To have reading intraspecific version regarding recombination rates during the maize, we authored a couple of half-sib panels, one to to have Damage and one having Flint inbred outlines. Drop and you can Flint are two maize gene pools that are crucial having crossbreed reproduction into the European countries . Both 50 % of-sib panels made up a maximum of twenty four complete-sib family members. The brand new Dent committee comprises 10 crosses off a main Reduction inbred range (F353) which have varied Dent originator inbreds of the Eu Reduction gene pool jak działa down dating that were created in European countries and North america. On Flint panel a main Flint inbred line (UH007) is crossed in order to eleven naturally varied Flint inventor inbreds of European Flint breeding procedure. The newest Flint founder contours originate from very early maize introductions so you can Spain as well as regarding thus-titled North Flints of France and you can Germany. On the other hand, a few reciprocal crosses among them central Reduction and you may Flint lines was indeed reviewed and also in per committee one mix into the Us Drop line B73 try provided due to the fact a link with the us nested relationship mapping (NAM) society .
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.
Results
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 most crosses, brand new haploid inducer line was applied because the male parent when crossed to your F
Since the an initial step-in the research out of recombination, individual genetic maps was built to possess 23 out of the 24 communities and every of the 10 chromosomes. Chart statistics are given inside the Desk step 1 with additional details within the Extra document step three, plus the over directory of marker ranking in all maps that have the latest brutal segregation info is considering in A lot more document 4. In total, 39,439 SNPs of the MaizeSNP50 number could well be mapped for the at least one people. Overall populations, to 33,884 COs was seen in dos,233 people meioses and you can, typically, eleven,988 SNPs was indeed mapped in a single considering populace. The average having Dent ? Drop communities (all the CFD except CFD01) was thirteen,247 markers mapped and Flint ? Flint communities (all CFF but CFF01 and CFF02) the average was 9,874. For population CFF05, and therefore made up just 34 DHs, zero secure chart could be received. The full length of hereditary maps ranged from 1,180 centiMorgan (cM) inside population CFD05 to 1,893 cM in CFF03 which have a suggest of 1,508 ± 185 cM (mean ± fundamental deviation). An average hereditary chart duration from the ten Reduction ? Drop communities (CFD02 so you’re able to CFD12) are step 1,353 ± 99 cM, since eleven hereditary charts away from Flint ? Flint populations (CFF03 in order to CFF15) was basically, normally, stretched during the 1,645 ± 154 cM. The three maps regarding crosses anywhere between Damage and you may Flint mothers (CFD01, CFF01, CFF02) got an advanced average length of 1,570 ± 85 cM. The most significant pit during the a hereditary chart are 53.eight cM to your long arm from chromosome 7 (7L) within the population CFF13, where no SNPs was indeed polymorphic between your moms and dads, probably on account of name-by-descent (IBD). Information about genome-wider range and you can IBD areas anywhere between mothers of mapping populations are in Additional document dos. Synteny and you can colinearity of genetic maps are compared to the brand new B73 AGPv2 genome construction. Overall, a high arrangement is receive, demonstrating the new higher texture away from marker order all over communities, that have couples exclusions given that discussed in Extra file 2.