Mark Coggeshall | University of Missouri Columbia (original) (raw)

Papers by Mark Coggeshall

Information about the flood tolerance of most plants has been obtained from either observations f... more Information about the flood tolerance of most plants has been obtained from either observations following natural floods or pot studies with amended soils. To better evaluate and compare flood tolerance among hardwood seedlings and ground covers for use in riparian buffer and bottomland plantings, a large outdoor facility with natural floodplain soils is needed where flood timing, depth, flow, and duration can be controlled and replicated. In 1999, the University of Missouri Center for Agroforestry constructed a field facility at the Horticulture and Agroforestry Research Center on the floodplain adjacent to Sulphur Creek. Using soil excavated to create a retention pond, 6-m wide by 2-m high berms were constructed on the original floodplain soil with minimal disturbance to soils within twelve parallel 6-m wide x 180-m long channels. Water from the retention pond can be pumped independently into each channel to control timing, depth, and duration of either standing or flowing water. First year survival of spring planted seedlings of black walnut (Juglans nigra L.) in the control channels has continued to increase each year with annual modifications to lower the high water table caused by seepage and improved post-flood draining of channels. On-going studies include evaluating genotypic variation in response to flooding within hardwood species and seedling flood tolerance among hardwood species and forage crops.

Applications in Plant Sciences, Dec 1, 2013

BMC Genomics, May 30, 2017

Background: Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly... more Background: Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage. Results: Our sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1. 8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×. Conclusions: The ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data.

Genetic Resources and Crop Evolution, Nov 22, 2012

New Forests, Apr 24, 2012

Molecular markers have been used in several walnut species to help reconstruct breeding program p... more Molecular markers have been used in several walnut species to help reconstruct breeding program pedigrees, to characterize genetic structure in natural Juglans populations, to determine the impact of different timber harvest scenarios on residual levels of genetic diversity, and to quantify the effects of interspecific hybridization on subsequent reproduction success. Pijut et al. (2007) reviewed technological applications of molecular markers used on several temperate hardwood tree species. Modern genomics-based tools are currently being used in several black walnut (J. nigra) studies.

Tree Genetics & Genomes, Dec 17, 2022

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in Nort... more Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F 1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia "Chandler" V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

G3: Genes, Genomes, Genetics

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree nat... more Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfam...

Butternut (Juglans cinerea), a native riparian forest tree, has suffered significant decline thro... more Butternut (Juglans cinerea), a native riparian forest tree, has suffered significant decline throughout most of its range due to a fatal fungal disease, butternut canker (caused by Sirococcus clavigignenti-juglandacearum). It has also been subject to natural hybridization pressures from Japanese walnut (J. ailantifolia), first introduced to North America ~1850. Butternut is now listed as a “species of concern” in Canada and similarly classified in several states of the United States. Previous experience indicates site-related shifts in fitness for Japanese walnut × butternut hybrids compared to “pure” butternuts. The presence of at least putative “tolerance” to butternut canker in some butternuts resulted in the establishment of a multi-state effort to restore this species by establishing a series of ex situ germplasm collections in the northeastern United States. Both nuclear and chloroplast markers developed at the University of Notre Dame were used to define the hybrid status of ...

Annals of Forest Research, 2017

Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (G... more Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (Gleditsia triacanthos) using Illumina transcriptome and low-coverage genome sequencing. A diversity panel of 40 honeylocust samples covering large parts of the species distribution range was characterized. As expected the level of genetic variation was lower in EST-SSRs than for non-genic genomic SSRs. This is the first report of EST-SSRs for honeylocust. All markers are polymorphic and produce clear single locus amplification products and can be used for genetic diversity and gene flow analyses. The transcriptome sequencing data provide a rich resource for new marker development.

PLOS ONE, 2018

Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders ha... more Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders have historically utilized only open-pollinated half-sib families. An alternate approach called "breeding without breeding," consists of genotyping open-pollinated progeny using DNA markers to identify paternal parents and then constructing full-sib families. In 2014, we used 12 SSR markers to genotype 884 open-pollinated half-sib progeny harvested from two clonal orchards containing 206 trees, comprised of 52 elite timber selections. Seed was harvested in 2011 from each of two ramets of 23 clones, one upwind and one downwind, based on prevailing wind direction from the west-southwest. One orchard was isolated from wild black walnut and composed of forward selections while the other orchard was adjacent to a natural forest containing mature black walnut composed of backward selections. Isolation significantly increased within-orchard pollination (85%) of the progeny from the isolated orchard compared to 42% from the non-isolated orchard. Neither prevailing wind direction nor seed tree position in the orchard affected paternity patterns or wild pollen contamination. Genetic diversity indices revealed that progeny from both orchards were in Hardy-Weinberg equilibrium with very little inbreeding and no selfing. A significant level of inbreeding was present among the forward selected parents, but not the first generation (backward selected) parents. Some orchard clones failed to sire any progeny while other clones pollinated upwards of 20% of progeny.

