The Integrated Mapping Project: Interval mapping of visibles with RFLPs --Ed Coe, Dave Hoisington, Shiaoman Chao, Susan Melia-Hancock and Jack Gardiner In the spring and summer of 1989, families segregating for about 125 visible factors (naked-eye polymorphisms, NEPs) have been grown, classified, and sampled for RFLP characterization. Selection of NEPs to be interval-mapped was made primarily as follows: (1) map location has been previously defined; (2) the utility of the factor as a marker is established; and (3) whenever possible a multiple-factor F2 family in cis arrangement was available from the Stock Center or other source (we greatly appreciate the advice, encouragement and help of Earl Patterson in making the selections and supplying seed of most of these materials from the Stock Center collection). Some additional viable seed or seedling traits have been included toward the potential of adding to the bank of useful markers. The accompanying list identifies factors that are currently projected for interval mapping, plus isozymes that we plan to incorporate as well. We hope to be able to interval-map a major part of this ambitious list. Our intention has been to make a first-priority mapping selection of NEPs, not to exclude anyone's favorite locus on assumption that someone else would map it.

Loci (NEPs and Isozymes) Projected for Mapping

Chromosome 1: sr1 vp5 zb4 ms17 ts2 P1 dek1 nec2 as1 rs2 hm1 Amp2 br2 br1 Vg1 f1 Mdh4 an1 id1 bz2 ad1 Kn1 Adh1 D8 gs1 Phi1 vp8 Ts6 bm2

Chromosome 2: ws3 al1 lg1 gl2 d5 B1 gs2 sk1 Les1 wt1 fl1 ts1 ba2 v4 w3 Ht1 Ch1 spt1 whp1

Chromosome 3: g2 E8 cr1 Cg1 d1 ra2 cl1 rt1 Lg3 Rg1 gl6 ys3 ts4 pm1 vp1 ig1 lg2 ba1 na1 a3 Mdh3 a1 sh2 et1 ga7 h1

Chromosome 4: Aco1 Ga1 Ts5 la1 fl2 st1 su1 bt2 zb6 gl4 Tu1 j2 gl3 o1 c2 dp1

Chromosome 5: Pgm2 Mdh5 am1 anl1 lu1 gl17 a2 vp2 ps1 bm1 bt1 v3 bv1 td1 ae1 pr1 gl8 lw2 ys1 v2 eg1 sh4

Chromosome 6: hcf26 Pgd1 po1 l11 rgd1 Enp1 w15 l12 y1 l10 si1 pb4 wi1 pg11 Dt2 Pl1 Bh1 su2 sm1 Pt1 Hex2 py1 w14 w1 Idh2 Mdh2

Chromosome 7: Hs1 o2 y8 in1 v5 vp9 ms7 o5 ra1 gl1 Tp1 sl1 ij1 bd1 Pn1

Chromosome 8: Bif1 ats1 fl3 gl18 nec1 pro1 v16 ms8 j1 v21 Idh1

Chromosome 9: Dt1 yg2 C1 sh1 bz1 l7 baf1 lo2 w11 wx1 d3 pg12 ar1 v1 ms2 gl15 bk2 v30 Wc1 Bf1 bm4 da1 Acp1

Chromosome 10: sr3 oy1 Og1 y9 zn1 du1 bf2 Glu1 nl1 li1 ms10 Tp2 g1 cm1 R1 Lc1 Mst1 l1 w2 o7 l13 sr2 ms11

To maximize information and statistical accuracy with minimal laboratory effort and cost, it is preferable to carry out molecular probing on a selection of plants rather than on all members of the F2 (see Hoisington and Coe, Stadler Genet. Symp., in press). The interval mapping approach, in simplest terms, is to select the recessive class for the marker (the mutant if the trait is recessive, the normal if the trait is dominant) in an F2 segregating for the trait and for whatever RFLP loci along that chromosome inherently segregate in the family. RFLPs in the DNA of the recessive individuals are probed to ask which RFLP alleles have stayed together, compared to checks in the dominant class. The interval that has stayed together will have the highest probability of containing the marker. A particular efficiency of the F2 design is that each F2 plant characterized by the molecular probing carries two strands, either or both of which may show recombination between the marker and RFLP loci at increasingly distant points on the map: one plant characterized by probing means two strands tested.

We anticipate that interval mapping against the core map of RFLPs will be advanced during the spring of 1990, and that a considerable integration across the genome should be available by the next Newsletter.


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