8/17/2023 0 Comments Touchdown pcr microbiome![]() ![]() ![]() Here, with the help of deep RNA-seq of kernels at 15 DAP in a diverse panel with 368 inbred lines 5, we characterized the extreme variation at the transcript level (ePAV), relative to the reference genome and performed association studies between ePAVs and more than 600 quantitative traits. Recently, the maize pan-transcriptome and its diversity have been studied in diverse lines 9, 12, however, we still lack knowledge about many dispensable gene function at the genome-wide level. The construction of the maize pan-transcriptome is especially useful for the discovery of functional dispensable genes. Compared to genome sequencing, RNA-seq is more economical, especially in the exploration of the complex maize genome containing more than 85% repetitive sequences 11. RNA sequencing (RNA-seq) has been successfully used to define the transcriptome and to find novel transcripts absent from the reference genome 10. The rapid development of next generation sequencing technology and the decrease in cost provide us an opportunity to sequence many individuals within a species to build up the pan genome, or the sequences which, taken as a whole from all individuals, define a species. The widespread dispensable genes, i.e those showing present/absent variation, have been proposed to be important for phenotypic diversity in inbred collections and for heterotic performance in hybrids 8, 9. The genome-wide comparison between B73 and Mo17 6 and within an expanded panel including teosinte (ancestral maize) lines 7 demonstrated that a considerable portion of the genome (~50%) was not shared. It is now recognized that a portion of the genomic content is only present in a subset of individuals within a species, (termed the dispensable genome) especially in diverse species, such as maize. Most genome-wide genetic studies focus the genetic elements present in the reference genome. Thus it is essential to characterize the ePAV genes and their possible functions. ![]() The ePAV not only reflect genomic structural variation, but also the variations in genetic and epigenetic regulatory elements. PAV at the genomic level would be reflected in the transcriptome ePAV (expression Presence and Absence Variation). ![]() Presence/absence genomic sequence variation (PAV) is important in reshaping individual performance 6. As it becomes clear that the differences in transcript abundance are a major contributor to phenotypic evolution 3, 4, allelic variation effects on the transcriptome, which reflect both genetic and epigenetic regulation, should be explored at a genome-wide level 5. Phenotypic variation has been explored by QTL mapping and genome-wide association studies (GWAS) 2. Maize shows an amazing degree of phenotypic variation due to the outcrossing nature and to natural and artificial selection during the rapid worldwide population expansion 1. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |