High-occurrence genetic map structure from inside the maize full-sib families

To own training intraspecific version regarding recombination rates in maize, i authored a few half-sib boards, one to to own Dent plus one getting Flint inbred contours. Reduction and you can Flint are a couple of maize gene pools which might be essential to have crossbreed reproduction into the Europe . Both 50 % of-sib boards manufactured a maximum of twenty-four full-sib household. The Reduction committee comprises ten crosses off a main Drop inbred line (F353) that have varied Drop maker inbreds of your own Western european Damage gene pond that have been designed in European countries and you will United states. On Flint committee a central Flint inbred range (UH007) is entered so you can eleven genetically varied Flint inventor inbreds of the Eu Flint reproduction point. The fresh Flint founder traces come from early maize introductions so you’re able to Spain also out-of thus-entitled Northern Flints of France and you may Germany. In addition, one or two mutual crosses between the two central Drop and you will Flint traces was reviewed as well as in for every single committee you to definitely mix for the All of us Damage range B73 are integrated since the a link with the united states nested association 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.

Efficiency

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, the newest haploid inducer range was utilized since the men father or mother whenever crossed on F

As a primary help the research out-of recombination, personal hereditary charts was developed for 23 outside of the twenty-four populations and each of 10 chromosomes. Chart analytics are provided inside Dining table step one with an increase of details inside the Additional file 3, as well as the over range of marker positions in all charts having the brutal segregation data is given in A lot more document cuatro. In total, 39,439 SNPs of one’s MaizeSNP50 array might be mapped inside the during the the very least one people. Over all communities, up to 33,884 COs was seen in dos,233 lady meioses and, typically, eleven,988 SNPs had been mapped in one single offered population. The common to have Dent ? Dent communities (most of the CFD except CFD01) is actually thirteen,247 indicators mapped as well as for Flint ? Flint communities (most of the CFF but CFF01 and you will CFF02) the average try 9,874. To have populace CFF05, hence made-up just 34 DHs, zero secure chart was obtained. The full length of hereditary charts ranged from one,180 centiMorgan (cM) into the inhabitants CFD05 to one,893 cM inside CFF03 that have an indicate of 1,508 ± 185 cM (imply ± standard departure). The average hereditary chart size regarding the 10 Damage ? Damage communities (CFD02 so you can CFD12) is actually 1,353 ± 99 cM, because the 11 genetic maps of Flint ? Flint populations (CFF03 to CFF15) was in fact, on average, prolonged at the 1,645 ± 154 cM. The three maps out of crosses anywhere between Reduction and you can Flint parents (CFD01, CFF01, CFF02) had an intermediate average amount of 1,570 ± 85 cM. The biggest gap for the an inherited chart is 53.seven cM into the long-arm regarding chromosome 7 (7L) inside society CFF13, where no SNPs had been polymorphic between your mothers, probably because of identity-by-ancestry (IBD). Factual statements about genome-greater range and you may IBD locations between mothers of your mapping communities come in More file 2. Synteny and colinearity of the hereditary charts was compared to this new B73 AGPv2 genome set-up. As a whole, a top arrangement is located, indicating the fresh highest consistency of marker buy across the populations, having couples exclusions given that demonstrated in Extra document dos.