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Title: Transcriptome analysis of a breeding program pedigree examines gene expression diversity and reveals target genes for malting quality improvement

item MUNOZ-AMATRIAIN, MARIA - University Of Minnesota
item XIONG, Y - University Of Minnesota
item Schmitt, Mark
item BILGIC, H - University Of Minnesota
item Budde, Allen
item Chao, Shiaoman
item SMITH, K - University Of Minnesota
item MUEHLBAUER, G - University Of Minnesota

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2010
Publication Date: 11/23/2010
Citation: Munoz-Amatriain, M., Xiong, Y., Schmitt, M., Bilgic, H., Budde, A.D., Chao, S., Smith, K., Muehlbauer, G. 2010. Transcriptome analysis of a breeding program pedigree examines gene expression diversity and reveals target genes for malting quality improvement. Biomed Central (BMC) Genomics. 11:653.

Interpretive Summary: Among all the different types of barley, only a distinct subset have the select range of properties needed to be useful in the commercial production of malt. These malting barley varieties have variable useful lifetimes in production agriculture, all eventually being replaced by newer varieties that have improved agronomic, disease resistance, or malting quality characteristics. However, even with useful improvements in agronomic or disease resistance traits, the new varieties must still exhibit malting quality characteristics that fall within the same narrow range as existing varieties. Because of these constraints, it is easier and faster to breed new varieties by recombining established varieties. But this only is feasible if there is sufficient variability in the varieties used as parents. In this study we use several techniques to show that current varieties in the University of Minnesota barley breeding program retain substantial genetic variation in malting-related gene expression. This validates the use of current malting barley genotypes as parents for continued selection in the breeding program. Being able to use the current advanced germplasm from the University of Minnesota breeding program as parents for further malting barley breeding will have a significant positive impact on the development of new barley varieties, ensuring timely introduction of useful malting barley varieties.

Technical Abstract: Advanced cycle breeding utilizes crosses among elite lines and is a successful method to develop new inbreds. However, it results in a reduction in genetic diversity within the breeding population. The development of malting barley varieties requires the adherence to a narrow malting quality profile and thus the use of advanced cycle breeding strategies. Although attention has been focused on diversity in gene expression and its association with genetic diversity, there are no studies performed in a single breeding program examining the implications that consecutive cycles of breeding have on gene expression variation. Fifteen lines representing a historically important pedigree of the University of Minnesota six-rowed malting barley breeding program were genotyped with 1,524 SNPs, phenotypically examined for six malting quality traits, and analyzed for transcript accumulation during germination using the Barley1 GeneChip array. Significant correlation was detected between genetic and transcript-level variation. We observed a reduction in both genetic and gene expression diversity through the breeding process, although the expression of many genes have not been fixed. A high number of quality-related genes whose expression was already fixed in the older members of the pedigree was identified, indicating that much of the diversity reduction was associated with the improvement of the complex phenotype “malting quality”, the main goal of the University of Minnesota breeding program. We also identified 49 differentially expressed genes between the most recent lines of the program that were correlated with one or more of the six primary malting quality traits. These genes constitute potential targets for the improvement of malting quality within the breeding program. The present study shows the repercussion of advanced cycle breeding on gene expression diversity within an important barley pedigree. A reduction in gene expression diversity was detected, although there is diversity still present after forty years of breeding that can be exploited for future crop improvement. In addition, the identification of candidate genes for enhancing malting quality may be used to optimize the selection of targets for further improvements in this economically important phenotype.