Sugarcane genomics: depicting the complex genome of an important tropical crop

Grivet, Laurent; Arruda, Paulo

doi:10.1016/s1369-5266(02)00234-0

Cited by 267 publications

(194 citation statements)

References 49 publications

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“…Modern cultivars have 2n = 100-130 chromosomes, which are often recombined or lost. This exceptionally complex polyploid aneuploid genome can be thought of as being composed of multiple variant copies of the closely related Sorghum genome 48 . To assess genetic diversity between related chromosomes and to identify lines for optimal crosses, linked-read technologies could be applied to generate a number of haplotypes that are aligned to the Sorghum 'baseline' genome.…”

Section: Combined Approaches To Genome Sequencing and Assemblymentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

311

218

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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Section: Combined Approaches To Genome Sequencing and Assemblymentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

311

218

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“…Because of its diverse origin, sugarcane is thought to have one of the most complex plant genomes, carrying variable chromosome numbers. Modern cultivars generally have between 100 and 130 chromosomes (Grivet and Arruda, 2002). In situ hybridization studies have suggested that modern cultivars inherit approximately 80% of their chromosomes entirely from S. officinarum, approximately 10% entirely from S. spontaneum, and approximately 10% as the result of recombination among the remaining ancestral species (D'Hont et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Use of differential levels of mean observed heterozygosity in microsatellite loci of commercial varieties of sugarcane (Saccharum spp)

Maranho¹,

Augusto²,

Mangolin³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. In this study, we measured the genetic diversity within and among a set of 9 commercial sugarcane varieties used for alcohol and sugar production using 17 microsatellite DNA markers. The UGSM148 and UGSM59 primers were monomorphic for all 74 sugarcane samples. The estimated proportion of simple sequence repeated (SSR) polymorphic loci was 88.23%; 17 alleles were detected. The mean gene diversity of all SSR loci was 0.7279. The

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“…This is the case of sugarcane, an important crop that is cultivated in the tropics for its high sucrose accumulation in the stalk. Among the cultivated crops, sugarcane possesses perhaps one of the most complex genomes (for a review see Grivet and Arruda, 2002). Modern sugarcane cultivars are hybrids derived from the crossing of Saccharum officinarum, usually having 2n = 80 chromosomes and Saccharum spontaneum, 2n = 40 -128 chromosomes.…”

Section: Introductionmentioning

confidence: 99%

“…Modern sugarcane cultivars are hybrids derived from the crossing of Saccharum officinarum, usually having 2n = 80 chromosomes and Saccharum spontaneum, 2n = 40 -128 chromosomes. In view of the structural differences between chromosomes of the two species, the hybrids possess different proportions of chromosomes, varying chromosome sets and complex recombinational events (Grivet and Arruda, 2002). This imposes tremendous difficulties in applying conventional plant breeding techniques to sugarcane.…”

Section: Introductionmentioning

confidence: 99%

The libraries that made SUCEST

et al. 2001

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A large-scale sequencing of sugarcane expressed sequence tags (ESTs) was carried out as a first step in depicting the genome of this important tropical crop. Twenty-six unidirectional cDNA libraries were constructed from a variety of tissues sampled from thirteen different sugarcane cultivars. A total of 291,689 cDNA clones were sequenced in their 5' and 3'end regions. After trimming low-quality sequences and removing vector and ribosomal RNA sequences, 237,954 ESTs potentially derived from protein-encoding messenger RNA (mRNA) remained. The average insert size in all libraries was estimated to be 1,250bp with the insert length varying from 500 to 5,000 bp. Clustering the 237,954 sugarcane ESTs resulted in 43,141clusters, from which 38% had no matches with existing sequences in the public databases. Around 53% of the clusters were formed by ESTs expressed in at least two libraries while 47% of the clusters are formed by ESTs expressed in only one library. A global analysis of the ESTs indicated that around 33% contain cDNA clones with full-length insert.

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Sugarcane genomics: depicting the complex genome of an important tropical crop

Cited by 267 publications

References 49 publications

Genomic innovation for crop improvement

Genomic innovation for crop improvement

Use of differential levels of mean observed heterozygosity in microsatellite loci of commercial varieties of sugarcane (Saccharum spp)

The libraries that made SUCEST

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