Identification of quantitative trait loci influencing annual height- and diameter-increment growth in loblolly pine (Pinus taeda L.)

 Quantitative trait loci (QTLs) for annual height- and diameter-increment growth were estimated in each of two three-generation loblolly pine pedigrees. Annual height-increment was measured in three consecutive years in the BASE pedigree and in four consecutive years in the QTL pedigree. Annual diameter-increment was measured only in the QTL pedigree for two consecutive years. An interval mapping-approach was used to estimate the number of QTLs, the magnitude of QTL effects, and their position on genetic linkage maps. Thirteen different height-increment and eight different diameter-increment QTLs were detected, suggesting that the these traits are, at least in part, controlled by a few genes of large effect. Little evidence was found for the expression of individual QTLs in multiple years or in multiple genetic backgrounds. These results were discussed in terms of the power of the experiment and their consequences for marker-assisted breeding. Received: 12 July 1998/Accepted: 5 August 1998     

Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones

 We report a strategy for developing codominant PCR-based genetic markers by using sequenced cDNA clones from loblolly pine (Pinus taeda L.). These clones were previously used as probes for detecting restriction fragment length polymorphisms (RFLPs) to generate linkage maps. After assessing the complexity of banding patterns from Southern blots, we selected clones representing relatively simple gene families, and then determined nucleotide sequences for about 200 bp at each end of the cDNA inserts. Specific PCR primers were designed to amplify samples of genomic DNA derived from two loblolly pine mapping populations. Polymorphisms were detected after digesting the amplified DNA fragments with a battery of restriction endonucleases, and most polymorphisms were inherited in a Mendelian fashion. These newly identified genetic markers are codominant and relatively simple to use. By assaying DNA from individuals used to construct RFLP maps, we show that most of these markers map to the same position as the RFLP loci detected using their corresponding cDNAs as probes, implying that these markers have been converted from RFLP to PCR-based methods. These PCR-based markers will be useful for genome mapping and population genetics. Received: 10 February 1998 / Accepted: 25 February 1998     

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

The development and application of genomic tools to loblolly pine (Pinus taeda L.) offer promising insights into the organization and structure of conifer genomes. The application of a high-throughput genotyping assay across diverse forest tree species, however, is currently limited taxonomically. This is despite the ongoing development of genome-scale projects aiming at the construction of expressed sequence tag (EST) libraries and the resequencing of EST-derived unigenes for a diverse array of forest tree species. In this paper, we report on the application of Illumina’s high-throughput GoldenGate™ SNP genotyping assay to a loblolly pine mapping population. Single nucleotide polymorphisms (SNPs) were identified through resequencing of previously identified wood quality, drought tolerance, and disease resistance candidate genes prior to genotyping. From that effort, a 384 multiplexed SNP assay was developed for high-throughput genotyping. Approximately 67% of the 384 SNPs queried converted into high-quality genotypes for the 48 progeny samples. Of those 257 successfully genotyped SNPs, 70 were segregating within the mapping population. A total of 27 candidate genes were subsequently mapped onto the existing loblolly pine consensus map, which consists of 12 linkage groups spanning a total map distance of 1,227.6 cM. The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of QTLs influencing wood property traits in loblolly pine ( Pinus taeda L.). II. Chemical wood properties

Chemical wood property traits were analyzed for the presence of quantitative trait loci (QTLs) in a three-generation outbred pedigree of loblolly pine (Pinus taeda L.). These traits were assayed using pyrolysis molecular beam mass spectrometry and include mass spectrum peak intensities associated with carbohydrates, α-cellulose and hemicellulose sugars, and lignin. Models for projection to latent structures (PLS) were used to also estimate the chemical composition of cell walls (i.e., α-cellulose, galactan and lignin) from mass spectrum data using multivariate regression. Both earlywood and latewood fractions from the fifth annual ring were analyzed for each trait. An interval mapping approach designed for an outbred pedigree was used to estimate the number of QTLs, the magnitude of QTL effects, and their genomic position. Eight unique QTLs influencing cell wall chemistry were detected from multiple peak intensities and/or PLS estimates using the one- and two-QTL models. Significant differences in chemical contents were observed among the populations from North Carolina vs Oklahoma, and results from QTL×environment analyses suggest that QTLs interact with environmental location. QTLs should be verified in larger experiments and in different genetic and environmental backgrounds. QTL mapping will help towards eventually identifying genes having a major effect on chemical wood properties. Received: 19 January 2001 / Accepted: 31 May 2001     

Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). I. Physical wood properties

Physical wood property traits for loblolly pine (Pinus taeda L.) were analyzed for the presence of quantitative trait loci (QTLs) in a three-generation outbred pedigree. These traits include wood specific gravity (wsg), volume percentage of latewood (vol%), and microfibril angle (mfa). Phenotypic data were collected for rings 2–11 for wsg and vol%, and rings 3, 5 and 7 for mfa. Both earlywood and latewood were analyzed for each trait. An interval mapping approach designed for an outbred pedigree was used to estimate the number of QTLs, the magnitude of QTL effects, and their genomic position. Nine unique QTLs were detected for composite traits (average of all rings) for wsg, five for vol%, and five for mfa. The majority of these QTLs were verified by analyses of individual-ring traits. Additional QTLs for each trait were also detected by these individual-ring analyses. Most QTLs for wsg were specific to either earlywood or latewood, whereas each QTL for mfa was detected for both earlywood and latewood. Before these QTLs are utilized in a breeding program, they should be verified in larger experiments and in different genetic and environmental backgrounds. Received: 15 February 2000 / Accepted: 31 March 2000     

Wood properties and ring width responses to long-term atmospheric CO2 enrichment in field-grown loblolly pine (Pinus taeda L.)

Loblolly pine (Pinus taeda L.) were grown in the field, under non-limiting nutrient conditions, in open-top chambers for 4 years at ambient CO₂ partial pressures (pCO₂) and with a CO₂-enriched atmosphere (+ 30 Pa pCO₂ compared to ambient concentration). A third replicate of trees were grown without chambers at ambient pCO₂. Wood anatomy, wood density and tree ring width were analysed using stem wood samples. No significant differences were observed in the cell wall to cell lumen ratio within the latewood of the third growth ring formed in 1994. No significant differences were observed in the density of resin canals or in the ratio of resin canal cross-sectional area to xylem area within the same growth ring. Ring widths were significantly wider in the CO₂-enrichment treatment for 3 of 4 years compared to the ambient chamber control treatment. Latewood in the 1995 growth ring was significantly wider than that in the ambient control and represented a larger percentage of the total growth-ring width. Carbon dioxide enrichment also significantly increased the total wood specific gravity (determined by displacement). However, when determined as total sample wood density by X-ray densitometry, the density of enriched samples was not significantly higher than that of the ambient chamber controls. Only the 1993 growth ring of enriched trees had a significantly higher maximum latewood density than that of trees grown on non-chambered plots or ambient chambered controls. No significant differences were observed in the minimum earlywood density of individual growth rings between chambered treatments. These results show that the most significant effect of CO₂ enrichment on wood production in loblolly pine is its influence on radial growth, measured as annual tree ring widths. This influence is most pronounced in the first year of growth and decreases with age.     

Segregation and linkage relationships of isoenzymes in shortleaf pine (Pinus echinata Mill.)

 Segregation and linkage relationships were analyzed between 28 isoenzyme loci in ten natural stands representing much of the natural range of Pinus echinata Mill. (shortleaf pine). A total of 203 possible two-locus combinations were tested. Three linkage groups were revealed in this study at a linkLOD of 4.0. The first linkage group (A) consisted of Pgi and Adh-1; Gdh, Idh, Skdh-2, G6pd-2 and Aco were mapped to the second linkage group (B); the third group (C) had 2 loci: Mdh-2 and Mdh-3. A moderate linkage between Mnr-2 and Dia-2 and weak linkages between Mnr-1 and Dia-1, and Got-2 and 6pgd-2 were also detected. The significance of these results in shortleaf pine is discussed and compared to linkage maps previously reported in other conifers, including pines. Received: 7 April 1997 / Accepted: 25 April 1997     

Expressed sequence markers for genetic analysis of bulb onion (Allium cepa L.)

