Meiotic crossovers characterized by haplotype-specific chromosome painting in maize

Lívia Do Vale Martins,Fan Yu,James A Birchler,Nick Lauter,Addie Thompson,Zuhu Deng,Hainan Zhao,Jiming Jiang,Jean-Marie Rouillard,Haiyan Wang,Kassandra Semrau,Tesia Dennison

doi:10.1038/s41467-019-12646-z

Abstract

Meiotic crossovers (COs) play a critical role in generating genetic variation and maintaining faithful segregation of homologous chromosomes during meiosis. We develop a haplotype-specific fluorescence in situ hybridization (FISH) technique that allows visualization of COs directly on metaphase chromosomes. Oligonucleotides (oligos) specific to chromosome 10 of maize inbreds B73 and Mo17, respectively, are synthesized and labeled as FISH probes. The parental and recombinant chromosome 10 in B73 x Mo17 F1 hybrids and F2 progenies can be unambiguously identified by haplotype-specific FISH. Analysis of 58 F2 plants reveals lack of COs in the entire proximal half of chromosome 10. However, we detect COs located in regions very close to the centromere in recombinant inbred lines from an intermated B73 x Mo17 population, suggesting effective accumulation of COs in recombination-suppressed chromosomal regions through intermating and the potential to generate favorable allelic combinations of genes residing in these regions.

Highlights

Meiotic crossovers (COs) play a critical role in generating genetic variation and maintaining faithful segregation of homologous chromosomes during meiosis
We identified B73 oligos that are absent in the Mo17 genome and vice versa, which were named presence-absence variation (PAV) oligos
Physical mapping of a large number of recombination nodules (RNs) indicated the lack of recombination in the pericentromeric regions of maize chromosomes, such analysis was conducted only in a single inbred line KYS32

Summary

Introduction

Meiotic crossovers (COs) play a critical role in generating genetic variation and maintaining faithful segregation of homologous chromosomes during meiosis. Meiotic recombination, which generates genetic variation via exchange of DNA between homologous parental chromosomes, is essential for plant and animal breeding. Physical mapping in plants can be achieved by using cytogenetic stocks[8,9], or by fluorescence in situ hybridization (FISH) of DNA markers directly on chromosomes[10,11,12,13,14]. The identified oligos are based on presence-absence variation (PAV), single nucleotide polymorphisms (SNPs), and/or insertions and deletions (indels) in chromosome 10 sequences derived from the two inbreds. These oligos are massively synthesized and labeled as FISH probes. We intend to use this FISH technique to detect and quantify meiotic COs derived from the two homologous chromosome 10 in different maize populations

Methods

Results

Conclusion