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

Abstract

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.

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

“…In addition, mapping populations of inter-mated B73xMo17 recombinant inbred lines and doubled haploids have been generated to facilitate genetic analyses 9,10 . Numerous comparative genomics studies of other maize cultivars and wild ancestors have examined the origin of maize as well as events of adaptation and artificial selection [11][12][13][14][15][16][17] . However, the studies are limited to comparisons of non-repetitive and low-repetitive sequences.…”

The wheat pangenome: assembly and analysis

“…However, it is only recently that large scale pangenomic studies of plants have been undertaken. The 1001 Arabidopsis genome project (Alonso-Blanco et al), the rice pangenome assembly and gbrowse , the maize pantranscriptome and pangenome analysis (Jin et al, 2016, Hirsch et al, 2014, the construction of soybean pangenome draft (Li et al, 2014c) and the recent construction and analysis of the Brassica oleracea pangenome (Brassica genome C) (Golikz, 2016, Golicz et al, 2016b are all the first attempts at unveiling the hidden genetic diversity of crop plant gene pools.…”

“…A recent study by Liu et al (2016) assembled unmapped reads from chromosome 3B of cultivar CRNIL1A and determined that up to 8.3 Mbp of sequences present in the CRNIL1A 3B chromosome were absent in its Chinese Spring counterpart and estimated that 159.3 Mbp present in the CRNIL1A could be absent in the Chinese Spring reference genome. Additionally, the authors assembled RNA-seq data from 28 wheat cultivars and aligned the assembled transcripts to the IWGSC reference genome, the TGAC v1 genome, the W7984 assembly and the assembly of 16 wheat cultivars described here.…”

“…The authors found that 10% of the transcripts not found in any Chinese Spring reference assembly were found in the assembly of the 16 Australian wheat cultivars we provided (Liu et al, 2016). The assembly provided by us did not include the assembly of unmapped reads from the W7984 and OpataM85 genomes.…”

“…In bacteria, lateral gene transfer is a major mechanism in the acquisition of new genetic material, species with high rates of horizontal gene transfer tend to have larger pangenomes, and the fraction of their core genome tends to be smaller , Tettelin et al, 2008, Medini et al, 2005. Meanwhile, the origin of variable genes in plants is largely affected by gene loss, genome duplication followed by diversification and activity of transposable elements (Jin et al, 2016, Hirsch et al, 2014.…”