Sequencing of cDNA clones previously screened for ability to reveal RFLPs in bulb onion has been completed and a further 128 ESTs from 111 clones have been deposited in public databases. A putative function was assigned to 66% (84/128) of ESTs by BLASTX searches against public databases and FASTA comparisons were used to determine similarity among clones, including those which detected linked RFLP loci. Cleavage amplified polymorphisms (CAPs) and single-stranded conformation polymorphisms (SSCP) were evaluated as strategies for converting onion expressed sequence tags (ESTs) into PCR-based assays for gene mapping. We screened 14 ESTs with 8 to 12 restriction enzymes and detected two CAPs, which mapped in the ’Brigham Yellow Globe’ (BYG15–23)×’Ailsa Craig’ (AC43) mapping population. A wider survey of CAPs for ESTs among eight bulb onion populations with six frequently cutting restriction enzymes detected variation, but too little to be practical for routine gene mapping. By contrast, non-radioactive SSCP of amplicons from 3′ UTRs of ESTs was found to detect useful levels of variation within bulb onion germplasm. In addition to SSCPs, homo- and hetero-duplex polymorphisms (duplex polymorphisms) were also frequently observed on the same gels. Of a total of 31 ESTs surveyed, 26 exhibited SSCP/duplex variation among bulb onion populations. SSCP/duplex polymorphisms in 11 ESTs were mapped in the ’BYG15–23’×’AC43’ family and, of these, ten were linked to an RFLP locus revealed by the original cDNA. The SSCP/duplex assays of five additional ESTs showed Mendelian segregations in the ’Colossal Grano’×’Pukekohe Longkeeper’ (P12) F₂ population. Two of these markers were linked, as predicted from linkage of their corresponding RFLPs in the ’BYG15–23’×’AC43’ family. Ninety two percent (12/13) of EST PCR products that amplified in Allium roylei exhibited marked differences in SSCP patterns from bulb onion. ESTs for invertase and sucrose-sucrose fructosyltransferase were mapped by SSCP and an ATP sulfurylase gene cloned by RT-PCR revealed SSCP/ duplex polymorphism within bulb onion. These results demonstrate that SSCP/duplex is an efficient and economical technique for exploiting onion EST information for gene mapping in onion. Received: 18 September 2000 / Accepted: 15 February 2001     

Genetic variation and migration pathways of maritime pine (Pinus pinaster Ait) in the Iberian peninsula

The genetic variability and migration pathways of Pinus pinaster after glaciation in the Iberian peninsula was studied by means of 18 loci from 12 natural populations of the species. The analysis showed the existence of three groups of populations with different levels of diversity and patterns of recolonization. The southern Iberian group displays a high level of diversity, with a stepping-stone model of variation. The presence of rare alleles in this group and their position in the phylogenetic tree suggest the existence of refugia during glaciations in this zone. The eastern Iberian group also has high levels of diversity but is clearly separate from the first group based on their genetic distances. The Atlantic group displays a low level of diversity that could be interpreted as a rapid recolonization of the entire area by the Eastern group that has not yet developed to a divergence in this area. The southern Iberian range is indicated to be the dispersal centre of the species after the last glaciation. Received: 15 February 1999 / Accepted: 30 April 1999     

Genetic variability and structure of natural and domesticated populations of Caribbean pine (Pinus caribaea Morelet)

 Isozyme analysis of seed samples derived from natural and managed populations of the tropical pine Pinus caribaea vars ‘bahamensis’ and ‘caribaea’ was used to assess population genetic structure in its native range and to detect changes occurring during early domestication of the species. Baseline data from natural populations of the two varieties showed that populations sampled as seed are characterized by high gene diversity (mean H_e=0.26) and a low level of inbreeding ( mean F_is=0.15). A UPGMA tree of genetic relatedness among populations indicates that the two varieties represent distinct evolutionary units. Within each variety there is significant differentiation among populations, and this is greater for the more fragmented populations of var ‘bahamensis’ (F_st=0.08) than for var ‘caribaea’ (F_st=0.02). Seed from a seed orchard population of var ‘caribaea’ established within its natural range showed no change in genetic diversity but did show a reduced inbreeding coefficient (F_is=0.09) compared with its progenitor populations, suggesting a decrease in selfing and/or biparental inbreeding. A bulked seed sample from an exotic plantation of var ‘bahamensis’ in Australia displayed a large increase in the inbreeding coefficient (F_is=0.324) compared with that found in natural populations, possibly due to elevated self-fertilization. Finally, a bulked seed sample from an exotic plantation population of var ‘caribaea’ from China showed enhanced genetic diversity, an increase in the inbreeding coefficient and more linkage disequilibrium than its presumed progenitor populations. It was also genetically divergent from them. RFLP analysis of chloroplast DNA variation in the Chinese sample suggested that seeds of the related taxa P. elliottii and P. taeda, or seeds derived from hybridization with these taxa growing in the seed production area, had been included in the seed crop during harvesting. We conclude that monitoring of appropriate genetic markers may be an effective means of identifying potentially deleterious genetic changes occurring during forest tree domestication. Received: 10 August 1998 / Accepted: 8 September 1998     

