Natural variations in a barley aldehyde oxidase 1 gene affect seed germination and malting quality

Abstract

Multiple phytohormones, including gibberellin (GA), abscisic acid (ABA), and indole-3-acetic acid (IAA), regulate seed germination. In this study, a barley aldehyde oxidase 1 (HvAO1) gene was identified, which is located near the SD2 (seed dormancy 2) region at the telomeric end of chromosome 5H. A doubledhaploid population (AC Metcalfe/Baudin) was used to characterize HvAO1 and validated its association with seed germination and malting quality. Aldehyde oxidase is predicted to catalyse the oxidation of various aldehydes, such as indoleacetaldehyde and abscisic aldehyde, into IAA and ABA, which is the final step of IAA/ABA biogenesis. This process influences the final IAA/ABA concentration in the seed, affecting the seed dormancy. Sequence analysis revealed substantial variations in the HvAO1 promoter regions between AC Metcalfe and Baudin. The combining seed germination tests, genetic variation analysis, gene expression, and phytohormone measurements showed that Baudin, which displays strong seed dormancy, has a specific sequence variation in the promoter region of the HvAO1 gene. This variation is associated with a higher expression level of the HvAO1 gene and an increased level of ABA than those in AC Metcalfe, which shows weak dormancy and lacks this sequence variation. In addition to its strong effect on the SD2 gene, HvAO1 shows excellent potential to fine-tune malting quality and seed dormancy, as evidenced by genotyping with HvAO1-specific markers, dormancy phenotypes, and malting quality. Our findings provide a new strategy for introducing favourable HvAO1 alleles to achieve the desired level of seed dormancy and high malting quality in barley.

Headnote

ARTICLE INFO

Article history:

Received 21 February 2024

Revised 14 November 2024

Accepted 19 November 2024

Available online 21 December 2024

Keywords:

Barley (Hordeum vulgare L.)

Dormancy

Germination

Malting quality

Aldehyde oxidase

ABSTRACT

Multiple phytohormones, including gibberellin (GA), abscisic acid (ABA), and indole-3-acetic acid (IAA), regulate seed germination. In this study, a barley aldehyde oxidase 1 (HvAO1) gene was identified, which is located near the SD2 (seed dormancy 2) region at the telomeric end of chromosome 5H. A doubledhaploid population (AC Metcalfe/Baudin) was used to characterize HvAO1 and validated its association with seed germination and malting quality. Aldehyde oxidase is predicted to catalyse the oxidation of various aldehydes, such as indoleacetaldehyde and abscisic aldehyde, into IAA and ABA, which is the final step of IAA/ABA biogenesis. This process influences the final IAA/ABA concentration in the seed, affecting the seed dormancy. Sequence analysis revealed substantial variations in the HvAO1 promoter regions between AC Metcalfe and Baudin. The combining seed germination tests, genetic variation analysis, gene expression, and phytohormone measurements showed that Baudin, which displays strong seed dormancy, has a specific sequence variation in the promoter region of the HvAO1 gene. This variation is associated with a higher expression level of the HvAO1 gene and an increased level of ABA than those in AC Metcalfe, which shows weak dormancy and lacks this sequence variation. In addition to its strong effect on the SD2 gene, HvAO1 shows excellent potential to fine-tune malting quality and seed dormancy, as evidenced by genotyping with HvAO1-specific markers, dormancy phenotypes, and malting quality. Our findings provide a new strategy for introducing favourable HvAO1 alleles to achieve the desired level of seed dormancy and high malting quality in barley.

© 2024 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/

1. Introduction

Quick seed germination is a prerequisite for brewing barley [1]. A lack of seed dormancy leads to viable seeds that cannot germinate even under favorable conditions. Compared with wild barley, cultivated barley exhibits a continuous decline in dormancy level due to artificial breeding selection [2,3]. Seed dormancy and germination are tightly regulated by the major phytohormones abscisic acid (ABA) and gibberellin (GA), and dormancy is determined by the sensitivity of the embryo to the ratio of GA to ABA [4]. The 8 -hydroxylation of ABA results in the accumulation of inactive phaseic acid (PA) and dihydrophaseic acid (DPA). ABA-glucose ester (ABA-GE) is the most widespread storage form of ABA [5].

