Pericentromeric heterochromatin in tomato contains a high frequency of repetitive DNA, primarily due to the presence of transposable elements. Repeated sequences prevent the placement of the unique oligonucleotide probes necessary for successful chromosome walking . The reference genome sequence of cultivated tomato may be helpful in overcoming this problem, because probes may be designed targeting nonrepetitive coding sequences interspersed within the pericentromeric heterochromatin. However, there is no publicly available genome sequence for S. habrochaites, and it is possible that the gene or genes underlying the QTL for resistance to P. infestans and horticultural traits within this region may be unique to S. habrochaites.The complex genetic architecture of P. infestans resistance and horticultural traits within the region of chromosome 11 from S. habrochaites presents both opportunities and challenges for breeding applications of the resistance QTL and useful horticultural trait QTL. Challenges include linkage and/or pleiotropy between P. infestans resistance QTL and horticultural trait QTL, the pericentromeric location of these QTL, and the presence of QTL · E for some traits. If unfavorable repulsion phase linkages of QTL are broken through recombination and recombinants are recovered, then the beneficial QTL alleles we have identified may prove useful for breeding tomato cultivars. In our study, we were able to separate some QTL alleles with negative effects from other desirable QTL alleles through recombination. However, because recombination is suppressed to less than 3% of the genome-wide average  within the marker interval TG147–At5g04590 , it is likely that large numbers of progeny will need to be screened to identify individuals with recombination between QTL within this region. In our present study, all loci with QTL · E have undesirable phenotypic effects when the S. habrochaites allele is present . If suitable environments and/or complementary genetic backgrounds for QTL deployment are identified,vertical farming hydroponic then negative effects may not preclude the use of the P. infestans resistance QTL linked to or pleiotropic to these horticultural QTL .

The two sub-NILs with the highest P. infestans resistance contained nonover lapping S. habrochaites introgressions, consistent with our prior findings of multiple QTL for resistance within the lb11b region . The level of resistance in these sub-NILs was comparable but their horticultural phenotypes differed, with 08GH8032 being significantly later maturing than E6203, whereas 08GH3999 was not. Sub-NIL 08GH8032 also had shorter and wider FS, whereas 08GH3999 had taller and narrower FS. Both lines suffered a significant reduction in 30Wt, but yield was not significantly reduced in either line compared with E6203. Sub-NIL 08GH3999 had the best combination of P. infestans resistance and horticultural trait phenotypes, and likely can be used directly as a donor line for MAS breeding to improve P. infestans resistance in tomato cultivars . 08GH3999 can also be used as a parent for pyramiding resistance QTL alleles in crosses with other QTL donor lines . Pyramiding of genes and QTL has been successful in many breeding efforts, including increasing barley stripe rust resistance , increasing barley yellow dwarf virus resistance , and improving rice yield and quality . Sub-NIL 08GH3999 could be crossed with selected sub-NILs containing late blight disease resistance QTL from chromosome 5 to combine resistance QTL from two chromosomes and potentially increase the level of quantitative resistance to P. infestans. Additional research would be required to isolate the P. infestans resistance QTL in 08GH8032 from the linked horticultural QTL through recombination before it will be useful for tomato cultivar improvement. Based on the marker genotype of 08GH8032, its wild species introgression spans the centromere , so this work may be difficult, possibly requiring testing of thousands of progeny to recover favorable recombinants. Even so, the estimated large physical size of the S. habrochaites introgression in 08GH8032 suggests that obtaining desirable recombinants will be possible. Collectively, our results suggest that the resistance QTL alleles from S. habrochaites will eventually be useful for improving quantitative resistance to P. infestans in cultivated tomato.The cottontail rabbit has been identified by nursery growers as the primary cause of damage to irrigation systems and plants, causing economic loss to ornamental tree nurseries in southern California through vegetation destruction and chewing of drip irrigation lines.

This damage can be recognized by characteristic 45°-angle cuts to the spaghetti irrigation tubing, similar to rabbit damage on browsed twigs . One large commercial tree nursery in San Diego County reported more than $10,000 annually in costs due to plant loss, plus at least $12,000 for labor and materials to repair irrigation lines. Damage to plants from rabbit feeding and from water stress due to damaged irrigation lines has not been determined, but these are believed to be significant. Cottontails in California are believed to have a life span of 12-15 months. They can have up to 6 litters per year, with a litter size of 3-4 offspring . In the western U.S., natural predators of cottontails are mountain lion, coyote, weasel, gray fox, badger, bobcat, raccoon, skunk, mink, kit fox, red-tailed hawk, Cooper’s hawk, Swainson’s hawk, golden eagle, great horned owl, gopher snake, and rattlesnakes . The cottontail has evolved to survive the heat extremes of the southwest U.S., and it has a remarkable adaptability to feed on a variety of plants depending on seasonal availability . Cottontails are known to regularly travel 30 m or more from cover , have foraging areas with a diameter of 213 m , and have been observed to travel 1,006 m from the point of capture . While one strategy to reduce damage from brush rabbits is to establish buffer zones of cleared space between natural areas and resources needing protection , given the large distances that cottontails will venture from cover to find feed, it is unreasonable to expect such habitat modifications will effectively reduce cottontail damage. Cottontail rabbits are legally classified as game animals, and surveys of game hunting licensees by the California Department of Fish and Game document rabbit take in several California counties . Cottontail control with anticoagulant bait was conducted from the mid-1990s thru 2004 in Orange County California, but that use was temporarily discontinued pending a legal review. A recent opinion by the California Attorney General allows the use of anticoagulant bait to take cottontail rabbits that are causing damage to crops or property . CDFG Code Section 4186 allows landowners or their agents to take cottontails when damage to crops or forage is observed. Little is documented about the actual impact to nursery production caused by rabbit damage, or the types of growing practices that make a nursery crop most vulnerable to damage.

