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Crop Science 43:1043-1052 (2003)
© 2003 Crop Science Society of America

CELL BIOLOGY & MOLECULAR GENETICS

Comparative Mapping of ß-Amylase Activity QTLs among Three Barley Crosses

J. A. Clancya, F. Hanb, S. E. Ullrich*,a and the North American Barley Genome Project

a Dep. of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420
b Pioneer Hi-Bred Intl. Inc., 7200 NW 62nd Ave., Johnston, IA 50131

* Corresponding author (ullrich{at}wsu.edu)


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
ß-Amylase (BA) is one of the starch-degrading enzymes active in germinating barley (Hordeum vulgare L.). Unlike {alpha}-amylase (AA), it is not synthesized de novo at the onset of germination, but accumulates during seed development. BA activity is an important malting quality parameter and is a major contributor, along with AA, to diastatic power (DP). The objectives of this study were to (i) measure and map BA activity in three crosses of North American barleys, (ii) compare quantitative trait loci (QTLs) for BA among various crosses, and (iii) determine the relationship between BA and previously mapped DP QTLs. Comparative mapping was done by means of a consensus map with common markers from F1 doubled haploid mapping populations from the crosses of ‘Steptoe’ x ‘Morex’ (S/M), ‘Harrington’ x TR306 (H/T), and Harrington x Morex (H/M). BA activity analyses were performed with field-grown seed from the three mapping populations and parents. Relatively normal frequency distributions for enzyme activity were obtained from each of the mapping populations. QTLs for BA were identified in all three crosses and on all seven chromosomes. Seven QTLs were located in S/M, the most genetically diverse cross, while only three each were found in H/T and H/M. As expected, BA QTLs were almost always found in conjunction with previously identified DP QTLs. A survey of QTL literature of populations of diverse germplasm showed many QTLs for BA and DP in common with those identified herein and some unique QTLs as well. The results of this study suggest the benefits of identifying markers closely associated with major BA QTLs are to allow for further molecular studies and for marker assisted selection of this trait.

Abbreviations: BA, ß-amylase • AA, {alpha}-amylase • DP, diastatic power • S/M, Steptoe x Morex • H/M, Harrington x Morex • H/T, Harrington x TR306 • QTL, quantitative trait locus • MAS, marker assisted selection • NABGP, North American Barley Genome Project


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
ß-AMYLASE (BA) is one of the starch-degrading enzymes active in germinating barley. It is an exoenzyme that releases maltose by hydrolyzing from the nonreducing ends of the dextrins generated by AA. Unlike the other starch-degrading enzymes in barley malt, BA is not synthesized de novo during germination but accumulates during seed development (Hardie, 1975). The joint amylolytic activity of primarily BA and AA (Arends et al., 1995), but also limit dextrinase, and {alpha}-glucosidase is termed diastatic power, one of the major malting quality parameters in barley (Bamforth and Barclay, 1993). Some recent work has focused on the value of amylase enzyme activity as a predictor of DP. Arends et al. (1995) found limit dextrinase (r = 0.37), AA (r = 0.64), and BA (r = 0.77) to be correlated to DP. Georg-Kraemer et al. (2001) found only BA correlated to DP (r = 0.57), and Gibson et al. (1995) found BA, limit dextrinase, and AA correlated to DP with r-values of 0.79, 0.69, and 0.61, respectively. All three research groups concluded that BA was the best predictor of DP.

Two structural genes coding for BA (Bmy1 and Bmy2) were previously mapped to barley chromosomes 4 and 2, respectively (Nielsen et al., 1983; Kreis et al., 1988). QTLs for BA activity have been identified in several crosses in one other study (Langridge et al., 1996 and Li et al., 1996). The development of QTL analyses not only provides the map locations of these genes, but also identifies markers linked to them. Therefore, marker assisted selection (MAS) as an alternative selection strategy for quantitative traits has become possible.