Multiple quantitative trait loci (QTL) associated with dormancy in barley were identified through genetic mapping with mapping populations constructed from the hybrid offspring of Australian and Canadian malting barley [6-8]. Two major dormancy QTL on chromosome 5H, designated SD1 (seed dormancy 1) located near the centromere and SD2 (seed dormancy 2) in the telomeric region, have been consistently reported [6-9]. The germination rate of barley qsd1 and qsd2 mutants was significantly lower than that of the wild type, suggesting that the barley dormancy level could be regulated by manipulating the qsd1 and qsd2 alleles [10]. Genes in the SD2 antagonize the regulation of dormancy and malt quality [6,7,11,12]. Thus, exploring new genes in or near the SD2 loci that may achieve an optimal level of dormancy while maintaining superior malt is worth further study.

Malting quality is a measure of the value of barley grains used in malting and brewing [13]. Among malting-quality parameters, amylase catalyzes the hydrolysis of starch into smaller carbohydrate molecules. Diastatic power (DP) measures a malted grain's starch-degrading enzymatic content, mainly a-amylase (AA) and b-amylase. b-glucanase (BG) is a measure of the degree of cell wall modification. High BG activity hinders the hydrolysis process in malt. The hot water extract (HWE) is a trait of interest for industrial purposes. Free amino nitrogen (FAN) measures the concentration of individual amino acids and small peptides (one to three units), which can be utilized by beer yeast for growth and proliferation. FAN content is an indicator of beer quality, whereas excessive levels of FAN may lead to poor malt extract recovery. Soluble protein (SP) is a parameter for evaluating wort quality and measures soluble protein after hot water extraction from malt [14].

Based on previous QTL analysis and RNA sequencing in germinating embryos of AC Metcalfe-Baudin, we identified differentially expressed genes (DEGs) in the hormone synthesis and catabolism pathways. We identified the aldehyde oxidase gene (HvAO1) as a potential regulator of seed germination and malting quality.

Aldehyde oxidases (AOs) possess different substrate specificities for the oxidation of various aldehydes [15-19]. AtAO1 has been suggested to be involved in indole-3-acetic acid biosynthesis [16]. AO2 homodimers catalyse the oxidation of 1-naphthaldehyde [15]. AO3 in wheat regulates the accumulation of carotenoids, and OsAO3 in rice has been confirmed to be responsible for ABA synthesis and seed germination [17,18]. AO4 may oxidize benzaldehyde to benzoic acid to delay silique senescence [19]. Three AOs in barley are distributed in roots, stems and leaves and can oxidize various fatty and aromatic aldehydes [20].

The objective of this study was to evaluate the associations of HvAO1 with seed germination and malting quality in the AC Metcalfe and Baudin DH population. The experimental approach was to identify sequence variation in the HvAO1 promoter region and measure the expression of HvAO1 and phytohormones in AC Metcalfe and Baudin. The phytohormone levels (ABA and IAA) in isogenic lines were also analyzed. Our results indicate HvAO1 may balance moderate dormancy characteristics and superior malt quality in barley breeding programs.

2. Materials and methods

2.1. Plant materials

This study selected the barley (Hordeum vulgare L.) varieties AC Metcalfe and Baudin. The Australian barley cultivar Baudin and the Canadian barley variety AC Metcalfe are high-quality malting barleys. Baudin has moderate dormancy, whereas AC Metcalfe is preharvest sprouting sensitive. Seeds were obtained from the Department of Primary Industries and Regional Development in Western Australia.

We used a doubled-haploid population from AC Metcalfe/Baudin (138 lines) cross to evaluate their associations with germination. Four near-isogenic lines (Table S1) derived from the AC Metcalfe Baudin DH population were used for phytohormone measurement.

