Genetic diversity among sugarcane clones using Target Region Amplification Polymorphism (TRAP) markers and pedigree relationships

Genetic diversity is indispensable to sustain genetic gain in breeding programs. Cultivated sugarcane is a highly heterozygous hybrid derived from crossing two highly heterozygous parents. Sugarcane breeders traditionally rely on pedigree records to select parents. Molecular markers now make it possible to assess genetic diversity at the DNA level. Sixty three sugarcane clones were characterised using Target Region Amplification Polymorphism (TRAP) markers and pedigree relationship (Coefficient of parentage (COP)). The TRAP is a PCR-based marker with a fixed primer designed from Expressed Sequence Tag (EST) sequences paired with an arbitrary primer. It is supposed to unravel trait based polymorphism in the intronic- or exonic-regions of the genome. Ten genes evidently involved in sucrose accumulation (SUC), cold tolerance (CT) and trichome development (TRICH) were paired with four arbitrary primers. A total of 3,170 bands were scored of which 2,684 (85%) were polymorphic. Cluster and Multi Dimensional Scaling (MDS) analyses revealed a very narrow genetic diversity among the entries with genetic similarity (GS) ranging from 78 to 94%. Parentage did not seem to contribute to the grouping pattern in either the overall or individual gene family (SUC, CT and TRICH) clusters which was confirmed by the lack of correlation (r = -0.008) between the TRAP and COP-derived GS matrices. The complex genome of sugarcane and the strict assumptions inherent with estimating COP may account for this disparity. Analysis of Molecular Variance (AMOVA) revealed no structure in the population with regards to era of release (Pre- versus post-1980) with among clones accounting for up to 99% of the total variation and only 1% of variation attributable to era of release. Mixed Model Analysis on the MDS axes generally revealed no significant differences among era of release. Thus, pedigree records can enhance interpretation of marker-derived information especially in an interspecific crop like sugarcane where ancestral species possess and contribute different characteristics. Results from this study needs to be supplemented with sequence analysis of TRAP fragments to definitively relate the derived information to trait variation

Evolution and domestication of Saccharum using transcriptomic analyses

Artificial selection during crop domestication has dramatically shaped many wild plant species into high yielding food, fiber, medicinal, and biofuel crops. The trajectory from wild to domesticated is a long and complex process that leaves strong signatures of selection on the genome. Here we use a population genetics approach and transcriptome survey to scan for signatures of selection and domestication in sugarcane (Saccharum), the leading source of global sugar production. The sugarcane genome is highly complex, with ploidy levels ranging from 8n-14n. This complexity has hindered advances in marker assisted breeding and subjects sugarcane to a unique set of evolutionary forces not experienced during the domestication of most diploid crop species. Modern sugarcane is an interspecific hybrid mainly between the cultivated S. officinarum (2n=80) and the wild species S. spontaneum (2n=40-128), with some marginal contribution from S. robustum (2n=60-200) in a few breeding stations. We screened 48 representative accessions of the domesticated S. officinarum and the wild species S. spontaneum and S. robustum to identify genes selected during domestication. 2.8 million single nucleotide polymorphisms (SNPs) were found from 2.2 billion RNA-seq reads generated from leaf and stalk tissue. S. officinarum has twice as much inter-population allelic diversity compared to S. spontaneum and to S. robustum. The stalk transcriptome has more allele diversity than the leaf, reflective of gene expression changes during domestication. The allele diversity in Saccharum is characterized by the prevalence of intermediate-allele frequency typical of a balancing selection and reflective of the high degree of heterozygosity in this species. The population structure of sugarcane does not render to conventional population genetics tests for signals of selection due to the dynamics imposed by fixed heterozygosity. Site frequency spectrum (SFS) pattern describes higher per-site heterozygosity in genes that might be targets of domestication. Around 200 candidate domestication genes were detected in S. officinarum based on the prevalence of balancing selection among ~3000 SNPs. To gain insight into the nature of gene expression divergence in Saccharum, we conducted a comparative transcriptome profiling of leaf and stalk developmental stages in S. officinarum, S. spontaneum and S. robustum. A summary of all the pairwise differential expression tests shows 3,346 genes were differentially expressed between the cultivated and the wild species, most of which were observed in immature stalk and mature leaf tissues. Maturation of stalks and leaves seems to be associated with significant transcript abundance in gene networks related to post-embryonic morphogenesis, lipid localization and perturbation of the phenylpropanoid pathway. This suggests that expression between the cultivated and wild Saccharum are related to differences related to maturation and response to external stimuli, in general, and the biomass accumulation, in particular. In addition, genes associated with sugar metabolism and transport have dynamic expression in the surveyed tissues, reflective of the known source-sink feedback signaling for sucrose accumulation in the sugar-bearing Saccharum species. While these studies might highlight the unique challenges imposed by a complicated genome of Saccharum, the results presented also elucidate the population genetics and expression pattern dynamics of this highly complex, heterozygous, autopolyploid crop