The use of molecular markers in genome mapping has led to direct comparisons of the relative order of homologous sequences along the chromosomes of closely and distantly related species and development of the concept of genome synteny. Comparative genome mapping provides insights into genome evolution and genetic information between divergent species. Comparisons among major grass species revealed remarkable marker order conservation over large chromosomal regions as well as within small chromosomal segments (Ahn and Tanksley, 1993; Kurata et al., 1994; Moore et al., 1995; Dunford et al., 1995; Kilian et al., 1995; Han et al., 1998).

Since important quantitative traits among different species vary, such as milling and baking quality in wheat (Triticum aestivum L.) but not in barley, and malting quality in barley but not in rice (Oryza sativa L.), comparative mapping of QTLs among species may not have practical significance. The more interesting and practical question is whether QTLs are conserved among genotypes of the same species. This question is especially important for MAS. If QTLs are not conserved among different intraspecific genetic backgrounds, then tagging of QTLs becomes very difficult. QTL mapping would have to be performed for each specific cross to identify linked molecular markers. Of course if the parents of a cross have the same allele for a given QTL, the QTL would not be detected, but for breeding purposes the QTL would be fixed in the progeny of that cross.

Whereas, AA and DP are routinely analyzed in malting quality evaluations, BA is not. BA analysis is not typically done for various reasons, not the least of which is its analysis difficulty relative to AA and DP analyses. BA activity is an important parameter and genetic as well as linked marker knowledge would be valuable in the overall effort to understand malting quality traits and their improvement. The objectives of this study then were to (i) map BA activity QTLs in three crosses of North American barleys, (ii) compare QTLs among the various crosses analyzed in barley, and (iii) determine the relationship of BA activity QTLs to the closely related malt quality trait, DP, to determine the feasibility of using MAS to screen breeding populations for the economically important DP trait.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
Mapping Populations and Map Construction
The North American Barley Genome Project (NABGP) developed genetic maps from three mapping populations from crosses of S/M, H/T, and H/M (Kleinhofs et al., 1993; Kasha and Kleinhofs, 1993; Kleinhofs, 1996) that were used in this study. The population sizes ranged from 144 to 150 doubled haploid lines. Steptoe is a six-row feed barley, Morex is a North American standard for six-row malting barley, Harrington is a standard for two-row malting barley, and TR306 is a two-row feed barley line. The three maps were aligned on the basis of common molecular markers (Kleinhofs, 1996; Qi et al., 1996). These aligned maps were used for mapping of the BA activity QTLs, as well as, comparing BA and DP QTLs mapped in previous studies.

Analysis of ß-Amylase Activity
The three mapping populations and parents were grown in the field at Spillman Agronomy Farm, Pullman, WA, under dryland conditions on a Palouse silt loam soil (fine-silty, mixed mesic Pachic Ultic Haploxeroll) in a randomized complete block design with two replications of one row plots 6 m long (S/M in 1991, H/T in 1993, H/M in 1995). The bulked seeds from the two replications were used for BA activity analysis. The nurseries in which the populations were grown were for NABGP general agronomic and malting quality QTL analyses (Hayes et al., 1993; Tinker et al., 1996; Mather et al., 1997; Marquez-Cedillo et al., 2000). Malting quality analyses from these nurseries indicated normal quality parameters in terms of protein and malt extract contents and enzyme activities (AA and DP). Protein especially can influence AA, BA, and DP enzyme development and activity (Agu and Palmer, 1998). In this study, proteins averaged within American Malting Barley Association quality specifications (115–135 g kg-1) at 116, 128, and 131 g kg-1 for S/M, H/T, and H/M, respectively.

BA was analyzed by the betamyl method with the BA assay kit (K-Beta) from Megazyme, USA Inc., Bozeman, MT, USA. The assay was performed in duplicate according to the kit directions with the following modifications based on the optimization of the procedure for barley flour by Santos and Riis (1996). The extraction buffer contained 50 mM Trizma base, 1 mM EDTA, 1 mg/mL bovine serum albumin, pH adjusted to 8.0 with 0.2 M HCl. Cysteine (100 mM) was added just before use and the pH was readjusted to 8.0 with 4 M NaOH. Samples were extracted on a shaker for 1 h with manual inversion of the tubes every 15 min. Following extraction, samples were centrifuged and diluted (1250 fold) with the buffer A according to the kit instructions. The dilution allowed all samples to be within the linear range of the standard curve. The assay was conducted with 50 µL betamyl/substrate and 50 µL diluted extract as per directions. Data were expressed on both microgram per gram flour and microgram per milligram protein (analyzed by standard Kjeldahl method). One betamyl unit is defined as the amount of enzyme required, in the presence of excess {alpha}-glucosidase, to release one micromole of p-nitrophenol from PNPG5 in 1 min under the defined assay conditions. Since the trait analyzed is enzyme activity, data expressed as per milligram protein takes into account protein concentration differences among samples.

QTL Analysis
The average value of duplicates for each sample was used for BA activity QTL analysis. Interval mapping was performed by MAPMAKER/QTL (Lincoln et al., 1992). QTL affects were considered significant if they exceeded a LOD score of 2.0 (P < 0.001) for a sparse map case (Lander and Botstein, 1989). DP QTLs from the three NABGP crosses were taken from the literature (Hayes et al., 1993; Han and Ullrich, 1993; Han et al., 1997; Larson et al., 1997; Mather et al., 1997; Ullrich et al., 1997; Marquez-Cedillo et al., 2000), but S/M and H/M samples from the Pullman nurseries described above contributed to the literature values. All H/T DP data were from Canadian nurseries. DP was not reanalyzed because remnant seed samples were not large enough for micromalting and malt analyses.


   RESULTS AND DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
CONCLUSIONS
 REFERENCES
 
ß-Amylase Values
BA activity for the S/M doubled haploid lines varied from 492 to 1571 U/g flour because of the large difference in BA activity of the parental lines (Fig. 1A) . All but one of the progeny fell within the parental values. In H/T, the other malt x feed cross, the parents were close in BA values probably due to TR306 having common ancestry with Harrington and reportedly being identical at 22% of loci (Tinker et al., 1996). Harrington and Morex, both malting types, were also similar in BA activity. H/T and H/M had 58 and 55% of their progeny, respectively, with higher or lower BA activity than the parents. Morex, the malting type parent in the S/M cross, had the higher BA activity on a units per gram flour and units per milligram protein basis (Fig.1B). However in the H/T cross, Harrington, the malting type parent, was lower in BA activity than TR306 on a units per gram flour basis but higher on a units per milligram protein basis because of TR306 having approximately 20 g kg-1 higher protein. Agu and Palmer (1998) have shown that ß-amylase activity is positively associated with grain nitrogen and protein concentration.



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  		Fig. 1. Distribution of ß-amylase (BA) activity among parents and progeny of three doubled haploid populations: Steptoe x Morex (S/M), Harrington x TR306 (H/T), Harrington x Morex (H/M). A) BA activity as U/g flour. B) BA activity as U/mg protein.

 
Quantitative Trait Loci
BA QTLs were identified on all seven barley chromosomes (Fig. 2) . A study with three different crosses from those reported here involving six diverse parents from four continents also found BA QTLs on all 7 chromosomes. (Langridge et al., 1996; Li et al., 1996). In the malt/feed barley crosses, all the positive (higher value) alleles for the BA QTLs were attributed to the malting type parent. In the H/M cross, both malting type parents contributed positive alleles. DP QTLs previously located in the three crosses studied here (Hayes et al., 1993; Han and Ullrich, 1993; Han et al., 1997; Larson et al., 1997; Mather et al., 1997; Ullrich et al., 1997; Marquez-Cedillo et al., 2000) are included in Fig. 2 for comparison purposes. Since DP is predominantly a function of the combined activity of both BA and AA, DP QTLs would be expected to be coincident with BA and/or AA QTLs.









