Chromosome-level genome assembly of a regenerable maize inbred line A188

Abstract

Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii

“…To understand the haplotype of the Lr42 locus, publicly available whole genome sequencing (WGS) Illumina data were used to first examine polymorphisms between TA2450 ( Lr42 resistant line) and TA10132 (susceptible reference line) 27 . The result from Comparative Genomics Read Depth (CGRD) analysis using WGS data 28 , which provides similarities and copy number variation of low-repetitive regions between the two genomes, revealed two relatively conserved segments (8.24–8.67 Mb and 8.70–8.82 Mb on 1D) and other divergent regions (Fig. 3a ).…”

“…The public WGS Illumina data of TA10132 (the reference susceptible line, SRS7974112) and TA2450 (the Lr42 parental resistant line, SRS7973948) were downloaded 27 . The data were used for genome comparison through CGRD [ https://github.com/liu3zhenlab/CGRD ] 28 , identifying conserved and variable regions on the Ae. tauschii reference genome between the two genomes.…”

“…The RL1 gene amplified by RLI_F1/R1 (Supplementary Data 8 ) was used as the reference gene for normalizing gene expression data 64 . Primer efficiencies for the target and reference genes were in the range of 100–110%, therefore, gene expression data were analyzed using the CT method 28 , 65 . Three biological replicates were used for expression analysis.…”

“…Primers Lr42-qRT_F6 and Lr42-qRT _ R6 (Supplementary Data 8 ) were used for Lr42 , and primers actin_F1 and actin_R1 (Supplementary Data 8 ) were used for the actin gene as the control. The thermocycling conditions were initial denature at 95 °C for 3 min, 40 cycles of 95 °C for 10 s, 60 °C for 30 s. The CT method was used to determine the relative expression of Lr42 28 , 65 .…”

Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture

“…The dynamics of DNA methylation have already been reported to be an important way to actively reprogram, which plays critical roles in transposon silencing, genome stability and gene expression regulation during cell fate transition in both plants and animals (Feng et al, 2010;Zhang et al, 2010). In plant tissue culture, genome wide hypo-and hypermethylation were predominantly observed during the process of dedifferentiation (callus induction) and redifferentiation (shoots induction), respectively, in a variety of plant species (Neelakandan and Wang, 2012;Ghosh, 2016;Hesami et al, 2020;Lin et al, 2021), that was in accordance with our findings. There is little information concerning alterations in DNA methylation following consecutive stages of tissue culture from explants to outplanting.…”