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PubMed2002

Transmission of herbicide resistance from a monoecious to a dioecious weedy Amaranthus species.

The genus Amaranthus includes several important monoecious and dioecious weed species, and several populations of these species have developed resistance to herbicides. These species are closely related and two or more species often coexist in agricultural settings. Collectively, these attributes raise the concern that herbicide resistance might transfer from one weedy Amaranthus species to another. We performed research to determine if a dominant allele encoding a herbicide-insensitive form of acetolactate synthase (ALS) could be transferred from a monoecious species, A. hybridus, to a dioecious species, A. rudis. Numerous F(1) hybrids were obtained from controlled crosses in a greenhouse between A. rudis and herbicide-resistant A. hybridus, and most (85%) of these hybrids were herbicide-resistant. Molecular analysis of the ALS gene was used to verify that herbicide-resistant hybrids contained both an A. rudis and an A. hybridus ALS allele. Although hybrids had greatly reduced fertility, 42 BC(1) plants were obtained by backcrossing 33 hybrids with male A. rudis. Fertility was greatly restored in BC(1) progeny, and numerous BC(2) progeny were obtained from a second backcross to A. rudis. The herbicide-resistance allele from A. hybridus was transmitted to 50% of the BC(1) progeny. The resistance allele was subsequently transmitted to and conferred herbicide resistance in 39 of 110 plants analyzed from four BC(2) families. Parental species, hybrids, and BC(2) progeny were compared for 2C nuclear DNA contents. The mean hybrid 2C nuclear DNA content, 1.27 pg, was equal to the average between A. rudis and A. hybridus, which had 2C DNA contents of 1.42 and 1.12 pg, respectively. The mean 2C DNA content of BC(2) plants, 1.40 pg, was significantly (alpha < 0.01) less than that of the recurring A. rudis parent and indicated that BC(2) plants were not polyploid. This report demonstrates that herbicide resistance can be acquired by A. rudis through a hybridization event with A. hybridus.

Journal Article↗

PubMed2002

The origin of intermediate species of the genus Sorbus.

The genus Sorbus in Europe contains five diploid species, Sorbus aria, Sorbus aucuparia, Sorbus torminalis, Sorbus chamaemespilus and Sorbus domestica, classified into five different subgenera. The subgenus Aria (or the S. aria aggregate) contains apomictic triploid and tetraploid species. Within the genus there are, in addition, a number of species, morphologically intermediate between plants of the four main subgenera, which are considered to reproduce partly, or exclusively, by apomixis. These are believed to have originated by hybridisation between species in the S. aria aggregate and a species from another subgenus (either S. aucuparia, S. torminalis or S. chamaemespilus). We have used restriction fragment length polymorphism (RFLP) analysis on a total of 178 Sorbus accessions to test this model. The genome relationships of the different groups have been assessed, and the hybrid nature of the major intermediate groups is unequivocally demonstrated. Polyploid species in the S. aria aggregate show genetic variation, indicating the possibility of multiple origins and/or facultative apomictic breeding behaviour. A major finding, confirmed by microsatellite analysis, is that the 'intermediate' species S. intermedia is shown to have genomes from S aria, S aucuparia and S torminalis. Polymorphic mitochondrial DNA markers were used to determine the direction of the crosses that gave rise to new 'hybrid species'; in the majority of cases the pollen was provided by the parent from the S aria aggregate.

Journal Article↗

PubMed2002

Genomic relationships between Medicago murex Willd. and Medicago lesinsii E. Small. investigated by in situ hybridization.

Medicago murex Willd. is an annual species (2n = 14) widespread in the wild and of remarkable interest for pastures in regions with a mediterranean climate. It is considered closely related to Medicago lesinsii E. Small (2n = 16) but, up to now, there is no evidence demonstrating their genetic affinity. This research was undertaken to investigate the genomic relationships between M. murex and M. lesinsii by using genomic in situ hybridization (GISH). In this study GISH experiments were performed using both species as sources of chromosomes and genomic probes. To better evaluate the results of the hybridization, the labelled DNA of each species was hybridized to chromosomes of the same species and to chromosomes of the diploid Medicago littoralis (2n = 16). Strong hybridization signals were found on chromosomes of M. murex and M. lesinsii after GISH. Differences in the hybridization strength were not observed when slides from interspecific hybridization were compared with the control preparations. These results suggest that consistent divergences of the DNA sequences did not occur after the separation of the two species. Instead very reduced cross hybridization was found on chromosome spreads of M. littoralis hybridized with the DNA of M. lesinsii or M. murex. The distribution of the ribosomal genes (rDNA) investigated by fluorescent in situ hybridization (FISH) appeared similar in both M. murex and M. lesinsii. The GISH technique may be a valuable approach to obtain information on evolution of the 2n = 14 species and on the origin of the polyploids Medicago rugosa (2n = 30) and Medicago scutellata (2n = 30). The first attempt to investigate the genomic composition of M. scutellata using a genomic probe is reported in this paper.

Journal Article↗

PubMed2003

Construction and characterization of a half million clone BAC library of durum wheat ( Triticum turgidum ssp. durum).

Durum wheat ( Triticum turgidum ssp. durum, 2 n = 4 x = 28, genomes AB) is an economically important cereal used as the raw material to make pasta and semolina. In this paper we present the construction and characterization of a bacterial artificial chromosome (BAC) library of tetraploid durum wheat cv. Langdon. This variety was selected because of the availability of substitution lines that facilitate the assignment of BACs to the A and B genome. The selected Langdon line has a 30-cM segment of chromosome 6BS from T. turgidum ssp. dicoccoides carrying a gene for high grain protein content, the target of a positional cloning effort in our laboratory. A total of 516,096 clones were organized in 1,344 384-well plates and blotted on 28 high-density filters. Ninety-eight percent of these clones had wheat DNA inserts (0.3% chloroplast DNA, 1.4% empty clones and 0.3% empty wells). The average insert size of 500 randomly selected BAC clones was 131 kb, resulting in a coverage of 5.1-fold genome equivalents for each of the two genomes, and a 99.4% probability of recovering any gene from each of the two genomes of durum wheat. Six known copy-number probes were used to validate this theoretical coverage and gave an estimated coverage of 5.8-fold genome equivalents. Screening of the library with 11 probes related to grain storage proteins and starch biosynthesis showed that the library contains several clones for each of these genes, confirming the value of the library in characterizing the organization of these important gene families. In addition, characterization of fingerprints from colinear BACs from the A and B genomes showed a large differentiation between the A and B genomes. This library will be a useful tool for evolutionary studies in one of the best characterized polyploid systems and a source of valuable genes for wheat. Clones and high-density filters can be requested at http://agronomy.ucdavis.edu/Dubcovsky/BAC-library/BAC_Langdon.htm

Chromosomes, Artificial, Bacterial↗

PubMed2003

Genetic mapping and QTL analysis of fiber-related traits in cotton ( Gossypium).

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton ( Gossypium hirsutum L.) and Pima or Egyptian cotton ( G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F2 population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.

Chromosome Mapping↗

PubMed2003

A genetic linkage map of the diplosporous chromosomal region in Taraxacum officinale (common dandelion; Asteraceae).

In this study, we mapped the diplosporous chromosomal region in Taraxacum officinale, by using amplified fragment length polymorphism technology (AFLP) in 73 plants from a segregating population. Taraxacum serves as a model system to investigate the genetics, ecology, and evolution of apomixis. The genus includes sexual diploid as well as apomictic polyploid, mostly triploid, plants. Apomictic Taraxacum is diplosporous, parthenogenetic, and has autonomous endosperm formation. Previous studies have indicated that these three apomixis elements are controlled by more than one locus in Taraxacum and that diplospory inherits as a dominant, monogenic trait ( Ddd; DIP). A bulked segregant analysis provided 34 AFLP markers that were linked to DIP and were, together with two microsatellite markers, used for mapping the trait. The map length was 18.6 cM and markers were found on both sides of DIP, corresponding to 5.9 and 12.7 cM, respectively. None of the markers completely co-segregated with DIP. Eight markers were selected for PCR-based marker development, of which two were successfully converted. In contrast to all other mapping studies of apomeiosis to date, our results showed no evidence for suppression of recombination around the DIP locus in Taraxacum. No obvious evidence for sequence divergence between the DIP and non- DIP homologous loci was found, and no hemizygosity at the DIP locus was detected. These results may indicate that apomixis is relatively recent in Taraxacum.

Chromosome Mapping↗

PubMed2003

Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers.

The presence of a major resistance gene (Bru1) for brown rust in the sugarcane cultivar R570 (2n about 115) was confirmed by analyzing segregation of rust resistance in a large population of 658 individuals, derived from selfing of clone R570. A subset of this population was analyzed with AFLP and bulked segregant analysis (BSA) to develop a detailed genetic map around the resistance gene. Four hundred and forty three primer pairs were used resulting in the identification of eight AFLP markers surrounding the resistance gene in an interval of 10 cM, with the closest markers located at 1.9 and 2.2 cM on each side of the gene. Efficiency of the AFLP/BSA applied to the complex polyploid genome of sugarcane is discussed, as well as the potential of the newly identified AFLP markers for developing a map-based cloning approach exploiting, synteny conservation with sorghum.

Basidiomycota↗

PubMed2004

Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.).

In order to promote genome research on coffee trees, one of the most important tropical crops, a bacterial artificial chromosome (BAC) library of the coffee allotetraploid species, Coffea arabica, was constructed. The variety IAPAR 59, which is widely distributed in Latin America and exhibits a fair level of resistance to several pathogens, was chosen. High-efficiency BAC cloning of the high molecular weight genomic DNA partially digested by HindIII was achieved. In total, the library contains 88,813 clones with an average insert size of 130 kb, and represents approximately eight C. arabica dihaploid genome equivalents. One original feature of this library is that it can be divided into four sublibraries with mean insert sizes of 96, 130, 183 and 210 kb. Characterisation of the library showed that less than 4.5% of the clones contained organelle DNA. Furthermore, this library is representative and shows good genome coverage, as established by hybridisation screening of high-density filters using a number of nuclear probes distributed across the allotetraploid genome. This Arabica BAC library, the first large-insert DNA library so far constructed for the genus Coffea, is well-suited for many applications in genome research, including physical mapping, map-based cloning, functional and comparative genomics as well as polyploid genome analyses.

Blotting, Southern↗

PubMed2005

A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar.

Sugarcane varieties are complex polyploids carrying in excess of 100 chromosomes and are derived from interspecific hybridisation between the domesticated Saccharum officinarum and the wild relative S. spontaneum. A map was constructed in Denotes variety covered by Australian plant breeding rights., an Australian cultivar, from a segregating F1 population, using 40 amplified fragment length polymorphism (AFLP) primer combinations, five randomly amplified DNA fingerprints (RAF) primers and 72 simple sequence repeat (SSR) primers. Using these PCR-based marker systems, we generated 1,365 polymorphic markers, of which 967 (71%) were single-dose (SD) markers. Of these SD 967 markers, 910 were distributed on 116 linkage groups (LGs) with a total map length of 9,058.3 cM. Genome organisation was significantly greater than observed in previously reported maps for Saccharum spp. With the addition of 123 double-dose markers, 36 (3:1) segregating markers and a further five SD markers, 1,074 markers were mapped onto 136 LGs. Repulsion phase linkage detected preferential pairing for 40 LGs, which formed 11 LG pairs and three multi-chromosome pairing groups. Using SSRs, double-dose markers and repulsion phase linkage, we succeeded in forming 127 of the 136 LGs into eight homo(eo)logy groups (HG). Two HGs were each represented by two sets of LGs. These sets of LGs potentially correspond to S. officinarum chromosomes, with each set aligning to either end of one or two larger LGs. The larger chromosomes in the two HGs potentially correspond to S. spontaneum chromosomes. This suggestion is consistent with the different basic chromosome number of the two species that are hybridised to form sugarcane cultivars, S. spontaneum (x=8) and S. officinarum (x=10), and illustrates the structural relationship between the genomes of these two species. The discrepancy of coverage between HGs highlights the difficulty in mapping large parts of the genome.