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  		Fig. 2. QTL for ß-amylase (BA/F = BA/g flour, BA/P = BA/mg protein) and diastatic power (DP) on barley consensus maps of three doubled haploid populations: Steptoe x Morex (S/M), Harrington x TR306 (H/T), Harrington x Morex (H/M). Bars indicate approximate positions of QTL based on estimated order and position of markers (Qi et al., 1996). Number and letter below the bar indicate LOD score and parent contributing the QTL, respectively.

 
Chromosome 1 (7H)
A BA QTL on chromosome 1 with the positive allele attributed to Morex was apparent in both the S/M and H/M crosses. These QTLs accounted for 6.5 and 17.0% of the variation for BA in S/M and H/M, respectively. Since the positive QTL allele is not in the two-row cultivar Harrington, it may be a candidate for improving two-row malting barley, or at least Harrington types. QTLs previously reported for DP and AA in S/M (Hayes et al., 1993; Han and Ullrich, 1993; Han et al., 1997; Ullrich et al., 1997) and for DP in H/M (Marquez-Cedillo et al., 2000) are coincident with this BA QTL, again with the higher value alleles contributed by Morex. QTLs for AA and BA in approximately the same region were reported in the cross Galleon/Haruna Nijo (Li et al., 1996; Langridge et al., 1996). Oziel et al. (1996) found DP and AA QTLs adjacent to this region in another cross with a Morex parent. This QTL region may be the site of a single gene, perhaps a transcription factor, which controls these amylolytic enzymatic traits. However, this region overlaps Amy2, a known structural gene for AA, so there may be multiple QTLs which are too close to be separated in this type of analysis. Furthermore, this region contains QTLs for malt extract content, ß-glucan content, ß-glucanase activity, and dormancy (Hayes et al., 1993; Ullrich et al., 1993; Han et al., 1995; Ullrich et al., 1996; Han et al., 1997; Ullrich et al., 1997). In any case, this region is considered to be an important contributor to malting quality (Han et al., 1997).

Chromosome 2 (2H)
BA QTLs near the Bmy2 structural gene were identified in both the H/T and H/M crosses. These QTLs accounted for 10.8% of the variation for BA in both H/T and H/M. As these QTLs overlap and both the positive alleles come from Harrington, it is likely this is a single QTL. Not surprisingly there was a DP QTL in the H/M cross at the same location with the positive allele also from Harrington (Marquez-Cedillo et al., 2000). Since this chromosome 2 BA positive QTL allele has not been identified in Morex or other six-rows, then it may be a candidate for improving six-row malting barley. It is noteworthy that there was no QTL detected for BA activity in S/M near the Bmy2 site as Bmy2 was mapped in S/M by NABGP (Kleinhofs et al., 1993). However, it is not uncommon for structural genes to be absent in QTL analyses. For example in the NABGP crosses, no AA QTL has been found in S/M on chromosome 6 at the Amy1 structural gene site (Hayes et al., 1993), nor has any grain protein QTL been detected in the vicinity of the hordein protein gene families (Hor1, Hor2, Hor3) on chromosome 5 (Hayes et al., 1993; Mather et al., 1997; Marquez-Cedillo et al., 2000). Hordeins are prolamin storage proteins that make up over 50% of the total grain protein concentration. There is a DP QTL that overlaps with Bmy2, as well as an overlapping AA QTL (Hayes et al., 1993). Additional BA QTLs have been reported in Clipper/Sahara, Chebec/Harrington and Galleon/Haruna Nijo in the RbcS-MWG520A interval and another one near cMWG720 in Clipper/Sahara (Langridge et al., 1996).

Chromosome 3 (3H)
One or possibly two BA QTLs were located on chromosome 3 in H/T overlapping a region previously reported to contain a BA QTL in Clipper/Sahara (Langridge et al., 1996). Additional BA QTLs have been located between ABG 499 and ABG 495B in Galleon/Haruna Nijo and Clipper/Sahara (Langridge et al., 1996). DP (Larson et al., 1997) and AA (Hayes et al., 1993) QTLs have been located in the latter interval around WG110 in S/M and a DP QTL was also found here in Bleinheim/E224/3 (Thomas et al., 1996). The H/T QTL(s) accounted for 7.0% of the BA variation. This seems to be a minor QTL that is probably in both malting type parents, but is apparently not associated with a DP QTL.

