotypes of known rootstocks and indicated that these accessions may not accurately represent the indicated named clones. Sets of individuals with identical genotypes and similar cultivar names were assigned to sport families. These 23 sport families, comprised of 104 individuals, may have mutational differences that were not identified using the nine SSR loci. Five of the selected markers (CH01h01, CH02d08, CH01f02, G12, GD147) overlap with sets of markers that have been used to fingerprint European apple collections, thus making it possible to compare and coordinate collection inventories on a worldwide scale.
Gemma Reig, Jaume Lordan, Stephen Hoying, Michael Fargione, Daniel J. Donahue, Poliana Francescatto, Dana Acimovic, Gennaro Fazio, and Terence Robinson
We conducted a large (0.8 ha) field experiment of system × rootstock, using Super Chief Delicious apple as cultivar at Yonder farm in Hudson, NY, between 2007 and 2017. In this study, we compared six Geneva® rootstocks (‘G.11’, ‘G.16’, ‘G.210’, ‘G.30’, ‘G.41’, and ‘G.935’) with one Budagovsky (‘B.118’) and three Malling rootstocks (‘M.7EMLA’, ‘M.9T337’ and ‘M.26EMLA’). Trees on each rootstock were trained to four high-density systems: Super Spindle (SS) (5382 apple trees/ha), Tall Spindle (TS) (3262 apple trees/ha), Triple Axis Spindle (TAS) (2243 apple trees/ha), and Vertical Axis (VA) (1656 apple trees/ha). Rootstock and training system interacted to influence growth, production, and fruit quality. When comparing systems, SS trees were the least vigorous but much more productive on a per hectare basis. Among the rootstocks we evaluated, ‘B.118’ had the largest trunk cross-sectional area (TCSA), followed by ‘G.30’ and ‘M.7EMLA’, which were similar in size but they did not differ statistically from ‘G.935’. ‘M.9T337’ was the smallest and was significantly smaller than most of the other rootstocks but it did not differ statistically from ‘G.11’, ‘G.16’, ‘G.210’, ‘G.41’, and ‘M.26EMLA’. Although ‘B.118’ trees were the largest, they had low productivity, whereas the second largest rootstock ‘G.30’ was the most productive on a per hectare basis. ‘M.9’ was the smallest rootstock and failed to adequately fill the space in all systems except the SS, and had low cumulative yield. The highest values for cumulative yield efficiency (CYE) were with ‘G.210’ for all training systems except for VA, where ‘M.9T337’ had the highest value. The lowest values were for all training systems with ‘B.118’ and ‘M.7EMLA’. Regardless of the training system, ‘M.7EMLA’ trees had the highest number of root suckers. Some fruit quality traits were affected by training system, rootstock or system × rootstock combination.
Briana L. Gross, Gayle M. Volk, Christopher M. Richards, Patrick A. Reeves, Adam D. Henk, Philip L. Forsline, Amy Szewc-McFadden, Gennaro Fazio, and C. Thomas Chao
The USDA-ARS National Plant Germplasm System Malus collection is maintained by the Plant Genetic Resources Unit (PGRU) in Geneva, NY. In the 1990s, a core subset of 258 trees was hand-selected to be representative of the grafted Malus collection. We used a combination of genotypic and phenotypic data to compare the diversity of the 198 diploid trees in the original core subset with that of 2114 diploid trees in the grafted field collection for which data were available. The 198 trees capture 192 of the 232 total microsatellite alleles and have 78 of the 95 phenotypic characters. An addition of 67 specific individuals increases the coverage to 100% of the allelic and phenotypic character states. Several de novo core sets that capture all the allelic and phenotypic character states in 100 individuals are also provided. Use of these proposed sets of individuals will help ensure that a broad range of Malus diversity is included in evaluations that use the core subset of grafted trees in the PGRU collection.