Guoying Wang | Search bioRxiv

bioRxiv2016

Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere repeats, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Previously unknown genotype specific 45S rDNA sequences were discovered. The B73-specific 45S rDNA is not only located on the nucleolus organizer region (NOR) on chromosome 6 but also dispersed on all the chromosomes in B73, indicating the relatively recent spread of 45S rDNA from the NOR. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that dosage compensation operates for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 double haploids (DHs), genomic locations showing differential repetitive contents were genetically mapped. Analysis of WGS sequences of HapMap2 lines, including maize wild progenitor teosintes, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere repeats, 45S rDNA, knob, and retrotransposon sequences were found between teosinte and maize lines, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

Genomics↗

bioRxiv2015

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Variation in gene expression contributes to the diversity of phenotype. The construction of the pan-transcriptome is especially necessary for species with complex genomes, such as maize. However, knowledge of the regulation mechanisms and functional consequences of the pan-transcriptome is limited. In this study, we identified 13,382 nuclear expression presence and absence variation candidates (ePAVs, expressed in 5%~95% lines; based on the reference genome) by re-analyzing the RNA sequencing data from the kernels (15 days after pollination) of 368 maize diverse inbreds. It was estimated that only ~1% of the ePAVs are explained by DNA sequence presence and absence variations (PAV). The ePAV genes tend to be regulated by distant eQTLs when compared with non-ePAV genes (called here core expression genes, expressed in more than 95% lines). When the expression presence/absence status was used as the \" genotype\" to perform genome-wide association study, 56 (0.42%) ePAVs were significantly associated with 15 agronomic traits and 1,967 (14.74%) with 526 metabolic traits, measured from the mature kernels. While the above was majorly based on the reference genome, by using a modified assemble-then-align strategy, 2,355 high confidence novel sequences with a total length of 1.9Mb were found absent in the current B73 reference genome (v2). Ten randomly selected novel sequences were validated with genomic PCR. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes. Two novel validated sequences annotated as NBS_LRR like genes were found to associate with flavonoid content and their homologs in rice were also found to affect flavonoids and disease-resistance. Novel sequences absent in the present reference genome might be functionally important and deserve more attentions. This study provides novel perspectives and resources to discover maize quantitative trait variations and help us to better understand the kernel regulation networks, thus enhancing maize breeding.

Genetics↗