Dear Dr. Buckley, I am working on homeologous recombination in wheat and currently focusing on recombination hotspots and genetic mapping. Crossing over is very poor in terminal and pericentric regions and distributed in intercalary segments. At sequence level there are some signature sequences which are associated with homologous recombination and crossing over, such as Alu, Spo (topoisomerase like enzyme codes for meiosis specific double stranded breaks) etc. One can scan these signature sequences across the assembled and annotated sequence of an organism through bioinformatic or computational programs. There is one very good paper published in PloS ONE (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058916).  Wish you good luck for your research. 

Thank you, Pablo and Shailender, for your replies, especially for links to papers.

I am a breeder of American Bulldogs, with a large kennel having a near term goal of holding 40-50 breeding animals.  The price of sequencing an individual is falling, and the expectation of the $100.00US price-point provides an opportunity to trace crossover loci through a well-defined and controlled breeding pool.  With some reasonable fan-out and a number of generations, it should be possible to find any locus bias.

Comments?

Dear Dr. Buckley, 

I am wheat breeder and currently working in plant genomics and genetics. As per our previous discussion, there are several signature sequences  Apo, Spo etc. in DNA which may act as crossing over hotspots so crossing our must be locus biased.  Next question is how to identify this locus biasing? You have good population size and availability of funds and facility for sequencing, so you can go for genotyping by sequencing, identification of crossing over hotspots (through population genetics) or signature sequences (computational genomics). However, its difficult to trace out locus biasing in next generations due to number of recombination and crossing over events. In my case, In F1 generation its easier to identify the recombination hotspots but its very difficult to identify the recombination hotspots in subsequent generations.  Although till date, I hadn't worked on animal model but in our analysis of bread wheat (Hexaploid- ~80% repetitive genome) its difficult to identify the recombination hotspots in next generation.  

But, If one can identify the crossing over locus biasing in complex eukaryotic organisms (In subsequent next generations) than it will be very good contribution. I had got a clue in one article on Streptococcus and Staphylococus, where authors had studied inter and intraspecific recombination events (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002668). 

Wish you good luck

Shailender

If one has sequenced the genome of both parents and an offspring, it seems clear enough that a simple search of the chromosomes against each-other will show which portion of the offspring chromosome came from the mother chromosome, and which portion of the offspring chromosome came from the father chromosome.  I would not expect much deviation from exact match; unsequencible sections (show as regions of N in sequences) and SNP being the chief deviations.  Several generations of such mappings (perhaps not more than 20 or 30 will do) should provide definitive evidence for or against preferential crossover loci.

This paper my help you.

Campbell CL, Furlotte NA,Eriksson N, Hinds D,Auton A.

Escape from crossover interference increases with maternal age. Nat Commun. 2015 Feb 19;6:6260. doi: 10.1038.