Using Crossover Breakpoints in Recombinant Inbred Lines to Identify Quantitative Trait Loci Controlling the Global Recombination Frequency

Abstract

Recombination is a crucial component of evolution and breeding, producing new genetic combinations on which selection can act. Rates of recombination vary tremendously, not only between species but also within species and for specific chromosomal segments. In this study, by examining recombination events captured in recombinant inbred mapping populations previously created for maize, wheat, Arabidopsis, and mouse, we demonstrate that substantial variation exists for genomewide crossover rates in both outcrossed and inbred plant and animal species. We also identify quantitative trait loci (QTL) that control this variation. The method that we developed and employed here holds promise for elucidating factors that regulate meiotic recombination and for creation of hyperrecombinogenic lines, which can help overcome limited recombination that hampers breeding progress.A LTHOUGH natural selection is a powerful evolutionary process, it utilizes only the existing variation present in a population. Recombination of alleles is required to efficiently evolve new genetic varieties. Not surprisingly, theoretical predictions (Otto and Michalakis 1998) and empirical studies (Saleem et al. 2001) indicate that populations experiencing directional or strong selection pressures evolve increased recombination rates. Similarly to the natural evolutionary processes, combining many positive alleles into a single germplasm is the main objective of plant and animal breeding. The stacking of the favorable alleles is limited by the time and the number of meioses required to recombine numerous alleles from multiple parents. Consequently, a better understanding of the factors controlling recombination holds numerous implications for both academic and applied realms.To date, many of the genes involved in meiotic recombination have been identified and the mechanistic basis of recombination have begun to emerge (Krogh and Symington 2004;Cohen et al. 2006;Li and Ma 2006). However, the mechanisms that regulate recombination are poorly understood. Particularly, little is known about the control of genomewide recombination rates. Variation in recombination rates has been documented both within and between species, as well as between particular chromosomal regions (Rees 1961;Säll 1990;Beavis and Grant 1991;Tulsieram et al. 1992;Fatmi et al. 1993;Korol et al. 1994;Williams et al. 1995;Sanchez-Moran et al. 2002;Anderson et al. 2003;De Massy 2003;Myers et al. 2005; YandeauNelson et al. 2006). A minimum of one obligatory crossover per chromosome, or chromosome arm, occurs during meiosis as a requirement for proper chromosome segregation (Pardo-Manuel De Villena and Sapienza 2001). However, factors that control whether just this one or multiple crossovers occur per chromosome are poorly understood. Even though the idea that recombination frequencies can be genetically dissected, as any other quantitative trait, was first proposed long ago (Rasmusson 1927), to our knowledge, no quantitative trait loci (QTL) affecting recombination rates have been ...

Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping

“…S1). Consistent with these simulations, a survey of recombination rates in five A. thaliana RIL populations at the F 8 generation, showed that the mean number of recombination events ranged from 6.23 to 8.89 per individual (37). Relative to our doubled haploid population (4.89 recombination events per individual) these RILs have undergone an additional six generations of selfing and the average number of recombination events has increased approximately twofold.…”

The maize (Zea mays) desynaptic (dy) mutation defines a pathway for meiotic chromosome segregation, linking nuclear morphology, telomere distribution and synapsis

“…Relatedly, genetic control of recombination frequency in maize was subjected to QTL mapping by two groups, and in each study, the biggest effect QTL mapped to regions immediately adjacent to our dy mapping interval (Dole and Weber, 2007;Esch et al, 2007). These map positions were estimated to be between 166.0 and 168.5 MB (Esch et al, 2007) and at 181.1 MB (Dole and Weber, 2007) on the physical map of maize, which map just beyond our proximal and distal boundaries, respectively. Interestingly, the QTL with the greatest effect on recombination in Arabidopsis mapped near the end of chromosome 1, a region including At1G71360, predicted to encode a PM3-type SUN-domain.…”

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes inBrassica napusAllohaploids

“…Our knowledge of the genes and mechanisms involved in meiotic recombination and CO formation in plants has received a boost in the last 6 years with the use of Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays) as model systems (Mezard et al, 2007;Mercier and Grelon, 2008). However, little is known about natural variation in recombination rates within species (Sä ll, 1990;SanchezMoran et al, 2002;Anderson et al, 2003;Esch et al, 2007;Bovill et al, 2008), which is an important issue for understanding how recombination is regulated in the wild.…”