## 4 Discussion
### Improving the MAS Protocol  
Much progress has been achieved in development of molecular genetic markers for walleye since the native population was recognized [8], including 26 new microsatellite markers [28; 38; 39]. An evaluation of potential new markers for use in genetic marker-assisted selection was undertaken [35], but did not identify additional microsatellite alleles that mark native upper New River valleye. A particular microsatellite locus marks but a small proportion of the genome, perhaps 20 centiMorgans of recombinational distance bracketing the marker; with a genome likely of the order of 1000 centiMorgans in size, a few more markers would cover but a small increment of the genome. Further, MAS based on a limited number of nuclear loci will always be imprecise [30]. MAS based on mitochondrial markers [40] considers only the maternal ancestry of a focal individual. While our results showed that microsatellite markers provide a viable option, an approach combining mitochondrial and microsatellite markers would add to the rigor of an MAS protocol. Another concept might be applied to assess the efficacy of hatchery augmentation. [PERSON] and [PERSON] [41] described a \"family-printing\" approach to assess the contribution of hatchery-reared fish to an augmented population that uses multilocus microsatellite genotypes of individual mating adults to uniquely identify first- and second-generation offspring in the augmented mixture. The authors showed that with as few as seven allelesper locus using four loci scored without error, first-generation offspring can be uniquely assigned to the correct family. Using microsatellite DNA variation from an Atlantic salmon _Salmo salar_ restoration project on the Connecticut River, they showed 100% correct first-generation assignment and 97% correct second-generation assignment for sea-run returns using 14 marker loci. Parentage-based tagging is being used to provide information to managers in state, federal, and tribal agencies on the harvest, research, and conservation of Chinook salmon _Oncorhynchus tshawytscha_ and steelhead _Oncorhynchus mykiss_ in the Pacific Northwest of the United States [42]. [PERSON] et al. [43] reviewed application of the parentage-based tagging approach more generally. With the use of more microsatellite or other markers, family-printing might be applied to assess the success of stocking for future generations of native New River valleye. Single nucleotide polymorphisms (SNPs) could be developed to cover more of the genome and perhaps also to identify adaptive genetic variation between New River and other populations. Diagnostic SNP markers have been developed for Mobile basin [44] and Eastern Highlands [45; 46] valleye, and likely could be developed for upper New River and other valleye populations. A new GTSeq resource has been developed to facilitate research and management of valleye across the Great Lake region [47], some markers of which may prove useful for purposes of MAS for upper New River or other populations of walleye. Assays would have to be developed to score diagnostic SNP assays within 24 h of candidate broodstock collection in order to prove useful for MAS. We note that deep genomic coverage with SNPs that would clearly identify native New River valleye and estimate the extent of introgression (1) was not available when the program of MAS began, and (2) is not feasible for rapid screening of broodstock candidates given time constraints and the resources of a hatchery. Hatcheries have and, in the near term, will likely still rely on an incomplete and flawed picture of the genome for screening of broodstock candidates. Still, evaluative studies like that reported here can critically evaluate the costs and benefits of genetic screening and MAS.