There has been little research directed towards addressing the specific needs of container nursery production suffering rabbit damage. Experience has shown that damage by cottontail rabbits can be minimized by exclusion with 3-foot-tall fences secured tightly to the ground, allowing no means for rabbits to go under the fence . Although effective in a large nursery,vertical planters for vegetables fencing is expensive to install and maintain . Additionally, we observed that fencing interferes with the constant foot and machinery traffic that occurs during plant production. Fencing to prevent rabbit intrusion may be practical when the product has high monetary value and likelihood of damage .Most studies on habitat manipulation focus on enhancing populations for harvest purposes . However, a nursery may be able to apply those lessons to manipulate rabbit habitat to reduce populations and damage. To better understand the biology and ecology of rabbits in container nurseries, we studied rabbits in a commercial nursery to determine the characteristics of nursery production and their relationship to rabbit occurrence and damage. We tested methods to reduce damage to irrigation systems and exclude rabbits from crops. We also evaluated trapping strategies and made observations to determine rabbit habitat preference. The final objective was to define some feasible options that could be used by container nurseries for rabbit damage management. We found that most of the rabbit damage to irrigation was associated with drip irrigation using 0.64-cm spaghetti tubing and 68-L containers planted at high density. Beds with hanging drip lines or 1.9-cm tubing were seen to have less damage . Therefore, two studies were conducted to evaluate irrigation line covers to protect the 0.64 cm diameter spaghetti tubing. The first study tested various types of covers 46 cm in length and included PVC pipe, recycled black poly hose, clear vinyl tubing, vinyl hose, and duct tape. All types of covers reduced rabbit cutting of the tubing in comparison to the control. Covers using recycled 1.9-cm -diameter poly hose were easiest to install over the spaghetti tubing and may be the most economical, if they are reused. The second study used irrigation line covers 61 cm in length, made of 1.9-cm diameter poly hose. We measured a 96% decrease in damage waypoints, from an initial 27 waypoints to 1 damage waypoint . Black silt fence was evaluated as alternative exclusionary fence to the poultry fence normally recommended for rabbits. The advantage of this type of fence is its ease of installation and removal. The 76-cm -height silt fencing is a black fabric cloth with built-in wooden posts at 4.6-m intervals, which may be purchased at most hardware stores for the purpose of erosion control. In an observational study, 274 m of silt fence, installed with supplemental posts and soil covering the bottom flap, was used to closely encircle a bed containing rabbit-damaged jasmine in 1-gal pots.

No ill effects were observed due to the black plastic retaining heat or blocking airflow to the plants. The results of this demonstration plot indicate that silt fence was an excellent temporary exclusionary fence, preventing further rabbit damage. However, it should be recognized that exclusionary fencing is not practical in many situations, because it hinders normal nursery operations such as moving stock or getting equipment into the area. As part of the experimental trapping program at the nursery, one strategy was to use the black silt fencing as a drift fence in conjunction with trapping. The fence was placed in natural areas adjacent to production areas in the nursery, because rabbits were suspected of living in the natural areas and traveling to the planting beds. Doorways 0.3 – 0.9 m wide in the drift fence were monitored with Trailmaster™ infrared trail monitors and night photography to confirm that rabbits were being conditioned to use the drift fence and doorways. Once the rabbits were conditioned to the fence, #110 conibear traps and squirrel live traps 48 × 15 × 15 cm were set in the doorways, along the paths near the fence, and at paths at the end of the fence. The catch rates were 11-13% for trapping in conjunction with the drift fence . Where no fence was present to direct the rabbits into the trap, such as live traps set between containers in a growing bed, the trapping success was reduced to 3% . Rabbits continue to be an economic burden to nursery growers in southern California. Given the biology of cottontails with their dietary adaptability, variable range of movement, and their need for cover close to food sources, the typical nursery environment provides cottontails an optimal environment for high survivability and reproduction. In addition, nursery operations in southern California are in multi-use areas usually interspersed among residential neighborhoods, making some means of control such as use of firearms in conflict with city ordinances. Furthermore, nursery operations are usually limited to daylight operating hours, leaving the rabbits undisturbed during their most active crepuscular hours of dawn and dusk. Although our study nursery had natural and domestic cottontail predators , these predators appeared unable to control cottontail numbers, given the advantages for the cottontail in the nursery environment. We recommended that the nursery make ongoing efforts, as materials and time permit, to protect their business from rabbit damage. The efforts should include fencing or tabling potted plants known to be at high risk for rabbit browsing. Silt fence represents a flexible and easy-to-install method of exclusionary fencing in addition to the traditional use of chicken wire/poultry netting for those plantings of high value or that sustain heavy damage.