Transcriptome analysis unveils a potential novel role of VvAP1 in regulating the developmental fate of primordia in grapevine

The grapevine shoot meristem contains undifferentiated primordia known as anlagen, which can develop into either inflorescences or tendrils depending on vine age, growth status, hormone balance, and other factors. Interestingly, a gain-of-function mutation in the DELLA domain of VvDELLA1 in the dwarf mutant grape, Vitis vinifera L. cv. Pixie, virtually disrupts the normal developmental course of anlagen and reroutes tendril-bounded anlagen toward inflorescence development even at the juvenile stage. To understand the underlying mechanism(s), we compared the transcriptome profiles of V. vinifera cv. Pinot Meunier (from which Pixie was derived), Pixie, and three other V. vinifera grape cultivars (Dena, Gina, and Tia) which were derived from crosses involving Pixie and carry the same DELLA mutation. Our findings revealed significant mis-regulation of hundreds of genes, profoundly reshaping both transcriptome landscapes and regulatory pathways in the mutant grapes. Interestingly, VvAP1, a central positive flower regulator in annuals, was unexpectedly co-downregulated with VvTFL1a, a flowering repressor. We also found several other key flower regulators which were either upregulated (e.g., VvFT, VvLFY) or downregulated (e.g., VvSOC1s) in all mutant grapes, although the overall effect was moderate. These findings, along with the previous identification of tendril-specific expression of VvAP1 and inflorescence-specific expression of VvLFY, support that VvAP1 promotes anlagens to develop tendrils, whereas VvLFY favors inflorescences formation. The balance between these factors, particularly the abundance of VvAP1 transcripts, ultimately dictates whether anlagens develop into tendrils or inflorescences

Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep

Collection sites of wild Costa Rican papaya. Table S2. Summary of sequencing statistics of re-sequenced papaya genomes. Table S3 Annotation of polymorphisms. Table S4. Synonymous site diversity for genes in the X-linked region. (DOCX 37 kb

A key ‘foxy’ aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape ‘Concord’

‘Concord’, the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special ‘foxy’ aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key ‘foxy’ aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in ‘Concord’ and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the ‘foxy’ aroma trait and makes it genetically trackable and amenable in grapevine breeding

RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines

Abstract Background Gibberellins (GAs) and their regulator DELLA are involved in many aspects of plant growth and development and most of our current knowledge in the DELLA-facilitated GA signaling was obtained from the studies of annual species. To understand GA-DELLA signaling in perennial species, we created ten GA-insensitive transgenic grapevines carrying a DELLA mutant allele (Vvgai1) in the background of Vitis vinifera ‘Thompson Seedless’ and conducted comprehensive analysis of their RNA expression profiles in the shoot, leaf and root tissues. Results The transgenic lines showed varying degrees of dwarf stature and other typical DELLA mutant phenotypes tightly correlated with the levels of Vvgai1 expression. A large number of differentially expressed genes (DEGs) were identified in the shoot, leaf and root tissues of the transgenic lines and these DEGs were involved in diverse biological processes; many of the DEGs showed strong tissue specificity and about 30% them carried a DELLA motif. We further discovered unexpected expression patterns of several key flowering induction genes VvCO, VvCOL1 and VvTFL1. Conclusions Our results not only confirmed many previous DELLA study findings in annual species, but also revealed new DELLA targets and responses in grapevine, including the roles of homeodomain transcription factors as potential co-regulators with DELLA in controlling the development of grapevine which uniquely possess both vegetative and reproductive meristems at the same time. The contrasting responses of some key flowering induction pathway genes provides new insights into the divergence of GA-DELLA regulations between annual and perennial species in GA-DELLA signaling

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a three-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy. One population was the selfed progeny and the other one, an outcrossed progeny of a Vitis hybrid, 'Roger's Red'. We analyzed 13 375 expressed genes and carried out in-depth analyses of 324 of them, which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations. A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed. Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor. TCP3 and MYB12, which were known important for plant-form development, were among these transcription factors. More importantly, TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52, which is important to plant-form development. A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background