2.2. Genotyping, sequencing, and gene expression

DNA extraction, genotyping, and sequencing were performed as previously described [11]. Sequencing using the Sanger method was replicated three times to detect and validate variations in the promoter region of HvAO1 between AC Metcalfe and Baudin. The DNA sequences were compared using the blast function of BioEdit software. All primers used in this study are shown in Table S2.

Following Zhang et al. [21], we selected several DEGs to screen candidate genes according to their expression level, genetic variation, and gene annotation. Embryos isolated from 20 seeds were pooled, and total RNA was extracted using the ISOLATE II RNA Plant Kit according to the manufacturer's protocol. The first strand of cDNA was synthesized using the SensiFAST cDNA Synthesis Kit. PCR was performed with the SensiFASTTM SYBR No-ROX Kit (Bioline, Australia) following the manufacturer's instructions.

2.3. Dormancy test, and malting quality measurement

One hundred uniform seeds were imbibed in a Petri dish at room temperature with 4 mL of water in darkness (three replications). Seeds with emerged coleorhiza were counted as germinated. The experiment was replicated twice. Micro-malting and measurement of malting-quality parameters, including HWE, DP, AA, FAN and BG, followed Cu et al. [14].

2.4. Phytohormone sampling and quantification

Seeds were germinated at 18 ° £C under dark conditions for 24 h. Germinating embryos were excised, ground into fine powder, and freeze-dried. Phytohormone measurement in germinating AC Metcalfe and Baudin was performed at the Aquatic and Crop Resource Development Research Center, Canada. Phytohormone measurement in germinating near-isogenic lines derived from the AC Metcalfe Baudin DH population using HPLC-ESI-MS/MS was performed by Convinced Test Company in Nanjing, Jiangsu, China.

2.5. Association between genes, germination rates and malting quality

The effects of different HvAO1 alleles on germination traits were measured in one DH population. For genotyping, the AC Metcalfe and Baudin DH population were divided into two groups based on the SD2-specific marker GMS001 and four groups based on the HvAO1-specific InDel marker. The germination traits of these four groups were calculated and compared.

2.6. Phylogenetic tree construction

The deduced aldehyde oxidase amino acid sequences were retrieved from Phytozome (https://phytozome-next.jgi.doe.gov). A phylogenetic tree was constructed by the neighbor-joining method with 1000 bootstrap replicates.

2.7. Statistical analyses

Two-sample t-tests were conducted to compare the differences in germination rates, malting qualities, and phytohormone contents between varieties and populations. Data statistics were implemented using Excel 2021. Statistical significance was taken at P < 0.05.

3. Results and discussion

3.1. HvAO1 as a candidate gene influencing seed germination through phytohormone synthesis and regulation

The 24-h germination rates of AC Metcalfe and Baudin were 71.76% and 33.76%, respectively. The final germination rates at 72 h after germination increased to 94.7% and 94.0%, respectively. We retrieved previously published RNA-seq data and identified 78 differentially expressed genes (DEGs) responsible for phytohormone synthesis [21]. We focused on the candidate gene HORVU. MOREX.r2.5HG0429900 for further study for three reasons. First, HORVU.MOREX.r2.5HG0429900 is near previously reported QTL (SD2) controlling seed dormancy on chromosome 5H, and its gene annotation aldehyde oxidase (AO) is involved in phytohormone ABA and/or IAA biosynthesis. Second, the transcript level of the HORVU.MOREX.r2.5HG0429900 gene in Baudin was 2.5-, 1.4-, and 4.3-fold greater than that in AC Metcalfe after 24 h, 48 h, and 72 h germination, respectively, indicating that this gene may negatively regulate seed germination (Fig. S1A). Third, resequencing data of 19 barley varieties from the BarleyVar database (https:// 146.118.64.11/BarleyVar/) revealed genomic variations between AC Metcalfe and Baudin (Fig. S1B, C). L. Xu, P. Wang, X. Zhang et al. The Crop Journal 13 (2025) 299-303

The genomic DNA sequence of HORVU.MOREX.r2.5HG0429900 in the barley reference genome Morex has an 8.9 kb segment, comprising a 4.3 kb coding region and the full-length cDNA encoding a polypeptide of 1368 amino acids. AO comprises flavin cofactors, iron-sulfur centres and molybdenum cofactor (Moco) domains (Fig. S1C). Phylogenetic analysis and previous reports have shown that AO genes can be clustered into the AO1, AO2, and AO3 groups. AO1, AO2, and AO3 use indole acetaldehyde, 1-naphthaldehyde, and abscisic aldehyde as substrates. Phylogenetic analysis revealed that the candidate genes, which are marked in different colors in Fig. S2, belong to the AO1 group. Thus, the candidate gene was tentatively named HvAO1.

