High-density genetic linkage maps with over 2,400 sequence-anchored DArT markers for genetic dissection in an F2 pseudo-backcross of Eucalyptus grandis × E. urophylla

Kullan, Anand Raj Kumar; Dyk, M. M. van; Jones, N.B.; Kanzler, Arnulf; Bayley, A.D.; Myburg, Alexander Andrew

doi:10.1007/s11295-011-0430-2

Cited by 42 publications

(78 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The F2 backcross population was generated from a cross between an E. grandis × E. urophylla F1 interspecific hybrid parent (GUSAP1, Sappi Forest Research, South Africa) and an unrelated E. urophylla parent (USAP1) (18). At 3 y old, immature xylem tissue was harvested from 156 individuals as previously described (56).…”

Section: Methodsmentioning

confidence: 99%

“…The characterization of natural genetic perturbations segregating in phenotypically wild-type individuals offers an attractive alternative tool to study properties that emerge from permissible genetic variation (11,13). With the availability of high-throughput genotyping and high-resolution linkage maps in Populus (14,15) and Eucalyptus (16)(17)(18)(19), genetic approaches such as quantitative trait locus (QTL) (14,20,21) and LD-based association mapping (22)(23)(24)(25) are becoming feasible to…”

mentioning

confidence: 99%

See 1 more Smart Citation

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Mizrachi

Verbeke

Christie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.systems genetics | lignocellulosic biomass | cell wall | bioenergy | network-based data integration

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Mizrachi

Verbeke

Christie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…We assembled a non-redundant chromosome-scale reference (V1.0) sequence for BRASUZ1 based on 6.73 whole-genome Sanger shotgun coverage, paired bacterial artificial chromosome (BAC)-end sequencing and a high-density genetic linkage map 6 (see Methods and Supplementary Information section 1). An estimated 94% of the genome is organized into 11 pseudomolecules (605 megabases (Mb), Fig.…”

Section: Sequencing Assembly and Annotationmentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

Self Cite

761

750

View full text Add to dashboard Cite

Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

show abstract

“…More informative, codominant markers such as isozymes, RFLPs, and ESTs were indeed successfully used to map eucalypt genomes (Byrne et al 1995;Gion et al 2000;Thamarus et al 2002) but did not provide the levels of polymorphism and throughput required for routine mapping in multiple pedigrees. It was only with the more recent development of large numbers of highly polymorphic microsatellite (or SSR) markers for Eucalyptus (Brondani et al 1998(Brondani et al , 2006Glaubitz et al 2001;Ottewell et al 2005;Steane et al 2001) that comparative mapping could be performed and linkage map synteny established across multiple pedigrees (Brondani et al 2006;Freeman et al 2006;Marques et al 2002;Hudson et al 2011;Kullan et al 2012). …”

Section: Next-generation Sequencing Resourcesmentioning

confidence: 99%