Canadian Journal of Plant Science, Jun 1, 2018

Black walnut (Juglans nigra L.), a large tree native throughout the eastern United States, produc... more Black walnut (Juglans nigra L.), a large tree native throughout the eastern United States, produces a highquality edible nut. Our goal was to maintain the integrity of black walnut breeding programs by verifying the identity of accessions. We sampled 285 ramets of 78 cultivars from the black walnut nut breeding orchards and clonal repositories at the University of Missouri and Kansas State University. We employed both phenotypic and genotypic methods to identify and differentiate cultivars. Phenotypes were evaluated using seven phenological traits. Cultivars varied for all traits among each of the 4 yr, but the best morphological characteristics for evaluating cultivar identity were bud break date and date of first pistillate bloom. Samples (n = 285) were genotyped using 10 polymorphic microsatellite loci. The simple sequence repeats produced a total of 174 alleles and 17.2 alleles per locus. We detected 47 unique genotypes represented by more than one sample, including 128 instances of identical genotypes with different names (synonyms) and 106 instances of different genotypes with a shared name (homonyms). Our results indicated that multiple errors were committed during the propagation of these important cultivars. It may be difficult to determine which genotype is original to a cultivar name in the absence of a foundation plant materials collection or vouchered specimens. These results will assist black walnut breeders and producers by improving the integrity of breeding collections and by identifying the best phenological traits for rapid assessment of trueness to type.

John Wiley & Sons, Inc. eBooks, Jan 26, 2018

Biological Invasions, Mar 1, 2018

Biological invasions by insects that vector plant pathogens have altered the composition of natur... more Biological invasions by insects that vector plant pathogens have altered the composition of natural and urban forests. Thousand cankers disease is a new, recent example and is caused by the complex of walnut twig beetle, Pityophthorus juglandis, and the fungus, Geosmithia morbida, on susceptible hosts, notably some Juglans spp. and Pterocarya spp. Host colonization by P. juglandis may be particularly important for disease development, but the beetle's host range is not known. In the United States and Italy, this insect has expanded its geographic range by colonizing naïve hosts. The objective of this study was to characterize limits to, and variation within, the host range of P. juglandis and infer the extent to which hosts might constrain the geographic distribution of the insect. We examined colonization and reproduction by P. juglandis in no-choice laboratory experiments with 11 Juglans spp., one Pterocarya sp., and two Carya spp. over 2 years and found that all but the Carya spp. were hosts. Reproduction was generally greater on Juglans californica,

Acta horticulturae, Apr 1, 2010

Black walnuts (Juglans nigra L.) are valued for their uniquely fruity flavor and are often used a... more Black walnuts (Juglans nigra L.) are valued for their uniquely fruity flavor and are often used as an ingredient in baked goods and ice cream, or are eaten as a snack food. Although black walnuts can be harvested from wild trees, several cultivars have been selected for such characteristics as ease of cracking, size of kernel, and thickness of husks and shells. Other characteristics, such as date of bud break, time of flowering, length of season and date of harvest, are also important adaptive traits as there is considerable variation within the species. The University of Missouri Horticulture and Agroforestry Research Center (HARC) maintains a repository of more than 65 named cultivars of black walnut valued for their kernels. The identities of each of these cultivars have been confirmed by "fingerprinting", using a series of ten single sequence repeat microsatellite markers. A subset of cultivars maintained in the repository is used in an applied breeding program focusing on nut improvement. Average date of bud break, flower type, bloom period, pollination date, nut season length, and harvest date of cultivars were recorded from 2002 to 2006 at HARC. Such information offers a valuable resource to other breeders and producers in the identification of specific black walnut traits.

Annals of forest science, Aug 23, 2021

Key message Quercus rubra half sib progenies (N = 93) expressed high levels of variance for both ... more Key message Quercus rubra half sib progenies (N = 93) expressed high levels of variance for both growth and stem form traits in three locations in Indiana, USA at age 11 or 12. Height, diameter, and volume were measured and sweep, branch angle, forking, and branch retention were rated using a (+ / −) system. Families selected for volume showed no unfavorable increases in sweep or branch angle and only a slight increase in branch retention. Context Northern red oak (Quercus rubra L.) is the most planted hardwood in the central USA. Red oak seeds from sources with improved growth and form are unavailable in the Central Hardwood Region, in part because the absence of agreed methods for stem form evaluation diminishes the effectiveness of selection. Aims To identify red oak families improved for growth and to determine if a simple + / − rating system could identify red oak families with improved form. Methods We evaluated 93 open-pollinated families of 11 or 12-year-old red oak growing in three sites in central Indiana (USA) for height, diameter, volume, and four traits rated as + / − : sweep, branch angle, forking, and branch retention. Results Family × location effects were significant for all quantitative traits but not for any binary traits; differences among families were significant for all traits at all sites. Heritabilities for most traits were high. Selection of the top 20 families for volume at each site resulted in no change in population means for sweep or branch angle and only a small increase in the retention of large limbs. Conclusion A + / − rating system to evaluate hardwood form can help breeders deliver improved red oak to landowners when more complex systems are impractical.

Walnut is a unique species in both its timber and wood characteristics. Although market condition... more Walnut is a unique species in both its timber and wood characteristics. Although market conditions vary it is generally considered a valuable species. Because of these factors, setting quality (value) levels for both lumber and veneer can be involved. Lumber grades are quantitative thus straight forward once the system is understood. Determining quality in veneer is much more subjective. This paper will discuss important factors related to quality in both lumber and veneer. Landowners, foresters, researchers, and others concerned with the production of walnut timber for lumber and veneer should consider these factors before proceeding with their work.

Acta horticulturae, Apr 1, 2010

An applied breeding program focused on the improvement of eastern black walnut (Juglans nigra) fo... more An applied breeding program focused on the improvement of eastern black walnut (Juglans nigra) for edible nut production was initiated at the University of Missouri in 1996. Eighty four cultivars were grown as 158 trees in three replicated clonal repositories. Beginning in 2003, the collection was characterized using seven phenological descriptors: date of budbreak, first pistillate bloom, peak pistillate bloom, first pollen shed, peak pollen shed, nut harvest date and season length. In 2004, all trees were further characterized using 10 microsatellite markers. Genetic fingerprinting showed that the collection contained 57 cultivars rather than the expected 84, which we attribute to past propagation errors. Fingerprinting results generally agreed with the phenological data. The utility of phenological data for discriminating genotypes was affected by specific descriptor and tree size. First pistillate bloom, first pollen shed and season length calculated on a date basis had the smallest coefficients of variation for the seven phenological descriptors used in this study. INTRODUCTION An eastern black walnut (Juglans nigra L.) breeding program was initiated by the University of Missouri Center for Agroforestry in 1996. The long-term goal of this breeding program is to develop improved black walnut cultivars for new agroforestrybased plantings in Missouri that possess improved nut yield, nut and kernel quality characteristics, and resistance to anthracnose caused by Gnomonia leptostyla (Fr.) Ces. and de N. (Reid et al., 2004). Defining the levels of genetic variation associated with commercially important traits for this species was initiated in 2003 with the assessment of all nut cultivars using morphological and phenological descriptors. Numeric descriptor values originally developed for Persian walnut (J. regia L.) (IPGRI, 1994) have been utilized for an array of commercially important traits in black walnut including: disease tolerance, nut yield, precocity, bearing habit, season length, annual vs. alternate bearing and flowering phenology among others. In addition, important nut characteristics specific to black walnut including husk thickness, shell thickness, percent kernel, kernel color and ease of extraction have been assessed since 2005. It is anticipated that controlled crosses of specific parents in an applied breeding program will result in development of new intraspecific hybrids that exhibit desirable characteristics of both selected parents. Several phenological traits in Persian walnut exhibit heritabilities greater than 0.80, including leafing date, first pollen shed date, first pistil receptivity date and harvest date (Hansche et al., 1972). As a consequence, the pace of genetic improvement of these traits through an applied breeding program should be fairly rapid. Further, any environmental effects on phenotypic expression of such traits should be minimal, which suggests that they could be employed as an efficient assessment tool for delineating differences among specific cultivars. Unfortunately, heritability estimates are not yet available for commercially important phenological and morphological traits in eastern black walnut. However, previous work suggests that this species exhibits significant levels of genetic variation for many traits of interest (