To examine whether HvAO1 is involved in phytohormone regulation, we measured ABA and IAA in germinating AC Metcalfe and Baudin seeds. Overall, the contents of ABA and ABA catabolites were greater in Baudin than in AC Metcalfe, suggesting that higher levels of biologically active ABA may have been produced and further catabolized in Baudin (Fig. 1). Auxins are represented by the biologically active IAA and inactive amino acids conjugates such as IAA-Asp (aspartic acid). The overall auxin content and bioactive IAA levels were greater in Baudin than in AC Metcalfe, whereas the IAA-Asp level was lower in Baudin than in AC Metcalfe (Fig. 1). The lower accumulation of germination-inhibiting phytohormones (ABA and IAA) in AC Metcalfe may explain the faster germination of AC Metcalfe than that of Baudin.

Two pairs of near-isogenic lines (22669 vs. 22701, and 22,777 vs. 22813) derived from the AC Metcalfe Baudin DH population plus the parents were used in this study. These lines were divided into the AC Metcalfe type and the Baudin type based on the SD2 molecular marker: 22669Ac vs. 22701Ac , 22777Baudin vs. 22813Baudin , and these lines were further divided into different types: 22669Ac vs. 22701Baudin , 22777Ac vs. 22813Baudin , based on the molecular markers of HvAO1. After 24 h of germination, the ABA content and IAA content were greater in the BD-type groups than in the AC-type groups, except that the IAA content was parallel between 22,777 and 22813, possibly resulting from the strong effect of the SD2 locus (they were under the same SD2 background-Baudin type, Fig. 1).

3.2. Different alleles of HvAO1 have distinct effects on seed germination and malting quality

To determine whether HvAO1 plays a role in seed germination, we examined the associations of the genotypes using the HvAO1 gene-specific marker with the germination trait. Two InDel markers in the first intron were selected for HvAO1 genotyping in parental lines (AC Metcalfe and Baudin) and AC Metcalfe/Baudin DH populations. The distributions of the germination indices of the AC Metcalfe/Baudin DH populations and their parents are shown in Fig. S3 and Table S5. We first divided the 138 DH lines derived from AC Metcalfe/Baudin cross into AC Metcalfe types and Baudin types based on the markers of SD2 to accommodate the effect on seed germination of this locus. The HvAO1-specific markers were subsequently used to further divide the DH lines into four subgroups (subgroups AA, AB, BB and BA). Respectively 29, 33, 24, and 52 lines were obtained.

Among the progeny, the average germination rate of the AC Metcalfe type (subgroups AA and AB) was significantly greater than that of the Baudin type (subgroups BA and BB). Within the same SD2 background, the germination rates after 24 h germination of subgroup AA and subgroup AB (AC Metcalfe type) were 32% and 24%, respectively. Moreover, no differences were detected between the subgroups of the Baudin type (subgroups BA and BB, both at 6%) (Fig. 2). At 48 h after germination, 61.6% of the seeds in subgroup BA had germinated, which was greater than 46.4% of those in subgroup BB (both Baudin types) (Fig. 2). At 72 h, a similar pattern was observed, with 85% of the seeds in subgroup BA germinating, versus 72.7% in subgroup BB. The germination rate of subgroup AA was comparable to that of subgroup AB at 48 h and 72 h after germination (Fig. 2).

The DH populations are divided into AA, AB, BA and BB based on SD2 and HvAO1 specific marker. AA indicates the AC Metcalfe type considering the dormancy SD2 marker and AO1 locus, while AB indicates the AC Metcalfe type considering the SD2 marker and Baudin type considering the HvAO1 locus. BB indicates Baudin type considering the SD2 marker and AO1 locus, while BA indicates Baudin type considering the SD2 marker and AC Metcalfe type considering the HvAO1 locus. Different letters indicate differences between means (P < 0.05).

To evaluate whether HvAO1 could be utilized as a candidate gene to maintain the balance of dormancy and malting quality, we further measured the effect of HvAO1 on malting quality. The influence of genetic variation in the HvAO1 gene on malting quality was measured using the AC Metcalfe/Baudin DH population. Similarly, the DH lines were divided into AC Metcalfe (AA and AB) and Baudin (BA and BB) types based on the molecular markers of SD2. Each type was then divided into two subgroups based on the HvAO1-specific marker. No difference in diastatic power was found among the four groups. The amylase activity of the AA and BA groups was greater than that of the AB and BB groups. The amylase activity of the BA group was greater than that of the AB group. The BG and HWE of the AA group were greater than those of the AB group, whereas no difference was detected between the other groups. The FAN and SP contents of the AA and BA groups were greater than those of the AB and BB groups, respectively (Fig. 2). Previous studies have shown that the major QTL SD2 is also associated with malting quality parameters, including SP, BG, FAN, HWE, and AA [22]. Fig. 2. Germination rate and malting quality of AC Metcalfe/Baudin DH populations and their parents. (A) Germination rate of AC Metcalfe and Baudin after 24 h germination. (B) Germination rate of AC Metcalfe and Baudin after 48 h germination. (C) Germination rate of AC Metcalfe and Baudin after 72 h germination. (D) AA (a-amylase) activity in AC Metcalfe/Baudin DH populations. (E) BG (b-glucanase) in AC Metcalfe/Baudin DH populations. (F) HWE (hot water extract) in AC Metcalfe/Baudin DH populations. (G) SP (soluble protein) in AC Metcalfe/Baudin DH populations. (H) FAN (free amino nitrogen) in AC Metcalfe/Baudin DH populations. (I) MalYld (malt yield) in AC Metcalfe/Baudin DH populations. 302

3.3. Sequence variations in the HvAO1 promoter

With InDel markers in HvAO1 for AC Metcalfe and Baudin, we found large insertions in the intron regions. A search of a transposon database revealed that the insertion sequence did not have the typical characteristics of a transposon element [23]. Thus, we further searched the upstream regions for cis-regulatory elements that are known to mediate responses to GA, ABA or other phytohormones in the promoter regions (approximately 1 kb) of HvAO1 in AC Metcalfe and Baudin. In addition to 20 single-nucleotide polymorphisms, two 7-bp insertions, a 10-bp deletion and a 27- bp deletion, were detected in the promoter region of Baudin. A sulfur-responsive element (SURE, GAGAC) contains an auxin response factor (ARF)-binding sequence in the promoter region of HvAO1 in AC Metcalfe and Baudin at different positions [24]. The poly A (ATA) signal was detected only in the promoter region of Baudin, and it was consistently detected in rice alpha-amylase [25]. Two pyrimidine boxes (CCTTTT) were found exclusively in the Baudin promoter region, 956 bp and 1227 bp upstream from the translation start site. The pyrimidine box increases the expression of amy1 proteins and is involved in the GA response. GT1CONSENSUS (GRWAAW, R = A/G; W = A/T) and IBOXCORE (GATAA) were present only in the promoter of HvAO1 in Baudin, and they are conserved sequences upstream of light-regulated genes. One auxin response factor binding site, ARFAT (TGTCTC), and one auxin response element, SEBFCONSSTPR10A (YTGTCWC, W = A/T), were detected only in the Baudin promoter. ARFAT was found in the promoters of primary auxin response genes in Arabidopsis and the soybean auxin-responsive gene GH3 promoter. ARFAT was enriched in the 5 -flanking region of genes activated by IAA [26]. One ASF1 (TGACG) in the AC Metcalfe promoter region was mutated to the W-box. ASF1 is involved in the transcriptional activation of several genes induced by auxin and/or salicylic acid, which are light sensitive. The W-box element was detected in the barley iso-amylase 1 promoter (Table S6).

