Gbs-based Single Dosage Markers For Linkage And Qtl Mapping Allow Gene Mining For Yield-related Traits In Sugarcane

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. Results: We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. Conclusions: This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.18FINEP (Finaciadora de Estudos e Projetos)FAPESP (Fundacao de Amparo a Pesquisa de Sao Paulo) [08/52197-4]INCT-Bioetanol (Instituto Nacional de Ciencia e Tecnologia do Bioetanol) [FAPESP 08/57908-6]INCT-Bioetanol (CNPq, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico) [574002/2008-1]FAPESP [10/50091-4, 12/25236-4, 10/50549-0, 10/50031-1, 12/11109-0]CNPqCAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2 7 = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

<p>Abstract</p> <p>Background</p> <p>The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the <it>Quercus </it>family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.</p> <p>Results</p> <p>We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser <url>http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html</url>.</p> <p>Conclusions</p> <p>This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.</p

Africa, the Cradle of Human Diversity

This book brings together experts from several disciplines, reviewing and discussing our current knowledge of the complex history, biological diversity and behavioral evolution of African populations. The collection provides a valuable resource for students and researchers from various fields.; Readership: This book offers accessible knowledge from a multidisciplinary perspective to students, scholars and researchers interested in human evolutionary history, population genetics, archaeology, paleogenomics, anthropology, and related disciplines

Africa, the Cradle of Human Diversity

This book brings together experts from several disciplines, reviewing and discussing our current knowledge of the complex history, biological diversity and behavioral evolution of African populations. The collection provides a valuable resource for students and researchers from various fields.; Readership: This book offers accessible knowledge from a multidisciplinary perspective to students, scholars and researchers interested in human evolutionary history, population genetics, archaeology, paleogenomics, anthropology, and related disciplines

The genome of Eucalyptus grandis

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

QTL mapping in population originated from a bi-parental commercial cross of sugarcane

Orientadores: Anete Pereira de Souza, Monalisa Sampaio CarneiroTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: A cana-de-açúcar é uma fonte renovável de energia e com potencial para expansão. A complexidade genética da cana-de-açúcar decorrente de seu alto nível de ploidia e aneuploidia, aliada à natureza quantitativa da maioria dos caracteres agronômicos tem dificultado, atualmente, a obtenção de elevados índices de ganho genético através do melhoramento convencional. O desenvolvimento de marcadores moleculares e a construção de mapas genéticos podem auxiliar na elaboração de estratégias a serem introduzidas nos programas de melhoramento de forma a aumentar a eficiência dos processos de seleção e acelerar o desenvolvimento de novas cultivares. Desta forma, a proposta desta tese foi a construção de um mapa genético em cana-de-açúcar visando a identificação de regiões genômicas que controlam características de interesse através do mapeamento de QTL (Quantitative Trait Loci). Uma população de cana-de-açúcar com 153 indivíduos oriundos do cruzamento comercial bi-parental entre as cultivares SP80-3280 e RB835486 foi utilizada para alcançar os objetivos citados. O experimento de campo foi instalado em duas localidades, Araras-SP e Ipaussu-SP, usando o delineamento de blocos aumentados incompletos com 3 repetições. As avaliações fenotípicas foram realizadas ao longo de três anos (2011, 2012 e 2013). Empregou-se a abordagem de modelos mistos para análise das características fenotípicas relacionadas com componentes de produção e resistência à ferrugem marrom. Os dados de severidade à ferrugem marrom foram analisados, como uma primeira abordagem, via modelo misto linear generalizado. As estimativas de herdabilidade das características fenotípicas foram altas, variando de 0.78 (altura de colmos) a 0.92 (diâmetro de colmos), e a análise de severidade à ferrugem marrom mostrou que 66% dos clones possuem, no mínimo, 90% de probabilidade de serem resistentes à doença. Para construção do mapa genético integrado foram utilizados marcadores moleculares do tipo microssatélites (Simple Sequence Repeats, SSR), TRAP (Target Target Region Amplification Polymorphism), além de SNPs (Single Nucleotide Polymorphims) e indels (inserções e deleções) oriundos da técnica de GBS (Genotyping-by-Sequencing). Para descoberta de marcadores baseados em GBS foram utilizadas quatro pseudo-referências: genoma de sorgo (Sorghum bicolor), genoma metil-filtrado da cana-de-açúcar, transcriptoma da cana-de-açúcar (RNAseq) e sequências do projeto SUCEST. A ploidia e dosagem de cada loco bi-alélico foi estimada através do software SUPERMASSA. Utilizando o software Onemap (v. 2.0-4) e empregando-se LOD > 9.0 e fração de recombinação 9.0 and recombination fraction <0.10, a total of 993 markers in single dose were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups. The total length of the map was 3,682.04 cM with an average marker density of 3.70 cM. Using composite interval mapping (Composite Interval Mapping, CIM) were mapped seven QTLs considering four of the 11 phenotypic traits evaluated. The results suggest the presence of a stable QTL across locations to soluble solid content (BRIX) and sucrose content of the cane (POL%C). Furthermore, QTLs to BRIX and fiber content (FIB) traits had associated markers with candidate genes, which had great potential for validation and future use for molecular breeding in sugarcane. This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a population in sugarcane with posterior analysis to composite interval mappingDoutoradoGenetica Vegetal e MelhoramentoDoutor em Genetica e Biologia Molecular2010/50091-4 , 2008/52197-4FAPES