Information about the flood tolerance of most plants has been obtained from either observations f... more Information about the flood tolerance of most plants has been obtained from either observations following natural floods or pot studies with amended soils. To better evaluate and compare flood tolerance among hardwood seedlings and ground covers for use in riparian buffer and bottomland plantings, a large outdoor facility with natural floodplain soils is needed where flood timing, depth, flow, and duration can be controlled and replicated. In 1999, the University of Missouri Center for Agroforestry constructed a field facility at the Horticulture and Agroforestry Research Center on the floodplain adjacent to Sulphur Creek. Using soil excavated to create a retention pond, 6-m wide by 2-m high berms were constructed on the original floodplain soil with minimal disturbance to soils within twelve parallel 6-m wide x 180-m long channels. Water from the retention pond can be pumped independently into each channel to control timing, depth, and duration of either standing or flowing water. First year survival of spring planted seedlings of black walnut (Juglans nigra L.) in the control channels has continued to increase each year with annual modifications to lower the high water table caused by seepage and improved post-flood draining of channels. On-going studies include evaluating genotypic variation in response to flooding within hardwood species and seedling flood tolerance among hardwood species and forage crops.

Applications in Plant Sciences, Dec 1, 2013

BMC Genomics, May 30, 2017

Background: Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly... more Background: Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage. Results: Our sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1. 8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×. Conclusions: The ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data.

Genetic Resources and Crop Evolution, Nov 22, 2012

New Forests, Apr 24, 2012

Molecular markers have been used in several walnut species to help reconstruct breeding program p... more Molecular markers have been used in several walnut species to help reconstruct breeding program pedigrees, to characterize genetic structure in natural Juglans populations, to determine the impact of different timber harvest scenarios on residual levels of genetic diversity, and to quantify the effects of interspecific hybridization on subsequent reproduction success. Pijut et al. (2007) reviewed technological applications of molecular markers used on several temperate hardwood tree species. Modern genomics-based tools are currently being used in several black walnut (J. nigra) studies.

Tree Genetics & Genomes, Dec 17, 2022

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in Nort... more Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F 1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia "Chandler" V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

G3: Genes, Genomes, Genetics

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree nat... more Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfam...

Butternut (Juglans cinerea), a native riparian forest tree, has suffered significant decline thro... more Butternut (Juglans cinerea), a native riparian forest tree, has suffered significant decline throughout most of its range due to a fatal fungal disease, butternut canker (caused by Sirococcus clavigignenti-juglandacearum). It has also been subject to natural hybridization pressures from Japanese walnut (J. ailantifolia), first introduced to North America ~1850. Butternut is now listed as a “species of concern” in Canada and similarly classified in several states of the United States. Previous experience indicates site-related shifts in fitness for Japanese walnut × butternut hybrids compared to “pure” butternuts. The presence of at least putative “tolerance” to butternut canker in some butternuts resulted in the establishment of a multi-state effort to restore this species by establishing a series of ex situ germplasm collections in the northeastern United States. Both nuclear and chloroplast markers developed at the University of Notre Dame were used to define the hybrid status of ...

Annals of Forest Research, 2017

Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (G... more Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (Gleditsia triacanthos) using Illumina transcriptome and low-coverage genome sequencing. A diversity panel of 40 honeylocust samples covering large parts of the species distribution range was characterized. As expected the level of genetic variation was lower in EST-SSRs than for non-genic genomic SSRs. This is the first report of EST-SSRs for honeylocust. All markers are polymorphic and produce clear single locus amplification products and can be used for genetic diversity and gene flow analyses. The transcriptome sequencing data provide a rich resource for new marker development.

PLOS ONE, 2018

Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders ha... more Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders have historically utilized only open-pollinated half-sib families. An alternate approach called "breeding without breeding," consists of genotyping open-pollinated progeny using DNA markers to identify paternal parents and then constructing full-sib families. In 2014, we used 12 SSR markers to genotype 884 open-pollinated half-sib progeny harvested from two clonal orchards containing 206 trees, comprised of 52 elite timber selections. Seed was harvested in 2011 from each of two ramets of 23 clones, one upwind and one downwind, based on prevailing wind direction from the west-southwest. One orchard was isolated from wild black walnut and composed of forward selections while the other orchard was adjacent to a natural forest containing mature black walnut composed of backward selections. Isolation significantly increased within-orchard pollination (85%) of the progeny from the isolated orchard compared to 42% from the non-isolated orchard. Neither prevailing wind direction nor seed tree position in the orchard affected paternity patterns or wild pollen contamination. Genetic diversity indices revealed that progeny from both orchards were in Hardy-Weinberg equilibrium with very little inbreeding and no selfing. A significant level of inbreeding was present among the forward selected parents, but not the first generation (backward selected) parents. Some orchard clones failed to sire any progeny while other clones pollinated upwards of 20% of progeny.

