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Determining marker haplotypes associated with positive and negative QTL alleles in marker-phased sires, and tracing to elite dams and candidate bulls

The objective was to examine the feasibility of tracing chromosomal regions containing a QTL (QTLR) from a grandsire for whom marker-QTL linkage phase has been established, to progeny and grandprogeny, i.e., to a son or grandson. The main question considered was the number of markers that need to be followed to achieve accurate tracing. For this, we had three data sets. The first consisted of DNA samples of three pedigrees of RP1 (Pedigrees A, B, and C) each consisting of a grandsire, sire and 1, 13, and 3 grandsons, respectively. The second consisted of DNA samples of eight pedigrees of RP4 consisting of 8 grandsires, sires, 33 sons, and 117 grandsons.

The grandsons in all cases, were young recently purchased male calves, candidates for progeny testing. For these pedigrees, the specific objective was to trace chromosomal regions that carry QTL alleles with positive or negative effects on milk protein percent, from the grandsire (S0) (having known marker-QTL linkage phase) to his sons (S1) and grandsons (S2).

In addition, genotyping data were available for a large number of three generation male-line pedigrees in RP1, each ending in a set of granddaughters (genetically equivalent to grandsons). These were used for more extensive analyses of tracing success as a function of the width of QTLR traced, and the number of markers used for tracing.

Pedigree data, RP1: Materials and Methods: For purposes of tracing we examined a total of 18 markers in a 40cM region of BTA13 running from 39.6 to 96.0cM, but not all markers were genotyped in all individuals. Haplotypes were derived manually from the genotypes of the individuals in the table, with some cross referencing within half-sib families, and also with the program PowerMarker.

Results: Pedigree A: 16 markers were monitored. S0 transmitted a recombinant haplotype to S1, but this was not transmitted to S2. Pedigree B: 9 markers were monitored. S0 transmitted the positive haplotype to S1; this haplotype was transmitted to 3 grandsons (S2), while 3 grandsons did not receive any part of it; five grandsons received recombinant S1 haplotypes containing 1 to 8 marker alleles of S0 haplotype. Pedigree C: 6 markers were monitored. S0 transmitted the negative haplotype to S1; this haplotype was transmitted to three grandsons (S2), one grandson did not receive the haplotype..

Pedigree data, RP4: Materials and Methods. Tracing chromosomal regions containing a QTLR from a grandsire for whom marker-QTL linkage phase has been established, to sire and grandsons, was carried out for four QTLR: one on BTA11, two regions on BTA13, one on BTA14 and one on BTA20.

Results: For BTA11 (3 markers spanning 92.2 to 115.4 cM) the grandsire haplotype was traced for 19 out of 21 sires; for BTA13, region 1 (5 markers spanning 51.7 to 71.1) the grandsire haplotype was traced for 24 out of 27 sires; for BTA13, region 2 (3 markers, spanning 84.4 to 98 cM) the grandsire haplotype was traced for 24 out 30 sires; for BTA14 (6 markers, spanning 60.7 cM to 100 cM) the grandsire haplotype was traced for 20 out of 39 sires, and for BTA20 (5 markers, spanning 8.2 cM to 33.4 cM) the grandsire haplotype was traced for 30 out of 42 sires. Thus, in almost all cases it was possible to trace the QTLR from grandsire to grandson, and identify recombinants in transmission from S0 to S1, or from S1 to S2.

Tracing from grandsire to granddaughter, Materials and Methods: Data were taken from available three generation genotypes for BTA 1, 7, 11 and 13. In each chromosome a number of haplotypes were defined according to QTLR width (0 to 5cM; 5 to 10cM; 10 to 20cM) and markers per haplotype (2 to 8, depending on QTLR width). For haplotypes of width 0 to 5cM, 5 to 10cM and 10 to 20cM, a total of 2008, 2895, and 3860 haplotypes were traced respectively. Results were virtually independent of the width of the haplotypes, namely: for haplotypes defined by 2, 3, 4, and 5 or more markers, proportion of traced haplotypes (including recombinants) were 0.93, 0.96, 0.97, and 0.98, respectively. Thus, these results strongly confirm the ability to trace selected phased QTLR from grandsire to grandson. Conclusions: It is eminently feasible to trace phased QTLR from grandsire to sons and grandsons. Thus, tracing of QTLR should not pose a problem for MAS. This information is useful to organizations that are considering the application of MAS in their breeding programs.

Contacto

Moshe SOLLER, (Head of Unit)
Tel.: +972-2-6585144
Fax: +972-2-6584392
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