Three founding ancestral genomes involved in the origin of sugarcane.

BACKGROUND AND AIMS: Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. METHODS: To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. KEY RESULTS: The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. CONCLUSIONS: This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq.

A RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a "snakemake" pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values (< 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning.

Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids.

Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.

Genomic preselection with genotyping-by-sequencing increases performance of commercial oil palm hybrid crosses.

BACKGROUND: There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with almost 500 crosses for training and 200 crosses for independent validation. Genotyping-by-sequencing (GBS) yielded +5000 single nucleotide polymorphisms (SNPs) on the parents of the crosses. The genomic best linear unbiased prediction method gave genomic predictions using the SNPs of the training and validation sets and the phenotypes of the training crosses. The practical impact was illustrated by quantifying the additional bunch production of the crosses selected in the validation experiment if genomic preselection had been applied in the parental populations before progeny tests. RESULTS: We found that prediction accuracies for cross values plateaued at 500 to 2000 SNPs, with high (0.73) or low (0.28) values depending on traits. Similar results were obtained when parental breeding values were predicted. GS was able to capture genetic differences within parental families, requiring at least 2000 SNPs with less than 5% missing data, imputed using pedigrees. Genomic preselection could have increased the selected hybrids bunch production by more than 10%. CONCLUSIONS: Finally, preselection for yield components using GBS is the first possible application of GS in oil palm. This will increase selection intensity, thus improving the performance of commercial hybrids. Further research is required to increase the benefits from GS, which should revolutionize oil palm breeding.

Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut.

The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications.

Whole-genome duplications (WGDs) are widespread in plants, and three lineage-specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening. Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed. Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1-aminocyclopropane-1-carboxylate synthase (ACS), ethylene-insensitive 3-like (EIL), ethylene-insensitive 3-binding F-box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them. We propose that EIL and EBF genes were co-retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling.

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane.

Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It has the highest level of 'vertical' redundancy (2n=12x=120) of all polyploid plants studied to date. It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum. In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. Remarkably, all of the hom(oe)ologous genes were predicted as being functional (except for one gene fragment) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe. These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics.

Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

BACKGROUND: Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). RESULTS: Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. CONCLUSIONS: A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.