Manipulating the gene expression of HvAO1 could be used for different purposes in different environments. In regions with high humidity and precipitation during the harvest season, HvAO1Baudin may be preferred, whereas growers in drier environments may choose a different combination of SD2 markers and HvAO1. HvAO1 gene-specific markers could serve as polymorphic diagnostic markers in breeding programs.

CRediT authorship contribution statement

Le Xu: Writing - review & editing, Writing - original draft, Investigation, Data curation. Peng Wang: Investigation. Xiaoqi Zhang: Investigation. Qisen Zhang: Data curation. Penghao Wang: Data curation. Yanhao Xu: Data curation. Chengdao Li: Writing - review & editing, Supervision, Methodology. Wenying Zhang: Writing - review & editing, Funding acquisition.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

This work was supported by the Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education (KFT202302) and the National Natural Science Foundation of China (32372052). We thank Dr. Tianhua He for assistance with revision.

Footnote

* Corresponding authors.

E-mail addresses: [email protected] (C. Li), [email protected] (W. Zhang).

References

References

[1] G. Kaur, P.K. Toora, P.A. Tuan, C.A. McCartney, M.S. Izydorczyk, A. Badea, B.T. Ayele, Genome-wide association and targeted transcriptomic analyses reveal loci and candidate genes regulating preharvest sprouting in barley, Theor. Appl. Genet. 136 (2023) 202.

[2] Y. Jia, J.M. Barrero, J.R. Wang, M.J. Considine, S. Nakamura, C.D. Li, Seed dormancy, germination, and pre-harvest sprouting, Front. Plant Sci. 15 (2024) 1399510.

[3] K. Takeda, K. Hori, Geographical differentiation and diallel analysis of seed dormancy in barley, Euphytica 153 (2007) 249-256.

[4] W.E. Finch-Savage, G. Leubner-Metzger, Seed dormancy and the control of germination, New Phytol. 171 (2006) 501-523.

[5] X.M. Ji, B.D. Dong, B. Shiran, M.J. Talbot, J.E. Edlington, T. Hughes, R.G. White, F. Gubler, R. Dolferus, Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals, Plant Physiol. 156 (2011) 647-662.

[6] Y. Bonnardeaux, C.D. Li, R. Lance, X.Q. Zhang, K. Sivasithamparam, R. Appels, Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions, Crop Pasture Sci. 59 (2008) 517-526.

[7] L.T. Hickey, W. Lawson, V.N. Arief, G. Fox, J. Franckowiak, M.J. Dieters, Grain dormancy QTL identified in a doubled haploid barley population derived from two non-dormant parents, Euphytica 188 (2012) 113-122.

[8] R.D. Horsley, N.L.V. Lapitan, Z. Ma, P.B. Schwarz, QTL mapping of dormancy in barley using the Harrington/Morex and Chevron/Stander mapping populations, Crop Sci. 49 (2009) 841-849.

[9] S. Nakamura, M. Pourkheirandish, H. Morishige, Y. Kubo, M. Nakamura, K. Ichimura, S. Seo, H. Kanamori, J. Wu, T. Ando, G. Hensel, M. Sameri, N. Stein, K. Sato, T. Matsumoto, M. Yano, T. Komatsuda, Mitogen-activated protein kinase 3 regulates seed dormancy in barley, Curr. Biol. 26 (2016) 775-781.

[10] H. Hisano, R.E. Hoffie, F. Abe, H. Munemori, T. Matsuura, M. Endo, M. Mikami, S. Nakamura, J. Kumlehn, K. Sato, Regulation of germination by targeted mutagenesis of grain dormancy genes in barley, Plant Biotechnol. J. 20 (2021) 37-46.

[11] X. Jin, S. Harasymow, Y. Bonnardeaux, T. Allen, R. Appels, R. Lance, G. Zhang, QTLs for malting flavour component associated with pre-harvest sprouting susceptibility in barley (Hordeum vulgare L.), J. Cereal Sci. 53 (2011) 149-153.

