Transcriptomic and genomic analyses of Arabidopsis meiosis

Meiosis is essential for eukaryotic sexual reproduction and meiotic recombination plays a crucial role in redistributing genome variations at each generation. To investigate meiotic gene expression patterns, we analyzed Arabidopsis male meiocytes using RNA-seq and detected the expression of ~16,000 genes, with >800 genes showing preferentially expression in the meiocytes. Among 3,378 gene families, 3,265 contained meiocyte-expressed genes and 18 were overrepresented in male meiocytes, including genes encoding transcription factor. Moreover, many genes expressed in meiocytes are conserved in other organisms, including 503 single-copy genes shared between Arabidopsis, mouse and yeast. Arabidopsis natural variants are excellent for studying genetic variations and their meiotic redistribution, taking advantage of the unique feasibility of tetrad analysis in Arabidopsis among non-fungal organisms. We sequenced the Landsberg erecta (Ler) ecotype and eight meiotic progenies from two tetrads of a Col /Ler hybrid. Col and Ler showed > 300,000 single nucleotide polymorphisms (SNPs), >50,000 small insertions-deletions (indels), ~2,300 large indels and over 1,000 copy number variations (CNVs). Hundreds of genes have more than 10 amino acid differences between Col and Ler in the coding regions and are highly enriched in genes for defense response and programmed cell death. Furthermore, large indels affected >300 genes, including the complete removal of 130 coding regions in Ler. Using the newly detected SNPs, we found nine meiotic crossovers in each of two meioses, at least one between each pair of homologous chromosomes. The lengths of crossover tracts in Arabidopsis seemed shorter than those in yeast. We found and experimentally confirmed four noncrossover events. Our results provide the first insights into the effect of meiotic recombination on genome variation in a single generation and establish a system for further analysis in this important area.