Chromosome 4 (4H)
The QTL for BA found on chromosome 4 accounted for 10.5% of the BA variation and is coincident with reported QTLs for AA and DP in S/M (Hayes et al., 1993; Ullrich et al., 1997). The crosses studied by Langridge et al., (1996) had BA QTLs in mid-chromosome 4, medial to the area found in S/M, and overlapping the Bmy1 structural gene. DP QTLs for S/M (Hayes et al., 1993), Dicktoo/Morex (Oziel et al., 1996), and Calicuchima-sib/Bowman (Hayes et al., 1996) were also found near Bmy1. Interestingly, in both the S/M and Dicktoo/Morex crosses, the high DP allele was contributed by the nonmalting-type parent with no associated BA or AA QTLs observed. As in chromosome 2 in the case of Bmy2, the Bmy1 gene was not coincident with a BA QTL.

Chromosome 5 (1H)
A major QTL for BA found on chromosome 5 and a QTL for DP (Hayes et al., 1993) were located near the short-arm telomere of chromosome 5 in both S/M (accounted for 35.0% of BA variation) and H/T (accounted for 12.5% of BA variation) but not in H/M, which suggests that the positive alleles contributed by Morex and Harrington are probably the same. The Clipper/Sahara cross also had a BA QTL (Langridge et al., 1996) and Blenheim/E224/3 had a DP QTL (Thomas et al., 1996) in this same region. Another minor BA QTL on the long arm of chromosome 5 in S/M accounting for 6.8% of the BA variation was also associated with previously reported AA and DP QTLs in this same cross (Hayes et al., 1993). Overlapping this area between ABG452 and MWG912, additional BA QTLs were reported in Clipper/Sahara and Galleon/Haruna Nijo (Langridge et al., 1996).

Chromosome 6 (6H)
Two BA QTLs were found on chromosome 6 in S/M, with the favorable alleles coming from Morex. Each was coincident with DP QTLs in S/M (Hayes et al., 1993; Han and Ullrich, 1993). The BA variation accounted for by the short arm QTL was 6.9% and by the long-arm QTL was 9.6%. No BA QTLs were detected at these locations in the H/T or H/M populations, so the two malting types (Morex and Harrington) as well as TR306 may contain the same alleles. Clipper/Sahara also showed BA QTLs in these same two positions (Langridge et al., 1996). Mather et al. (1997) reported the presence of DP and AA QTLs in H/T in this general chromosome area. The BA QTL in H/M found in this study between ABC 170A and MWG798A was not evident in S/M despite the fact that the positive allele came from Morex, suggesting that Steptoe and Morex have the same allele at this locus. The magnitude of effect of this BA QTL was reflected as 9.2% of the variation.

Chromosome 7 (5H)
A minor BA QTL (accounted for 6.5% of BA variation) detected in S/M coincides with DP and AA QTLs in S/M (Hayes et al., 1993; Han and Ullrich, 1993) and Dicktoo/Morex (Oziel et al., 1996), as well as a DP QTL in Blenheim/E224/3 (Thomas et al., 1996). Additional QTLs for BA have been reported in Chebec/Harrington and Galleon/Haruna Nijo between MWG514B and MWG851B (Langridge et al., 1996). The DP QTL reported in H/T in this same region appears to be associated with an AA QTL only (Mather et al., 1997).

General
It might be expected that all previously reported DP QTLs would have either a BA or an AA QTL (or both) associated with them. This was the case for all but one of the 15 DP QTLs previously reported from the three crosses analyzed in this study. The exception is the DP QTL detected in S/M in which the positive allele was attributed to Steptoe, the nonmalting-type parent. Similarly, only three of the 13 BA QTLs detected in this study were not coincident with a DP QTL. One possible explanation for a lack of logical QTL associations between genes of these enzymatic traits might be that independently the BA and AA activities were not above the LOD threshold of significance but combined gave a significant DP QTL. Also, there are other enzymes (limit dextrinase, and {alpha}-glucosidase) that contribute to DP values.

