Duplication,divergence and persistence in the Phytochrome photoreceptor gene family of cottons (<Emphasis Type="Italic">Gossypium</Emphasis> spp.)

Background  

Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (Gossypium spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (G. herbaceum, G. raimondii) or allotetraploid (G. hirsutum, G. barbadense) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton.     

Sampling nucleotide diversity in cotton

Background  

Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum) × 3-79 (G. barbadense) have been developed to allow high-density genetic mapping of traits.     

Genetic transformation of cotton with a harpin-encoding gene <Emphasis Type="Italic">hpa</Emphasis><Subscript><Emphasis Type="Italic">Xoo</Emphasis></Subscript> confers an enhanced defense response against different pathogens through a priming mechanism

Background  

The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum). To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful.     

Expression of genes associated with carbohydrate metabolism in cotton stems and roots

Background  

Cotton (Gossypium hirsutum L) is an important crop worldwide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. Domesticated cotton makes these reserves available to developing seeds which impacts seed yield. The goals of these analyses were to identify genes and physiological pathways that establish cotton stems and roots as physiological sinks and investigate the role these pathways play in cotton development during seed set.     

The genetic diversity and evolution of field pea (<Emphasis Type="Italic">Pisum</Emphasis>) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

Background  

The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus.     

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.     

An interspecific somatic hybrid between upland cotton (<Emphasis Type="Italic">G. hirsutum</Emphasis> L. cv. ZDM-3) and wild diploid cotton (<Emphasis Type="Italic">G. klotzschianum</Emphasis> A.)

Somatic hybrids were produced through protoplast electrofusion between the tetraploid cotton Gossypium hirsutum L. cv. ZDM-3 and the wild diploid cotton G. klotzschianum. Hybrid plants were generated from 3 out of 24 callus lines that were derived from fused protoplasts. Hybrid plants were initially identified as somatic hybrids by ploidy analysis: the plants from the 3 callus lines had chromosome numbers near to sum of the two parents (78 = 52 + 26). The plants from the 3 lines were subsequently confirmed as hybrids by cytological, molecular, histological and morphological analyses. The morphology of hybrids was distinct from that of the parents, with elongated stigmas and malformed anthers lacking microspores and pollen, leading to male sterility. It is expected that the male sterility resulted from the high number of univalent and irregular multivalent chromosome pairings per meiocyte.     

Analysis of gene expression in cotton fiber initials

Background  

Cotton (Gossypium hirsutum L.) fibers are trichomes that initiate from the ovule epidermis. Little is known about the developmental pathway causing fiber to differentiate from ovular epidermal cells even though limits on the number of cells that differentiate into fiber will limit yield.     

Duplicate gene expression in allopolyploid <Emphasis Type="Italic">Gossypium</Emphasis>reveals two temporally distinct phases of expression evolution

Background  

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes.     

CWRML: representing crop wild relative conservation and use data in XML

Background  

Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange.     

Origins of the amphiploid species <Emphasis Type="Italic">Brassica napus</Emphasis>L. investigated by chloroplast and nuclear molecular markers

Background  

The amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species.     

Isolation and characterization of the dehydration stress-inducible GhRDL1 promoter from the cultivated upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>)

Cotton fiber is the basic raw material used in the textile industry. The fiber yield is severely affected by a number of biotic and abiotic factors, such as insects, viruses, drought and salinity. Drought is a major factor that negatively impacts the yields and quality of cotton fiber. Promoters that respond to stress conditions and up-regulate transgenes are of great significance in crop improvement using genetic engineering approach. Although dehydration-responsive gene promoters, such as RD22 and RD29 from Arabidopsis, have been characterized, not much information is available regarding stress-responsive promoters from Gossypium hirsutum, which accounts for approximately 90 % of cultivated cotton. In this study, we isolated and characterized the promoter of a dehydration-responsive gene (GhRDL1) from G. hirsutum using Agrobacterium-mediated transformation in tobacco and cotton. Transgenic tobacco plants expressing uidA under the GhRDL1 promoter showed GUS activity in the trichomes. Also, GUS expression was observed to some extent in leaf, stem and floral tissues. Similar results were observed when GhRDL1 promoter was tested in transgenic cotton. Most importantly, our study showed that the GhRDL1 promoter is up-regulated in the presence of polyethylene glycol that creates water stress under invitro conditions. Thus, the GhRDL1 promoter may find its usefulness in the development of stress-tolerant cotton and other crop species in the near future.     

