Polyploid formation created unique avenues for response to selection in Gossypium (cotton)

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.

A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population

An interspecific Gossypium hirsutum x Gossypium barbadense backcross population of 75 BC1 plants was evaluated for 1014 markers. The map consists of 888 loci, including 465 AFLPs, 229 SSRs, 192 RFLPs, and 2 morphological markers, ordered in 37 linkage groups that represent most if not all of the 26 chromosomes, altogether spanning 4400 cM. Loci were not evenly distributed over linkage groups, and 18 of the 26 long groups had a single dense region. This paper proposes a partially revised list of the 13 pairs of homoeologous A/D chromosomes of the 2n = 4x = 52 tetraploid cotton genome. The major revisions, which involve the c3-c17, c4-c22, c5-D08, and c10-c20 homoeologous pairs, are based on the mapping of 68 SSR and RFLP loci with a known chromosome assignment, as well as on comparative alignments with previously published G. hirsutum x G. barbadense maps. The overall congruency in the locus orders and distances of common SSR and RFLP loci in these maps allows for an estimation of the consensus length that reaches a minimum of 5500 cM, and is encouraging for future efforts aimed at developing an integrated map of cultivated cotton. The present map also provides a firm framework for precision mapping of Mendelian components of quantitative traits in cotton

Patterns of genome duplication within the Brassica napus genome

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.

Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids

We developed a set of genetic markers specific to the A and D genome types of cotton using representational difference analysis (RDA). These markers produce amplification products with genomic DNA from allotetraploid cotton Gossypium hirsutum. One of the markers is a polymorphic amplified restriction fragment (PARF) - a sequence found in both A and D genomes but differently flanked by restriction sites. Results of phylogenetic analysis of the PARF sequences from diploid cottons and from allotetraploid G. hirsutum agree with a previous observation of the interlocus concerted evolution (sequences corresponding to A and D genomes are homogenized to a D genome-type sequence). Our study shows how RDA can be used to develop genome-specific markers that can be used to study molecular evolution of allopolyploids.

What has QTL mapping taught us about plant domestication?

The aim of this paper is to survey the general area of quantitative trait locus (QTL) mapping, and its specific impact on current understanding of plant domestication. Plant domestication is not only of historical interest, but is also of ongoing importance as changing human needs and availability of nonrenewable resources impel continuing (and perhaps even accelerated) investigation of prospective new crops. New genomic tools applied in conjunction with now-established approaches such as QTL mapping are opening new doors into searches for the 'footprints' of domestication, and promise to accelerate and streamline the identification of specific genes integral to domestication(s), building on early successes. Better understanding of plant domestication promises to enhance knowledge about the developmental basis of some of the more striking evolutionary events known, to guide efforts to catalog plant biodiversity, and to accelerate progress in improving existing and new crops to sustain humanity. Contents Summary 591 I. Introduction 592 II. A backdrop: QTL mapping basics 593 III. The tempo of domestication 596 IV. Domestication and polyploidy 601 V. New approaches to identifying the footprints of domestication 603 VI. Perspectives 605 Acknowledgements 606 References 606.

Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species

Polyploidy creates severe genetic bottlenecks, contributing to the genetic vulnerability of leading crops. Cultivated peanut is thought to be of monophyletic origin, harboring relatively little genetic diversity. To introduce variability from diploid wild species into tetraploid cultivated Arachis hypogaea, a synthetic amphidiploid [[A. batizocoi K9484 x (A. cardenasii GKP10017 x A. diogoi GKP10602)](4x)] was used as donor parent to generate a backcross population of 78 progeny. Three hundred seventy RFLP loci were mapped onto 23 linkage groups, spanning 2210 cM. Chromatin derived from the two A-genome diploid ancestors (A. cardenasii and A. diogoi) comprised mosaic chromosomes, reflecting crossing over in the diploid A-genome interspecific F(1) hybrid. Recombination between chromosomes in the tetraploid progeny was similar to chromosome pairing reported for A. hypogaea, with recombination generally between chromosomes of the same subgenomic affinity. Segregation distortion was observed for 25% of the markers, distributed over 20 linkage groups. Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed.

Accelerated regulatory gene evolution in an adaptive radiation

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.

Polyploid formation in cotton is not accompanied by rapid genomic changes

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22 000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.Key words: polyploidy, genome evolution, cotton, Gossypium, amplified fragment length polymorphism (AFLP).

Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology

Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants; however, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight into understanding the evolution of complex traits both in crops and in wild plants.

Comparative development of fiber in wild and cultivated cotton

One of the most striking examples of plant hairs is the single-celled epidermal seed trichome of cultivated cotton. The developmental morphology of these commercial "fibers" has been well-characterized in Gossypium hirsutum, but little is known about the pattern and tempo of fiber development in wild Gossypium species, all of which have short, agronomically inferior fiber. To identify developmental differences that account for variation in fiber length, and to place these differences in a phylogenetic context, we conducted SEM studies of ovules at and near the time of flowering, and generated growth curves for cultivated and wild diploid and tetraploid species. Trichome initiation was found to be similar in all taxa, with few notable differences in trichome density or early growth. Developmental profiles of the fibers of most wild species are similar, with fiber elongation terminating at about two weeks post-anthesis. In contrast, growth is extended to three weeks in the A- and F-genome diploids. This prolonged elongation period is diagnosed as a key evolutionary event in the origin of long fiber. A second evolutionary innovation is that absolute growth rate is higher in species with long fibers. Domestication of species is associated with a further prolongation of elongation at both the diploid and allopolyploid levels, suggesting the effects of parallel artificial selection. Comparative analysis of fiber growth curves lends developmental support to previous quantitative genetic suggestions that genes for fiber "improvement" in tetraploid cotton were contributed by the agronomically inferior D-genome diploid parent.

Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton)

Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from interspecific hybridization in nature. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3662 BC3F2 plants derived from 24 different BC1 individuals of a cross between Gossypium hirsutum and G. barbadense, large and widespread deficiencies of donor (G. barbadense) chromatin were found, and seven independent chromosomal regions were entirely absent. This skewed chromatin transmission is best accounted for by multilocus epistatic interactions affecting chromatin transmission. The observed frequencies of two-locus genotypes were significantly different from Mendelian expectations about 26 times more often than could be explained by chance (P < or = 0.01). For identical pairs of loci, different two-locus genotypes occurred in excess in different BC3 families, implying the existence of higher-order interlocus interactions beyond the resolution of these data. Some G. barbadense markers occurred more frequently than expected by chance, indicating that genomic interactions do not always favor host chromatin. A preponderance of interspecific allelic interactions involved one locus each in the two different subgenomes of (allotetraploid) Gossypium, thus supporting several other lines of evidence suggesting that intersubgenomic interactions contribute to unique features that distinguish tetraploid cotton from its diploid ancestors.

Genetic and epigenetic interactions in allopolyploid plants

Allopolyploid plants are hybrids that contain two copies of the genome from each parent. Whereas wild and cultivated allopolyploids are well adapted, man-made allopolyploids are typically unstable, displaying homeotic transformation and lethality as well as chromosomal rearrangements and changes in the number and distribution of repeated DNA sequences within heterochromatin. Large increases in the length of some chromosomes has been documented in allopolyploid hybrids and could be caused by the activation of dormant retrotransposons, as shown to be the case in marsupial hybrids. Synthetic (man-made) allotetraploids of Arabidopsis exhibit rapid changes in gene regulation, including gene silencing. These regulatory abnormalities could derive from ploidy changes and/or incompatible interactions between parental genomes, although comparison of auto- and allopolyploids suggests that intergenomic incompatibilities play the major role. Models to explain intergenomic incompatibilities incorporate both genetic and epigenetic mechanisms. In one model, the activation of heterochromatic transposons (McClintock's genomic shock) may lead to widespread perturbation of gene expression, perhaps by a silencing interaction between activated transposons and euchromatic genes. Qualitatively similar responses, of lesser intensity, may occur in intraspecific hybrids. Therefore, insight into genome function gained from the study of allopolyploidy may be applicable to hybrids of any type and may even elucidate positive interactions, such as those responsible for hybrid vigor.

Contributions of plant molecular systematics to studies of molecular evolution

Dobzhansky stated that nothing in biology makes sense except in the light of evolution. A close corollary, and the central theme of this paper, is that everything makes a lot more sense in the light of phylogeny. Systematics is in the midst of a renaissance, heralded by the widespread application of new analytical approaches and the introduction of molecular techniques. Molecular phylogenetic analyses are now commonplace, and they have provided unparalleled insights into relationships at all levels of plant phylogeny. At deep levels, molecular studies have revealed that charophyte green algae are the closest relatives of the land plants and suggested that liverworts are sister to all other extant land plants. Other studies have suggested that lycopods are sister to all other vascular plants and clarified relationships among the ferns. The impact of molecular phylogenetics on the angiosperms has been particularly dramatic--some of the largest phylogenetic analyses yet conducted have involved the angiosperms. Inferences from three genes (rbcL, atpB, 18S rDNA) agree in the major features of angiosperm phylogeny and have resulted in a reclassification of the angiosperms. This ordinal-level reclassification is perhaps the most dramatic and important change in higher-level angiosperm taxonomy in the past 200 years. At lower taxonomic levels, phylogenetic analyses have revealed the closest relatives of many crops and 'model organisms' for studies of molecular genetics, concomitantly pointing to possible relatives for use in comparative studies and plant breeding. Furthermore, phylogenetic information has contributed to new perspectives on the evolution of polyploid genomes. The phylogenetic trees now available at all levels of the taxonomic hierarchy for angiosperms and other green plants should play a pivotal role in comparative studies in diverse fields from ecology to molecular evolution and comparative genetics.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Isolation, propagation and characterisation of Cryptosporidium

This review consists of 11 papers presented at the Consensus Conference on Cryptosporidium in Water (Parasitology Stream), held in Melbourne, Australia, from 5 to 6th October 1998. The conference was sponsored by the Water Services Association of Australia, the Australian Water and Wastewater Association, and the Collaborative Research Centre for Water Quality and Treatment. The papers summarise the advantages and disadvantages of various contemporary technologies applicable to parasite propagation and biochemical/molecular characterisation. Studies have detected distinct genetic differences between clinical isolates from humans and animals, and it is hoped that comprehensive documentation studies will facilitate the identification of environmental isolates in the not too distant future.

Rapid structural and epigenetic changes in polyploid and aneuploid genomes

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes.