Major paradigm shift in plant breeding since the availability of molecular marker technology is that mapping and characterizing the genetic loci that control a trait will lead to improved breeding. Often, one of the rationales for cloning of QTL is to develop the "perfect marker" for MAS, perhaps based on a functional polymorphism. In contrast, an advantage of genomic selection is precisely its black box approach to exploiting genotyping technology to expedite genetic progress. This is an advantage in our view because it does not rely on a "breeding by design" engineering approach to cultivar development requiring knowledge of biological function before the creation of phenotypes. Breeders can therefore use genomic selection without the large upfront cost of obtaining that knowledge. In addition, genomic selection can maintain the creative nature of phenotypic selection which couple's random mutation and recombination to sometimes arrive at solutions outside the engineer's scope. Currently, the lion's share of research on genomic selection has been performed in livestock breeding, where effective population size, extent of LD, breeding objectives, experimental design, and other characteristics of populations and breeding programs are quite different from those of crop species. Nevertheless, a great number of findings within this literature are very illuminating for genomic selection in crops and should be studied and built upon by crop geneticists and breeders. The application of powerful, relatively new statistical methods to the problem of high dimensional marker data for genomic selection has been nearly as important to the development of genomic selection as the creation of high-density marker platforms and greater computing power. The methods can be classified by what type of genetic architecture they try to capture.

Improvement of grain protein content (GPC), loaf volume and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcrossing (MABC) for introgression and pyramiding of the following genes:(i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24 and Sr24. GPC was improved by 0.8-3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines, allowed development of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the following four cultivars: NI5439, UP2338, UP2382 and HUW468.The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were developed in the backgrounds of following ve cultivars: Lok1, HD2967, PBW550, PBW621 and DBW1. The improved pre-bred lines developed during the present study should prove useful for development of cultivars with improved nutritional quality associated with rust resistance in future wheat breeding programmes.

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