Respiratory carbon use and carbon storage in mid‐rotation loblolly pine (Pinus taeda L.) plantations: the effect of site resources on the stand carbon balance

We used estimates of autotrophic respiration (R_A), net primary productivity (NPP) and soil CO₂ evolution (S_ff), to develop component carbon budgets for 12‐year‐old loblolly pine plantations during the fifth year of a fertilization and irrigation experiment. Annual carbon use in R_A was 7.5, 9.0, 15.0, and 15.1 Mg C ha^?1 in control (C), irrigated (I), fertilized (F) and irrigated and fertilized (IF) treatments, respectively. Foliage, fine root and perennial woody tissue (stem, branch, coarse and taproot) respiration accounted for, respectively, 37%, 24%, and 39% of R_A in C and I treatments and 38%, 12% and 50% of R_A in F and IF treatments. Annual gross primary production (GPP=NPP+R_A) ranged from 13.1 to 26.6 Mg C ha^?1. The I, F, and IF treatments resulted in a 21, 94, and 103% increase in GPP, respectively, compared to the C treatment. Despite large treatment differences in NPP, R_A, and carbon allocation, carbon use efficiency (CUE=NPP/GPP) averaged 0.42 and was unaffected by manipulating site resources. Ecosystem respiration (R_E), the sum of S_ff, and above ground R_A, ranged from 12.8 to 20.2 Mg C ha^?1 yr^?1. S_ff contributed the largest proportion of R_E, but the relative importance of S_ff decreased from 0.63 in C treatments to 0.47 in IF treatments because of increased aboveground R_A. Aboveground woody tissue R_A was 15% of R_E in C and I treatments compared to 25% of R_E in F and IF treatments. Net ecosystem productivity (NEP=GPP‐R_E) was roughly 0 in the C and I treatments and 6.4 Mg C ha^?1 yr^?1 in F and IF treatments, indicating that non‐fertilized treatments were neither a source nor a sink for atmospheric carbon while fertilized treatments were carbon sinks. In these young stands, NEP is tightly linked to NPP; increased ecosystem carbon storage results mainly from an increase in foliage and perennial woody biomass.     

Characterization of two laccases of loblolly pine (Pinus taeda) expressed in tobacco BY-2 cells

We previously showed that eight laccase genes (Lac 1–Lac 8) are preferentially expressed in differentiating xylem and are associated with lignification in loblolly pine (Pinus taeda) [Sato et al. (2001) J Plant Res 114:147–155]. In this study we generated transgenic tobacco suspension cell cultures that express the pine Lac 1 and Lac 2 proteins, and characterized the abilities of these proteins to oxidize monolignols. Lac 1 and Lac 2 enzymatic activities were detected only in the cell walls of transgenic tobacco cells, and could be extracted with high salt. The optimum pH for laccase activity with coniferyl alcohol as substrate was 5.0 for Lac 1 and between 5.0 and 6.0 for Lac 2. The activities of Lac 1 and Lac 2 increased as the concentration of CuSO₄ in the reaction mixtures increased in the range from 1 to 100 μM. Both enzymes were able to oxidize coniferyl alcohol and to produce dimers of coniferyl alcohol. These results are consistent with the hypothesis that Lac 1 and Lac 2 are involved in lignification in differentiating xylem of loblolly pine.     

Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.)

