STMS markers for grain protein content and their validation using near‐isogenic lines in bread wheat

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Abstract
The present study, undertaken as a continuation of an earlier study on quantitative trait loci (QTL) analysis of grain protein content (GPC) in bread wheat (Prasad et al. 1999), includes the following: (1) identification of an additional molecular marker associated with GPC; (2) development of near‐isogenic lines (NILs) for high GPC; and (3) the use of three sets of NILs (a total of 10 NILs) to validate the two available markers linked with QTL for GPC. A total of 114 sequence‐tagged microsatellite site (STMS) primer pairs (that were not used in the previous study) were used for detection of polymorphism between the two parents (PH132, with high GPC; WL711, with low GPC) of a mapping population of 100 recombinant inbred lines (RILs). A total of 95 primer pairs gave amplification products, of which only 30 detected reproducible polymorphism between the parental genotypes. Bulked segregant analysis was conducted using these 30 primers on two bulks (each comprising eight RILs) representing the two extremes of the normal distribution. A solitary primer pair (WMC415) showed association with GPC, which was further confirmed through selective genotyping. Subsequently, 100 RILs were genotyped. A single‐marker linear regression analysis showed significant association between the marker WMC415 and GPC, thus identifying a quantitative trait locus (designated as QGpcccsu‐5A1), which explained 6.21% of the variation for GPC among the RILs. The above STMS marker, together with the STMS marker (WMC41) identified earlier, explains approximately 25% of the variation for GPC. In order to conduct validation of the above two available markers, 10 NILs were developed for high GPC using two genotypes (WL711 and HD2329) with low GPC as recipient parents and another two genotypes (PH132 and PH133) with high GPC as donor parents. NIL 2233 (with 11.7% GPC), derived from HD2329, when tried with WMC41 gave a characteristic amplification profile similar to that of its donor parent PH132, and NIL 2215 (with 11.9% GPC) derived from WL711, when tried with WMC415 gave an amplification profile that resembled its donor parent PH133. The remaining eight NILs with high GPC gave patterns similar to those of their corresponding recipient parents with both the markers, suggesting that either the QTL, other than those associated with the above markers, were actually transferred from the donor parents and contributed to high GPC in these NILs or that recombination had occurred between the markers identified and the corresponding QTL. Thus, the marker validation conducted using NILs, while demonstrating the utility of these two microsatellite markers for use in marker‐assisted selection in plant breeding, also suggested that many more QTL exist that would need to be identified using closely linked molecular markers.