Canadian Journal of Plant Science, Jun 1, 2018

Black walnut (Juglans nigra L.), a large tree native throughout the eastern United States, produc... more Black walnut (Juglans nigra L.), a large tree native throughout the eastern United States, produces a highquality edible nut. Our goal was to maintain the integrity of black walnut breeding programs by verifying the identity of accessions. We sampled 285 ramets of 78 cultivars from the black walnut nut breeding orchards and clonal repositories at the University of Missouri and Kansas State University. We employed both phenotypic and genotypic methods to identify and differentiate cultivars. Phenotypes were evaluated using seven phenological traits. Cultivars varied for all traits among each of the 4 yr, but the best morphological characteristics for evaluating cultivar identity were bud break date and date of first pistillate bloom. Samples (n = 285) were genotyped using 10 polymorphic microsatellite loci. The simple sequence repeats produced a total of 174 alleles and 17.2 alleles per locus. We detected 47 unique genotypes represented by more than one sample, including 128 instances of identical genotypes with different names (synonyms) and 106 instances of different genotypes with a shared name (homonyms). Our results indicated that multiple errors were committed during the propagation of these important cultivars. It may be difficult to determine which genotype is original to a cultivar name in the absence of a foundation plant materials collection or vouchered specimens. These results will assist black walnut breeders and producers by improving the integrity of breeding collections and by identifying the best phenological traits for rapid assessment of trueness to type.

John Wiley & Sons, Inc. eBooks, Jan 26, 2018

Biological Invasions, Mar 1, 2018

Biological invasions by insects that vector plant pathogens have altered the composition of natur... more Biological invasions by insects that vector plant pathogens have altered the composition of natural and urban forests. Thousand cankers disease is a new, recent example and is caused by the complex of walnut twig beetle, Pityophthorus juglandis, and the fungus, Geosmithia morbida, on susceptible hosts, notably some Juglans spp. and Pterocarya spp. Host colonization by P. juglandis may be particularly important for disease development, but the beetle's host range is not known. In the United States and Italy, this insect has expanded its geographic range by colonizing naïve hosts. The objective of this study was to characterize limits to, and variation within, the host range of P. juglandis and infer the extent to which hosts might constrain the geographic distribution of the insect. We examined colonization and reproduction by P. juglandis in no-choice laboratory experiments with 11 Juglans spp., one Pterocarya sp., and two Carya spp. over 2 years and found that all but the Carya spp. were hosts. Reproduction was generally greater on Juglans californica,

Acta horticulturae, Apr 1, 2010

Black walnuts (Juglans nigra L.) are valued for their uniquely fruity flavor and are often used a... more Black walnuts (Juglans nigra L.) are valued for their uniquely fruity flavor and are often used as an ingredient in baked goods and ice cream, or are eaten as a snack food. Although black walnuts can be harvested from wild trees, several cultivars have been selected for such characteristics as ease of cracking, size of kernel, and thickness of husks and shells. Other characteristics, such as date of bud break, time of flowering, length of season and date of harvest, are also important adaptive traits as there is considerable variation within the species. The University of Missouri Horticulture and Agroforestry Research Center (HARC) maintains a repository of more than 65 named cultivars of black walnut valued for their kernels. The identities of each of these cultivars have been confirmed by "fingerprinting", using a series of ten single sequence repeat microsatellite markers. A subset of cultivars maintained in the repository is used in an applied breeding program focusing on nut improvement. Average date of bud break, flower type, bloom period, pollination date, nut season length, and harvest date of cultivars were recorded from 2002 to 2006 at HARC. Such information offers a valuable resource to other breeders and producers in the identification of specific black walnut traits.