Enrichment methods were optimised in order to isolate large numbers of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.), with the aim of developing a comprehensive set of loci for trait mapping and cultivar identification. Two libraries were constructed showing greater than 50% enrichment for a variety of SSR-motif types. Sequence characterisation of 1853 clones identified 859 SSR-containing clones, of which 718 were unique. Truncation of flanking sequences limited potential primer design to 366 clones. One-hundred selected SSR primer pairs were evaluated for amplification and genetic polymorphism across a panel of diverse genotypes. The efficiency of amplification was 81%. A relatively high level of SSR polymorphism was detected (67%), with a range of 2–7 alleles per locus. Mendelian segregation of alleles detected by selected SSR-locus primer pairs was demonstrated in the F₁ progeny of a pair cross. Cross-species amplification was detected in a number of related pasture and turfgrass species, with high levels of transfer to other Lolium species and members of the related genus Festuca. The identity of putative SSR ortholoci in these related species was confirmed by DNA sequence analysis. These loci constitute a valuable resource of ideal markers for the molecular breeding of ryegrasses and fescues. Received: 8 May 2000 / Accepted: 13 June 2000     

Development and characterisation of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.)

Highly informative molecular markers, such as simple sequence repeats (SSRs), can greatly accelerate breeding programs. The aim of this study was to develop and characterise a comprehensive set of SSR markers for white clover (Trifolium repens L.), which can be used to tag genes and quantitative trait loci controlling traits of agronomic interest. Sequence analysis of 1123 clones from genomic libraries enriched for (CA) _n repeats yielded 793 clones containing SSR loci. The majority of SSRs consisted of perfect dinucleotide repeats, only 7% being trinucleotide repeats. After exclusion of redundant sequences and SSR loci with less than 25 bp of flanking sequence, 397 potentially useful SSRs remained. Primer pairs were designed for 117 SSR loci and PCR products in the expected size range were amplified from 101 loci. These markers were highly polymorphic, 88% detecting polymorphism across seven white clover genotypes with an average allele number of 4.8. Four primer pairs were tested in an F₂ population revealing Mendelian segregation. Successful cross-species amplification was achieved in at least one out of eight legume species for 46 of 54 primer pairs. The rate of successful amplification was significantly higher for Trifolium species when compared to species of other genera. The markers developed in this study not only provide valuable tools for molecular breeding of white clover but may also have applications in related taxa. Received: 3 April 2000 / Accepted: 12 May 2000     

A linkage map of the pea (Pisum sativum L.) genome containing cloned sequences of known function and expressed sequence tags (ESTs)

 A linkage map of the pea (Pisum sativum L.) genome is presented which is based on F₂ plants produced by crossing the marrowfat cultivar ‘Primo’ and the blue-pea breeding line ‘OSU442-15’. This linkage map consists of 209 markers and covers 1330 cM (Kosambi units) and includes RFLP, RAPD and AFLP markers. By mapping a number of anchor loci, the ‘Primo’בOSU442-15’ map has been related to other pea linkage maps. A feature of the map is the incorporation of 29 loci representing genes of known function, obtained from other laboratories. The map also contains RFLP loci detected using sequence-characterized cDNA clones developed in our laboratory. The putative identities of 38 of these cDNA clones were assigned by examining public-sequence databases for protein or nucleotide-sequence similarities. The conversion of sequence-characterized pea cDNAs into PCR-amplifiable and polymorphic sequence-tagged sites (STSs) was investigated using 18 pairs of primers designed for single-copy sequences. Eleven polymorphic STSs were developed. Received: 18 June 1997 / Accepted: 11 August 1997     

Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map

Sugi, Cryptomeria japonica D. Don, is one of the most important forestry species in Japan. We here report the development of 217 CAPS markers derived from sugi cDNA libraries. More than half of a set of STS markers produced could be converted into CAPS markers using restriction endonuclease analysis. Of the 217 markers, 71 showed different patterns of polymorphism when they were digested with a range of endonucleases and, in total, 347 polymorphisms were found in the various combinations of STSs and endonucleases. When the polymorphisms gave co-dominant patterns in a screening program, the polymorphic information content (PIC) used to evaluate the value of the polymorphisms was relatively high (0.33, on average) compared to the information yielded by commonly used markers, like isozymes. The results of a segregation analysis suggest that approximately 80% of the CAPS markers developed here will show co-dominant inheritance. From logistic regression analysis, the polymorphisms were found to be associated more strongly with intron than with exon regions. Sixty two markers were subsequently mapped on the previously reported linkage map, 15 of which showed abnormal segregation, presumably caused by linkage with lethal factors. Received: 7 December 2000 / Accepted: 23 January 2001     

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome. Received: 5 May 1999 / Accepted: 16 August 1999