[12] D.W. Sweeney, T.E. Rooney, J.G. Walling, M.E. Sorrells, Interactions of the barley SD1 and SD2 seed dormancy loci influence preharvest sprouting, seed dormancy, and malting quality, Crop Sci. 62 (2021) 120-138.

[13] M.J. Edney, W.G. Legge, M.S. Izydorczyk, T. Demeke, B.G. Rossnagel, Identification of barley breeding lines combining preharvest sprouting resistance with "Canadian-type" malting quality, Crop Sci. 53 (2013) 1447- 1454.

[14] S.T. Cu, T.J. March, S. Stewart, S. Degner, S. Coventry, A. Box, D. Stewart, B. Skadhauge, R.A. Burton, G.B. Fincher, Genetic analysis of grain and malt quality in an elite barley population, Mol. Breed. 36 (2016) 129.

[15] S. Akaba, M. Seo, N. Dohmae, K. Takio, H. Sekimoto, Y. Kamiya, N. Furuya, T. Romano, T. Koshiba, Production of homo- and hetero-dimeric isozymes from two aldehyde oxidase genes of Arabidopsis thaliana, J. Biochem. 126 (1999) 395-401.

[16] M. Seo, S. Akaba, T. Oritani, M. Delarue, C. Bellini, C.T. Koshiba, Higher activity of an aldehyde oxidase in the auxin-overproducing superroot1 mutant of Arabidopsis thaliana, Plant Physiol. 4 (1998) 116.

[17] P. Colasuonno, M.L. Lozito, I. Marcotuli, D. Nigro, A. Giancaspro, G. Mangini, P. De Vita, A.M. Mastrangelo, N. Pecchioni, K. Houston, R. Simeone, A. Gadaleta, A. Blanco, The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments, BMC Genomics 18 (2017) 122.

[18] X. Shi, Q. Tian, P. Deng, W. Zhang, W. Jing, The rice aldehyde oxidase OsAO3 gene regulates plant growth, grain yield, and drought tolerance by participating in ABA biosynthesis, Biochem. Biophys. Res. Commun. 548 (2021) 189-195.

[19] S. Srivastava, G. Brychkova, D. Yarmolinsky, A. Soltabayeva, T. Samani, M. Sagi, Aldehyde oxidase 4 plays a critical role in delaying silique senescence by catalyzing aldehyde detoxification, Plant Physiol. 173 (2017) 1977.

[20] R.T. Omarov, S. Akaba, T. Koshiba, S.H. Lips, Aldehyde oxidase in roots, leaves and seeds of barley (Hordeum vulgare L.), J. Exp. Bot. 50 (1999) 63-69.

[21] Q.S. Zhang, X.Q. Zhang, F. Pettolino, G.F. Zhou, C.D. Li, Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos, J. Plant Physiol. 191 (2016) 127-139.

[22] J.F. Panozzo, P.J. Eckermann, D.E. Mather, D.B. Moody, C.K. Black, H.M. Collins, A.R. Barr, P. Lim, B.R. Cullis, QTL analysis of malting quality traits in two barley populations, Aust. J. Agric. Res. 58 (2007) 858-866.

[23] Z. Xu, H. Wang, LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Res. 35 (2007) 265-268.

[24] A. Maruyama-Nakashita, Y. Nakamura, A. Watanabe-Takahashi, E. Inoue, T. Yamaya, H. Takahashi, Identification of a novel cis-acting element conferring sulfur deficiency response in Arabidopsis roots, Plant J. 42 (2005) 305-314.

[25] J.C. Loke, E.A. Stahlberg, D.G. Strenski, B.J. Haas, P.C. Wood, Q.Q. Li, Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures, Plant Physiol. 138 (2005) 1457-1468.

[26] H. Goda, S. Sawa, T. Asami, S. Fujioka, Y. Shimada, S. Yoshida, Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis, Plant Physiol. 134 (2004) 1555-1573

Appendix A. Supplementary data

Supplementary data for this article can be found online at https://doi.org/10.1016/j.cj.2024.11.008.