Annals of forest science, Aug 23, 2021

Key message Quercus rubra half sib progenies (N = 93) expressed high levels of variance for both ... more Key message Quercus rubra half sib progenies (N = 93) expressed high levels of variance for both growth and stem form traits in three locations in Indiana, USA at age 11 or 12. Height, diameter, and volume were measured and sweep, branch angle, forking, and branch retention were rated using a (+ / −) system. Families selected for volume showed no unfavorable increases in sweep or branch angle and only a slight increase in branch retention. Context Northern red oak (Quercus rubra L.) is the most planted hardwood in the central USA. Red oak seeds from sources with improved growth and form are unavailable in the Central Hardwood Region, in part because the absence of agreed methods for stem form evaluation diminishes the effectiveness of selection. Aims To identify red oak families improved for growth and to determine if a simple + / − rating system could identify red oak families with improved form. Methods We evaluated 93 open-pollinated families of 11 or 12-year-old red oak growing in three sites in central Indiana (USA) for height, diameter, volume, and four traits rated as + / − : sweep, branch angle, forking, and branch retention. Results Family × location effects were significant for all quantitative traits but not for any binary traits; differences among families were significant for all traits at all sites. Heritabilities for most traits were high. Selection of the top 20 families for volume at each site resulted in no change in population means for sweep or branch angle and only a small increase in the retention of large limbs. Conclusion A + / − rating system to evaluate hardwood form can help breeders deliver improved red oak to landowners when more complex systems are impractical.

Walnut is a unique species in both its timber and wood characteristics. Although market condition... more Walnut is a unique species in both its timber and wood characteristics. Although market conditions vary it is generally considered a valuable species. Because of these factors, setting quality (value) levels for both lumber and veneer can be involved. Lumber grades are quantitative thus straight forward once the system is understood. Determining quality in veneer is much more subjective. This paper will discuss important factors related to quality in both lumber and veneer. Landowners, foresters, researchers, and others concerned with the production of walnut timber for lumber and veneer should consider these factors before proceeding with their work.

Acta horticulturae, Apr 1, 2010

An applied breeding program focused on the improvement of eastern black walnut (Juglans nigra) fo... more An applied breeding program focused on the improvement of eastern black walnut (Juglans nigra) for edible nut production was initiated at the University of Missouri in 1996. Eighty four cultivars were grown as 158 trees in three replicated clonal repositories. Beginning in 2003, the collection was characterized using seven phenological descriptors: date of budbreak, first pistillate bloom, peak pistillate bloom, first pollen shed, peak pollen shed, nut harvest date and season length. In 2004, all trees were further characterized using 10 microsatellite markers. Genetic fingerprinting showed that the collection contained 57 cultivars rather than the expected 84, which we attribute to past propagation errors. Fingerprinting results generally agreed with the phenological data. The utility of phenological data for discriminating genotypes was affected by specific descriptor and tree size. First pistillate bloom, first pollen shed and season length calculated on a date basis had the smallest coefficients of variation for the seven phenological descriptors used in this study. INTRODUCTION An eastern black walnut (Juglans nigra L.) breeding program was initiated by the University of Missouri Center for Agroforestry in 1996. The long-term goal of this breeding program is to develop improved black walnut cultivars for new agroforestrybased plantings in Missouri that possess improved nut yield, nut and kernel quality characteristics, and resistance to anthracnose caused by Gnomonia leptostyla (Fr.) Ces. and de N. (Reid et al., 2004). Defining the levels of genetic variation associated with commercially important traits for this species was initiated in 2003 with the assessment of all nut cultivars using morphological and phenological descriptors. Numeric descriptor values originally developed for Persian walnut (J. regia L.) (IPGRI, 1994) have been utilized for an array of commercially important traits in black walnut including: disease tolerance, nut yield, precocity, bearing habit, season length, annual vs. alternate bearing and flowering phenology among others. In addition, important nut characteristics specific to black walnut including husk thickness, shell thickness, percent kernel, kernel color and ease of extraction have been assessed since 2005. It is anticipated that controlled crosses of specific parents in an applied breeding program will result in development of new intraspecific hybrids that exhibit desirable characteristics of both selected parents. Several phenological traits in Persian walnut exhibit heritabilities greater than 0.80, including leafing date, first pollen shed date, first pistil receptivity date and harvest date (Hansche et al., 1972). As a consequence, the pace of genetic improvement of these traits through an applied breeding program should be fairly rapid. Further, any environmental effects on phenotypic expression of such traits should be minimal, which suggests that they could be employed as an efficient assessment tool for delineating differences among specific cultivars. Unfortunately, heritability estimates are not yet available for commercially important phenological and morphological traits in eastern black walnut. However, previous work suggests that this species exhibits significant levels of genetic variation for many traits of interest (