**4. Conclusions**

In conclusion, our study identified novel SNPs associated with bran friability and tentative SNPs associated with WRC. One of the SNP markers associated with bran friability was tagged to the well-characterized Pinb locus in wheat, which suggests that in addition to endosperm texture, Pinb may also have a role in bran texture (friability). The favorable alleles at the trait-associated SNP sites were

present in only a fraction of lines (mostly recent releases and very few heritage or older cultivars) in the HWWAMP, which comprises breeding lines from many of the breeding programs in the US. This result indicates that the traits beneficial for whole wheat flour are neither selected for or against, just randomly, and are relatively new in the breeding history. Additionally, the lines carrying favorable alleles for both traits were randomly distributed in a PCA biplot, suggesting the absence of groupings among lines carrying favorable alleles. A conscious e ffort is thus needed to breed for cultivars that would be more desirable for whole-grain milling. Upon validation in independent populations and multiple environments, the novel markers identified in this study may help breeders select lines that have high bran friability and low WRC, which are preferred in whole grain bread-making. Additionally, the lines carrying favorable alleles identified in this study can be used as parental lines while making new crosses in breeding programs for developing cultivars suitable for whole wheat grain flour. Further, if the genomic regions for bran friability and WRC are validated in multiple backgrounds and environments, they can then become potential targets for function characterization studies such as knockout or overexpression experiments and thus help narrow down genes important for these traits in bread wheat. These e fforts overall could lead to release of wheat lines with high whole grain flour functionality and identification and characterization of genes important for whole grain bread-making.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/11/8/838/s1, Figure S1: Principle components analysis biplot of the 297 genotypes in the HWWAMP using marker data, with the 46 lines carrying the GG favorable genotype for the friability marker, BS00000020\_51 (A), highlighted in color, and the 43 lines carrying the AA favorable genotype for the friability marker, Excalibur\_c49805\_63 (B), highlighted in color, Figure S2: Principle components analysis biplot of the 297 genotypes in the HWWAMP using marker data, with the 97 lines carrying CC favorable genotype for the WRC marker, IWA4867 (A), highlighted in color, and the 98 lines carrying CC favorable genotype for the WRC marker, IWA4698, highlighted in color, Table S1: Genotype information across HWWAMP lines for the markers associated with Friability and Water Retention Capacity traits.

**Author Contributions:** S.N., P.S.B. and D.J.R. contributed conception and design of the study; S.N. performed the experiments; P.S.B. organized, maintained, and produced the mapping population; S.N. and V.B. performed the quantitative genetics and statistical analyses; S.N. wrote the first draft of the manuscript; S.N., V.B., and D.J.R. wrote sections of the manuscript. All authors contributed to manuscript revision. All authors have read and agreed to the published version of the manuscript.

**Funding:** This study was partially supported by a gran<sup>t</sup> from the Agricultural Research Division of the University of Nebraska-Lincoln.

**Acknowledgments:** The authors acknowledge the helpful assistance of Eric Nkurikiye in completion of the bran friability and bran water retention capacity measurements. The authors would like to thank Triticeae Coordinated Agricultural Project (TCAP) for making the genotypic data publicly available. Also, we want to acknowledge Marry Guttieri and Nicholas Garst for their efforts in organization and growing of HWWAMP in Nebraska. Finally, we are grateful to the numerous wheat plant breeders and geneticists from the public and private sector who donated their lines to create the HWWAMP.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