Australia↗

PubMed2005

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases.

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars ('SP80-180' x 'SP80-4966') using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane.

Chromosome Mapping↗

PubMed2005

Genes involved in biosynthesis and signalisation of ethylene in Brassica oleracea and Arabidopsis thaliana: identification and genome comparative mapping of specific gene homologues.

The study reported was aimed at the identification and determination of the chromosomal organisation of genes involved in the ethylene biosynthesis and signalling pathways in Brassica oleracea, on the basis of the Arabidopsis thaliana DNA probes and in silico genome analysis. Because of its polyploidal origin, the B. oleracea genome is characterised by extensive gene redundancy. Therefore, an important aspect of gene expression in B. oleracea response to environmental stimuli is to identify the specific gene copy involved. This aspect should also be taken into consideration while studying the genetic basis of biosynthesis and signal transduction in relation to basic phytohormones. Our present work concerns the identification of homologue genes involved in ethylene biosynthesis such as SAM, ACS and ACO, as well as those involved in the ethylene signalling pathway, mainly ETR1, CTR1, MKK4, MKK5, EIN2, EIN3, EREBP, ERF5 and ERF7 on the basis of the restriction fragment length polymorphism (RFLP) and PCR mapping. In the case of ACC synthases, (ACSs) the in silico analysis of gene variants in the genome of A. thaliana was followed by the identification of homologues to ACS2, ACS6 and ACS7 in the B. oleracea database. In total, 22 loci with sequence homology to the genes under analysis were included in the existing B. oleracea RFLP chromosomal map. Based on the stress responsiveness of most of the A. thaliana genes analysed in this study, we performed initial functional analysis of some gene homologues mapped. With the use of the RT-PCR approach the conservation of differential transcriptional induction of ACS homologues in the B. oleracea and A. thaliana was demonstrated during ozone stress.

Arabidopsis↗

PubMed2005

Construction and characterization of a peanut HindIII BAC library.

Bacterial artificial chromosome (BAC) libraries have been an essential tool for physical analyses of genomes of many crops. We constructed and characterized the first large-insert DNA library for Arachis hypogaea L. The HindIII BAC library contains 182,784 clones; only 5,484 (3%) had no inserts; and the average insert size is 104.05 kb. Chloroplast DNA contamination was very low, only nine clones, and r-DNA content was 1,208, 0.66% of clones. The depth of coverage is estimated to be 6.5 genome-equivalents, allowing the isolation of virtually any single-copy locus. This rate of coverage was confirmed with the application of 20 overgos, which identified 305 positive clones from the library. The identification of multiple loci by most probes in polyploids complicates anchoring of physical and genetic maps. We explored the practicality of a hybridization-based approach for determination of map locations of BAC clones in peanut by analyzing 94 clones detected by seven different overgos. The banding patterns on Southern blots were good predictors of contig composition; that is, the clones that shared the same size bands and ascribed to the same overgos usually also located in the same contigs. This BAC library has great potential to advance future research about the peanut genome.

Arachis↗

PubMed2006

Characterisation of single nucleotide polymorphisms in sugarcane ESTs.

