Rare allele of HvLox-1 associated with lipoxygenase activity in barley (Hordeum vulgare L.)

Abstract

Key messageIdentification and allele-specific marker development of a functional SNP ofHvLox-1which associated with barley lipoxygenase activity.AbstractImproving the stability of the flavor of beer is one of the main objectives in breeding barley for malting, and lipoxygenase-1 (LOX-1) is a key enzyme controlling this trait. In this study, a modified LOX activity assay was used for null LOX-1 mutant screening. Four barley landraces with no detected level of LOX-1 activity were screened from 1,083 barley germplasm accessions from China. The genomic sequence diversity of the HvLox-1 gene of the four null LOX-1 Chinese landraces was compared with that of a further 76 accessions. A total of 104 nucleotide polymorphisms were found, which contained 83 single-nucleotide polymorphisms (SNPs), 7 multiple-nucleotide polymorphisms, and 14 insertions and deletions. Most notably, we found a rare C/G mutation (SNP-61) in the second intron which led to null LOX-1 activity through an altered splicing acceptor site. In addition, an allele-specific polymerase chain reaction marker was developed for the genotyping of SNP-61, which could be used in breeding programs for barley to be used for malting. The objective was to improve beer quality.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2362-3) contains supplementary material, which is available to authorized users.

Genetic variation of HvXYN1 associated with endoxylanase activity and TAX content in barley (Hordeum vulgare L.)

“…7b). Thus, the changes in the functional properties of the enzyme were likely caused by the change of bases [20, 57]. How the amino acid substitutions of different sequences impact the EA activity remains unclear.…”

“…Particularly in barley, xylanase can be synthesized and secreted in the aleurone layer [18]. However, due to the activity of xylanase in malt, a large amount of arabinoxylan is dissolved [13, 19], which in turn improves the viscosity, foam stability and sensory characteristics of beer [20].…”

“…Null LOX-1 activity varieties with stable foam in beer and better flavor of beer always were screened out as malting barley. Guo et al [20] identified a rare C/G mutation (SNP-61) in the second intron which result in null LOX-1 activity through an altered splicing acceptor site and the SNP could be used in breeding programs for barley to be used for malting. In general, superior malting quality requires a high conversion of starch to fermentable sugars.…”

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

“…The two main functions of AS are to increase protein diversity and regulate expression levels of specific transcripts by producing AS isoforms that are degraded by nonsense mediated decay (NMD) [28, 32, 39, 45, 54]. Extensive AS has been reported in barley [11, 26, 41, 59, 60] and allelic diversity further contributes to the landscape of AS transcript variation among genotypes through elimination and formation of splice sites and splicing signals [22, 33, 50].…”

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

“…The two main functions of AS are to increase protein diversity and regulate expression levels of specific transcripts by producing AS isoforms that are degraded by nonsense mediated decay (NMD) (Nilsen and Gravely, 2010;Kalyna et al, 2012;Reddy et al, 2013;Staiger and Brown, 2013;Lee and Rio, 2015). Extensive AS has been reported in barley (IBSC, 2012;Panahi et al, 2015;Calixto et al, 2016;Zhang et al, 2016a;Zhang et al, 2016b) and allelic diversity further contributes to the landscape of AS transcript variation among genotypes through elimination and formation of splice sites and splicing signals (Shirasu et al, 1999;Guo et al, 2014;Liu et al, 2015).…”