CA 15-3 has the advantage of being a serum based marker and therefore its measurement is less invasive.
The BIN system was used to realize chi-square tests to test the null hypothesis assuming independent distribution of BINs occupied with a Prx based markers and BINs occupied with a QTL peak marker or control molecular marker, as described previously [13] [14].
None of these tests indicated a significant association between the Prx based markers and such agronomic trait QTLs.
The chi-square test indicated a significant association between the distribution of Prx based markers and QTLs for basal resistance to P. hordei (P>0.05) (Table 3).
The possible association between Prx based markers and several types of resistance loci was investigated in this study.
We did not find such an association between resistance QTLs and markers based on random gene sequences and genomic sequences, nor between Prx based markers and QTLs for other agronomical traits than resistance (Table 4).
This enabled the construction of 2×2 contingency tables that allow tests of independence regarding the occupancy by Prx based markers and QTL peak markers (cf. [13], [14]).
The number of repeats for each of the repeat types is shown in Figure 1 with the average number being 9.59 repeats for the 112 di-nucleotide based markers and 6.18 repeats for the 136 tri-nucleotide based markers.
While SNP markers have a promising future in plant breeding applications, and may augment or displace SSR based marker systems, SNP based markers and associated technologies are in their infancy in most crops, including pigeonpea, while SSR marker technologies are better established for wide spread use in molecular breeding.
The RIL population was genotyped with 162 polymorphic markers including a gene based marker (GS3) and were used to construct a linkage map using the program MAPMAKER [ 54].
