Skip to main content
ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #311232
Title: A genome-wide association study of malting quality across eight U.S. barley breeding programs

Author
item MOHAMMADI, M - University Of Minnesota
item BLAKE, T - North Dakota State University
item Budde, Allen
item Chao, Shiaoman
item HAYES, P - Oregon State University
item HORSLEY, R - North Dakota State University
item OBERT, D - Montana State University
item ULLRICH, S - Washington State University
item SMITH, K - University Of Minnesota

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2014
Publication Date: 3/20/2015
Publication URL: http://handle.nal.usda.gov/10113/60605
Citation: Mohammadi, M., Blake, T.K., Budde, A.D., Chao, S., Hayes, P.M., Horsley, R.D., Obert, D.E., Ullrich, S.E., Smith, K.P. 2015. A genome-wide association study of malting quality across eight U.S. barley breeding programs. Theoretical and Applied Genetics. 128:705-721.

Interpretive Summary: Malting quality in barley is determined by a complex suite of traits. For some of these traits, there is consensus among the end-users for a target value while for other traits the specific target will depend on the market class (two-row or six-row), beer style, and brewing process. In the U.S., brewers that are members of the American Malting Barley Association (AMBA) have defined acceptable ranges and desired target values for 18 barley and malting quality traits. Barley producers that grow industry-endorsed cultivars that meet these standards will generally receive a premium price that is higher than feed barley. Previous genetic studies have detected at least 75 genes controlling these quality traits using wide crosses maximizing the differences between parents. Translation of such information to the trait improvement, however, has been limited. It would be more desirable if the genetic studies can be conducted using the elite barley breeding germplasm. This study leverages the breeding data of 1,862 breeding lines from eight U.S. barley breeding programs evaluated in 97 field trials. These lines were genotyped with over 3,000 DNA markers. A total of 4,976 grain samples were subjected to micro-malting analyses. Both the DNA marker and malting quality trait data were then used to perform genome-wide marker-trait association analysis to identify genes affecting malting quality. Results indicated that a total of 108 and 107 chromosome regions were significantly associated with trait expressions in six-row and two-row breeding programs, respectively. Only a handful of them were in common with those reported previously. The genetic architecture of malting quality and the distribution of favorable alleles present in different breeding programs suggests important strategies for marker assisted breeding and germplasm exchange.

Technical Abstract: This study leverages the breeding data of 1,862 breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The breeding lines were six-row and two-row barley advanced breeding lines from eight barley breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 10% of the QTL detected through association mapping had been detected in prior bi-parental mapping studies (Dicktoo × Morex, Steptoe × Morex, and Harrington × Morex). Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were in common. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual breeding programs six-row and two-row breeding programs, respectively indicating the most marker-trait associations were breeding population specific. Combing data sets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggests important strategies for marker assisted selection and germplasm exchange.