Commercial sugarcane cultivars (Saccharum spp. hybrids) are both polyploid and aneuploid with chromosome numbers in excess of 100; these chromosomes can be assigned to 8 homology groups. To determine the utility of single nucleotide polymorphisms (SNPs) as a means of improving our understanding of the complex sugarcane genome, we developed markers to a suite of SNPs identified in a list of sugarcane ESTs. Analysis of 69 EST contigs showed a median of 9 SNPs per EST and an average of 1 SNP per 50 bp of coding sequence. The quantitative presence of each base at 58 SNP loci within 19 contiguous sequence sets was accurately and reliably determined for 9 sugarcane genotypes, including both commercial cultivars and ancestral species, through the use of quantitative light emission technology in pyrophosphate sequencing. Across the 9 genotypes tested, 47 SNP loci were polymorphic and 11 monomorphic. Base frequency at individual SNP loci was found to vary approximately twofold between Australian sugarcane cultivars and more widely between cultivars and wild species. Base quantity was shown to segregate as expected in the IJ76-514 x Q165 sugarcane mapping population, indicating that SNPs that occur on one or two sugarcane chromosomes have the potential to be mapped. The use of SNP base frequencies from five of the developed markers was able to clearly distinguish all genotypes in the population. The use of SNP base frequencies from a further six markers within an EST contig was able to help establish the likely copy number of the locus in two genotypes tested. This is the first instance of a technology that has been able to provide an insight into the copy number of a specific gene locus in hybrid sugarcane. The identification of specific and numerous haplotypes/alleles present in a genotype by pyrophosphate sequencing or alternative techniques ultimately will provide the basis for identifying associations between specific alleles and phenotype and between allele dosage and phenotype in sugarcane.

Alleles↗

PubMed2006

Genetic variation for the response to ploidy change in Zea mays L.

Polyploidization is an important process in the evolutionary history of most eukaryotic species. It oftentimes causes large-scale genomic reorganizations and is accompanied by a wide variety of phenotypic alterations in morphology, niche preference and fitness characteristics. Despite their importance, the morphological effects of alterations in ploidy are not well understood. We investigated these changes in four diverse maize inbred lines, using monoploid, diploid, triploid and tetraploid derivatives, measuring 13 characters in a randomized field study. Employing several analysis of variance approaches, we find that all characters investigated strongly respond to alterations in ploidy. This response appears to have two sources: one source is shared by all inbred lines and constitutes a common response to ploidy change. The other source is genotype specific and results in a response to ploidy change that varies among inbred lines. This finding demonstrates the existence of genetic variation for the morphological response to ploidy change in Zea mays.

Analysis of Variance↗

PubMed2026

Genomic selection in timothy (Phleum pratense L.): a comprehensive evaluation of prediction models, multi-trait strategies, and forward validation across Norwegian environments.

This study presents a comprehensive evaluation of genomic selection (GS) in timothy (Phleum pratense L.), comparing nine prediction models across yield and quality traits at two Norwegian locations. Forward validation with independent full-sib (FS2) families revealed a substantial generalization gap, highlighting the need for realistic accuracy assessment in polyploid forage breeding. Timothy (Phleum pratense L.) is the most important forage grass in Northern Europe, yet genomic selection has not been systematically evaluated in this hexaploid species. We assessed 889 FS2-families originating from biparental crosses among 49 cultivars/populations. The FS2-families were genotyped with 30,698 SNP markers derived from genotyping-by-sequencing (GBS) and field tested for three harvest years at a highland and a lowland continental location in Southern Norway. Nine genomic prediction models were compared for six yield traits (dry matter yield per cut and total) and six quality traits (protein, digestibility, and fiber fractions) across three cuts/year. Within-training cross-validation accuracies were moderate to high (mean r = 0.62), with Random Forest and SVR consistently outperforming GBLUP. However, forward validation using 213 independent FS2-families revealed dramatically lower accuracies (mean r = 0.16), with only 16 of 30 trait-dataset combinations reaching statistical significance (p < 0.05). Genomic heritabilities (GREML), estimated across environments, ranged from near zero for the quality traits to 0.55 for the yield traits. Multi-trait models improved accuracy by 3-5% over single-trait approaches, while FS2 families-by-environment interaction models with Random Forest achieved the highest within-training accuracy (mean r = 0.71). Marker density analysis showed accuracy plateauing at approximately 15000 SNPs. Genetic correlations among the yield component traits were estimated by multi-trait REML; correlations among the quality traits could not be estimated reliably because their genomic heritabilities were low. A multi-trait selection index identified top-performing FS2-families for further crossing recommendations. These results provide a benchmark for GS implementation in hexaploid timothy and emphasize that cross-validation substantially overestimates prediction accuracy for truly independent material.