Development of Efficient Plant Regeneration and Transformation System for Impatiens Using <Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis>and Multiple Bud Cultures as Explants

Background  

Impatiens (Impatiens walleriana) is a top selling floriculture crop. The potential for genetic transformation of Impatiens to introduce novel flower colors or virus resistance has been limited by its general recalcitrance to tissue culture and transformation manipulations. We have established a regeneration and transformation system for Impatiens that provides new alternatives to genetic improvement of this crop.     

Exploring valid reference genes for gene expression studies in <Emphasis Type="Italic">Brachypodium distachyon</Emphasis>by real-time PCR

Background  

The wild grass species Brachypodium distachyon (Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data.     

Genetic and environmental control of the <Emphasis Type="Italic">Verticillium</Emphasis> syndrome in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background  

Verticillium spp. are major pathogens of dicotyledonous plants such as cotton, tomato, olive or oilseed rape. Verticillium symptoms are often ambiguous and influenced by development and environment. The aim of the present study was to define disease and resistance traits of the complex Verticillium longisporum syndrome in Arabidopsis thaliana (L.) Heynh. A genetic approach was used to determine genetic, developmental and environmental factors controlling specific disease and resistance traits and to study their interrelations.     

Construction of a complete set of alien chromosome addition lines from Gossypium australe in Gossypium hirsutum: morphological,cytological, and genotypic characterization

Key message

We report the first complete set of alien addition lines of G. hirsutum . The characterized lines can be used to introduce valuable traits from G. australe into cultivated cotton.

Abstract

Gossypium australe is a diploid wild cotton species (2n = 26, GG) native to Australia that possesses valuable characteristics unavailable in the cultivated cotton gene pool, such as delayed pigment gland morphogenesis in the seed and resistances to pests and diseases. However, it is very difficult to directly transfer favorable traits into cultivated cotton through conventional gene recombination due to the absence of pairing and crossover between chromosomes of G. australe and Gossypium hirsutum (2n = 52, AADD). To enhance the transfer of favorable genes from wild species into cultivated cotton, we developed a set of hirsutum–australe monosomic alien chromosome addition lines (MAAL) using a combination of morphological survey, microsatellite marker-assisted selection, and molecular cytogenetic analysis. The amphidiploid (2n = 78, AADDGG) of G. australe and G. hirsutum was consecutively backcrossed with upland cotton to develop alien addition lines of individual G. australe chromosomes in G. hirsutum. From these backcross progeny, we generated the first complete set of chromosome addition lines in cotton; 11 of 13 lines are monosomic additions, and chromosomes 7G^a and 13G^a are multiple additions. MAALs of 1G^a and 11G^a were the first to be isolated. The chromosome addition lines can be employed as bridges for the transfer of desired genes from G. australe into G. hirsutum, as well as for gene assignment, isolation of chromosome-specific probes, flow sorting and microdissection of chromosome, development of chromosome-specific ‘‘paints’’ for fluorochrome-labeled DNA fragments, physical mapping, and selective isolation and mapping of cDNAs for a particular G. australe chromosome.     

Large impact of the apoplast on somatic embryogenesis in <Emphasis Type="Italic">Cyclamen persicum</Emphasis> offers possibilities for improved developmental control <Emphasis Type="Italic">in vitro</Emphasis>

Background  

Clonal propagation is highly desired especially for valuable horticultural crops. The method with the potentially highest multiplication rate is regeneration via somatic embryogenesis. However, this mode of propagation is often hampered by the occurrence of developmental aberrations and non-embryogenic callus. Therefore, the developmental process of somatic embryogenesis was analysed in the ornamental crop Cyclamen persicum by expression profiling, comparing different developmental stages of embryogenic cell cultures, zygotic vs. somatic embryos and embryogenic vs. non-embryogenic cell cultures.     

Rapid linkage disequilibrium decay in the <Emphasis Type="Italic">Lr10</Emphasis> gene in wild emmer wheat (<Emphasis Type="Italic">Triticum dicoccoides</Emphasis>) populations

Introduction  

Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR).