Having discovering intraspecific type off recombination rate in the maize, we composed one or two half-sib panels, one to getting Damage and another having Flint inbred lines. Damage and you may Flint are a couple of maize gene swimming pools that will be extremely important to have crossbreed breeding within the Europe . Both half-sib panels made all in all, twenty-four complete-sib family members. The fresh Dent committee constitutes ten crosses out-of a main Reduction inbred line (F353) that have varied Dent inventor inbreds of your Eu Dent gene pond that were created in European countries and you will United states. On the Flint committee a main Flint inbred line (UH007) is actually crossed to help you 11 naturally diverse Flint creator inbreds of your European Flint breeding thing. This new Flint founder contours originate from early maize introductions in order to The country of spain and out-of very-titled Northern Flints of France and you will Germany. On the other hand, several reciprocal crosses between them main Drop and you can Flint outlines were reviewed and in each committee one to mix to the All of us Drop range B73 was provided given that a link with the us nested association mapping (NAM) population .
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.
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 profil gleeden haploid induction, so our maps reflect only female meioses. Details on the diversity analysis of the parental lines are given in Additional file 2.
Throughout crosses, new haploid inducer range was used as the men father or mother when crossed to the F
As the a primary part of the study from recombination, personal genetic charts were built to possess 23 from the twenty-four communities and every of the 10 chromosomes. Chart statistics are provided into the Dining table step one with information into the A lot more document step 3, and the over set of marker ranking throughout maps that have the latest intense segregation info is provided for the Most file 4. Altogether, 39,439 SNPs of the MaizeSNP50 selection would-be mapped in during the least one population. Over all populations, up to 33,884 COs had been observed in 2,233 girls meioses and, typically, eleven,988 SNPs were mapped in a single given society. An average for Reduction ? Dent communities (all of the CFD except CFD01) try thirteen,247 indicators mapped and also for Flint ? Flint populations (every CFF but CFF01 and you may CFF02) an average try nine,874. For population CFF05, and this made-up merely 34 DHs, zero stable chart will be acquired. The duration of hereditary maps varied from a single,180 centiMorgan (cM) when you look at the inhabitants CFD05 to 1,893 cM inside CFF03 which have a suggest of just one,508 ± 185 cM (suggest ± standard departure). The average genetic chart duration from the 10 Damage ? Reduction communities (CFD02 so you’re able to CFD12) is actually step 1,353 ± 99 cM, given that eleven hereditary charts out of Flint ? Flint communities (CFF03 in order to CFF15) had been, on average, lengthened during the step one,645 ± 154 cM. The 3 maps regarding crosses anywhere between Reduction and Flint moms and dads (CFD01, CFF01, CFF02) had an intermediate mediocre amount of 1,570 ± 85 cM. The biggest gap inside a genetic map is actually 53.7 cM into long arm regarding chromosome eight (7L) into the populace CFF13, where no SNPs was indeed polymorphic amongst the moms and dads, probably because of title-by-origin (IBD). Factual statements about genome-wider assortment and you will IBD areas anywhere between moms and dads of one’s mapping communities can be found in Even more file 2. Synteny and you may colinearity of the hereditary maps are compared to new B73 AGPv2 genome assembly. In general, a leading contract are found, appearing the fresh new higher structure regarding marker order all over communities, having couples exceptions given that described inside Additional file 2.