Norway↗

PubMed2026

From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.

Sugarcane (Saccharum spp.) underpins global sugar and bioenergy supply and is increasingly valued as a renewable biomass feedstock. Sustained improvement in commercial traits and resilience is constrained by long breeding cycles, clonal propagation, multi-stage testing, and a highly polyploid, heterozygous, and frequently aneuploid genome with substantial non-additive genetic variation. Genomic selection has demonstrated value for predicting elite-clone performance, yet its operational use remains limited at earlier decision points, including family selection, parent evaluation, and cross design. This review examines the biological, statistical, and genomic factors that shape these decisions, with emphasis on the Australian breeding context based on progeny assessment trials (PATs), clonal assessment trials (CATs), and final assessment trials (FATs). We evaluate challenges arising from family plot means, the use of different full-sib samples as nominal family replicates, spatial heterogeneity, competition, genotype-by-environment interaction, and the partitioning of additive and non-additive effects. We also assess the integration of pedigree and genomic relationship, genotype representation, allele-dosage estimation, aneuploidy, genomic prediction models, and training-population design. We then consider genomic prediction of cross performance and constrained mate allocation as approaches for improving expected family performance, accounting for cross-specific non-additive effects and managing relatedness. We propose a decision-centred framework that links family and clonal data across breeding stages, tracks the propagation of information and uncertainty, and supports parent recycling and cross allocation. We conclude with a practical research agenda for stage-integrated mixed-model and single-step analyses that connect early family evaluation with genomic prediction and cross-level decision support in sugarcane breeding.

Saccharum↗

PubMed2002

AFLP-based estimation of 2n gametophytic heterozygosity in two parthenogenetically derived dihaploids of Rosa hybrida L.

Two dihaploid Rosa hybrida L. genotypes, derived through parthenogenesis by using irradiated pollen, were crossed with clonally propagated plants of the diploid species Rosa rugosa Thunb. and Rosa wichuraiana Crép., respectively. Three progeny groups were obtained which contained numerous polyploids, as determined by flow cytometry. Production of fertile 2n female gametes is apparently very common in one of these R. hybrida dihaploid derivatives, whereas the other one is able to produce fertile 2n pollen. Hence, an amplified fragment length polymorphism (AFLP) study was performed on the parental plants and the resulting hybrid offspring in order to estimate (1) the respective genomic parental contributions, and (2) the level of heterozygosity transmitted by the 2n unreduced gametes. Comparison of the levels of transmitted parental heterozygosity revealed that two types of 2n gametes were produced simultaneously, presumably resulting from restitution at the first and at the second meiotic division, respectively.

Journal Article↗

PubMed2003

Evolution of vertebrate voltage-gated ion channel alpha chains by sequential gene duplication.

Phylogenetic analysis of alpha chains of voltage-gated ion channels revealed that extensive gene duplication has occurred among both Ca(2+) and Na(+)-channels since the origin of vertebrates. Rather than showing a pattern of gene duplication consistent with the hypothesis of polyploidization early in vertebrate history, both Ca(2+) and Na(+) channels showed patterns of sequential gene duplication associated with specialization of the gene products. In the case of Na(+) channels, the phylogeny supported the hypothesis that the ancestral vertebrate gene had an expression pattern including both central and peripheral nervous system cells and that duplication of vertebrate Na(+) channel genes has repeatedly been followed by specialization for the central nervous system, the peripheral nervous system, or muscle cells. Thus, cephalization in vertebrate evolution has been accompanied by specialization of this important family of neuromuscular proteins along the central-peripheral axis.

Animals↗