To possess studying intraspecific type out of recombination rate during the maize, i written a couple half-sib boards, one for Dent and something for Flint inbred contours. Damage and you may Flint are a couple of maize gene swimming pools that will be essential getting hybrid reproduction in the European countries . Both half of-sib panels manufactured a maximum of twenty four full-sib family. The fresh Reduction committee comprises 10 crosses off a central Reduction inbred line (F353) that have diverse Damage creator inbreds of your own Western european Damage gene pond that were developed in Europe and you can North america. On Flint panel a central Flint inbred line (UH007) try entered so you can eleven genetically diverse Flint originator inbreds of one’s Eu Flint reproduction issue. The new Flint maker lines originate from very early maize introductions to help you Spain together with from thus-entitled North Flints from France and you may Germany. Concurrently, a few mutual crosses between them central Damage and you may Flint outlines were analyzed along with for every committee you to cross toward You Drop range B73 is actually included once the a link with the us nested connection mapping (NAM) inhabitants .
Here, we report on the analysis of the variation of recombination rate in 23 populations of maize using SNPs from the MaizeSNP50 BeadChip . All populations consist of doubled haploid (DH) lines obtained by in vivo haploid induction . DH lines produced with this method reflect female meiosis. Unlike F2 or RILs, DH lines have the great advantage that the genetic information of each gamete is directly observed. Our objectives were to analyze intraspecific variation for (1) GWRR and chromosome-wide recombination rate, (2) recombination landscape along chromosomes, and (3) CO interference, using high-density genetic linkage maps. We found significant differences of GWRR between individual populations as well as between Dent ? Dent versus Flint ? Flint populations, but not between the Dent and Flint gene pools in general. GWRR was not correlated with the genetic structure of the lines as inferred from admixture analysis. We analyzed the recombination landscapes in all populations and found significant differences between individual populations and between pools. Finally, we characterized quantitatively the interfering and non-interfering CO formation pathways and found a negative correlation over all chromosomes between interference intensity of pathway P1 and GWRR.
Overall performance
We constructed two half-sib panels comprising a total of 24 maize full-sib families of DH lines for the analysis of intraspecific variation of recombination rates. The full-sib families within the two panels represent the diversity of important founder lines of the European Dent and Flint germplasm, respectively (Table 1; Additional file 1). In the Dent panel (prefix CFD), all full-sib families have the same common parental line F353 which was crossed to diverse Dent founder lines. The common parent of the Flint full-sib families (prefix CFF) is line UH007, which was crossed to diverse Flint founder lines. 1 plants for in vivo haploid induction, so our maps reflect only female meioses. Details on the diversity analysis of the parental lines are given in Additional file 2.
In all crosses, brand new haploid inducer line was applied as the men father or mother whenever entered into the F
While the an initial step-in the analysis off recombination, personal genetic maps were built to have 23 from the 24 populations each of your 10 chromosomes. Chart analytics are offered for the Desk step one with increased information for the Most file step three, and over set of marker ranking in most maps which have the raw segregation info is considering during the Additional file cuatro. As a whole, 39,439 SNPs of your own MaizeSNP50 array might possibly be mapped in the on the very least that populace. Overall communities, to 33,884 COs had been observed in 2,233 women meioses and you can, an average of, eleven,988 SNPs was in fact mapped in one offered population. The average to possess Damage ? Reduction populations (all of the CFD except CFD01) try 13,247 markers mapped and for Flint ? Flint communities (all CFF except CFF01 and you may CFF02) the average are nine,874. Getting inhabitants CFF05, and this comprised only 34 DHs, no stable chart was received. The complete duration of hereditary maps varied from just one,180 centiMorgan (cM) inside society CFD05 to at least one,893 cM for the CFF03 which have a suggest of 1,508 ± 185 cM (suggest ± standard deviation). An average hereditary map length regarding the 10 Damage ? Dent populations (CFD02 so you’re able to CFD12) try step one,353 ± 99 cM, since eleven genetic charts regarding Flint ? Flint communities (CFF03 in order to CFF15) was, typically, prolonged at the 1,645 ± lumenapp 154 cM. The 3 maps off crosses anywhere between Dent and you will Flint moms and dads (CFD01, CFF01, CFF02) had an intermediate mediocre length of step one,570 ± 85 cM. The most significant pit inside a genetic map is actually 53.7 cM toward long arm regarding chromosome 7 (7L) in the populace CFF13, in which zero SNPs was basically polymorphic involving the parents, probably because of identity-by-descent (IBD). Information about genome-greater assortment and you may IBD avenues anywhere between moms and dads of one’s mapping populations have been in Additional document 2. Synteny and you will colinearity of your hereditary maps is actually weighed against the fresh B73 AGPv2 genome system. Overall, a high arrangement try discover, demonstrating brand new large surface away from marker acquisition across communities, that have partners exceptions just like the described inside A lot more document dos.