BA QTLs were never detected in this study, and should not be expected to be, in all three crosses at a given chromosome location. A QTL might not be detected in any given cross for a number of reasons. Some favorable alleles may be absent even in malting varieties. Some crosses, particularly those between two malting types, may not show segregation at a particular locus due to a lack of polymorphism, and therefore, the QTL would not be detected. Considering the various studies on BA QTL analysis (Langridge et al., 1996; Li et al., 1996), different and often unique markers were used, which makes it difficult to compare the positions of the QTLs. Marker order and map distances vary among crosses, as determined in different labs, making accurate placement of QTLs on chromosomes difficult. Reports vary in thresholds of statistical significance and methods of analysis as well. Despite these shortcomings, through the use of a consensus map, valuable information has been gained for areas of the barley genome (Zale et al., 2000), and there is remarkable agreement between this study and a previous study (Langridge et al., 1996; Li et al., 1996).


   CONCLUSIONS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
REFERENCES
 
BA QTLs were detected on all seven barley chromosomes. Conservatively, among the 13 independently determined QTLs, 10 BA activity QTLs were detected among the three crosses studied. In three cases, two QTLs, which were independently detected in two different crosses, are probably the same QTL because there was a common parent and the common parent contributed the positive (high value) allele. Then among the 10 BA QTL regions identified in this study, six were coincident with BA QTL regions identified in a previous study (Langridge et al., 1996; Li et al., 1996), which involved other crosses. The previous study (Langridge et al., 1996; Li et al., 1996) also identified five BA QTL regions not coincident with any of the regions identified in the present study. On the basis of the previous and present studies together, a minimum of 15 chromosome regions affect BA activity in barley. Therefore, there appears to be a considerable number of genes operating for BA activity, which underlies its quantitative genetic nature.

The most consistent and promising QTL regions identified herein for MAS, on the basis of detection in at least two crosses, on both enzyme activity measurement methods, on relatively high magnitudes of effect, and coincidence with BA (Langridge et al., 1996; Li et al., 1996) and/or DP QTLs from other studies (Hayes et al., 1993; Thomas et al., 1996; Mather et al., 1997; Marquez-Cedillo et al., 2000) are ones on chromosome 1 between Brz and Amy2 (up to 17% of BA variation), on chromosome 2 between Bmy2 and ABC252 (10.8% of BA variation), and on chromosome 5 between Act8A and CDO099 (up to 35% of BA variation). The QTL region on chromosome 1 is a critical region for malting quality in general as pointed out above because of the plethora of relevant QTLs in the region (Han et al., 1997). The chromosome 5 QTL region is also important for BA and consequently DP (Arends et al., 1995; Gibson et al., 1995; Georg-Kraemer et al., 2001) because of the high magnitude of effect on BA activity. On the other hand, any of the QTLs could be important for fine tuning the ß-amylase activity trait or its downstream trait, diastatic power in malting type barley germplasm. Given adequate resources and priorities, choice of target QTL(s) (high or low magnitude of effect) for MAS will depend on how wide (genetically) the cross in question is and parental pedigrees in relationship to the occurrence of known positive alleles in related cultivars or lines. Ultimately with microarray technology, genetic knowledge about parents and MAS should become quite accurate and precise. The more knowledge that breeders have about the genes that control economically important traits, especially quantitatively inherited traits, the more directed crop improvement efforts can be. The study reported herein will contribute, in a small way, to the overall effort to improve barley malting quality, which involves a very genetically complex set of traits.


   ACKNOWLEDGMENTS
 
The authors wish to thank Drs. Andris Kleinhofs and Fred Muehlbauer for their critical review of this manuscript and funding through Washington State University, the Washington Barley Commission, the American Malting Barley Association, and the North American Barley Genome Mapping Project.


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
Dep. of Crop and Soil Sciences Scientific Paper Number 0208-03, Agricultural Research Center, Washington State University, Pullman, WA, Project 1006.

Received for publication August 29, 2001.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 





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