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Crop Science 43:556-561 (2003)
© 2003 Crop Science Society of America

CROP BREEDING, GENETICS & CYTOLOGY

Marker-Based Selection in Barley for a QTL Region Affecting {alpha}-Amylase Activity of Malt

M. Ayouba, E. Armstrongb, G. Bridgerc, M. G. Fortina and D. E. Mather*,a

a Dep. of Plant Sci., McGill Univ., 21111 Lakeshore Road, Ste-Anne-de-Bellevue, QC, H9X 3V9 Canada
b Brewing and Malting Barley Research Institute, 303-161 Portage Ave. E., Winnipeg, MB, R3B 2L6 Canada
c Health Canada, Pest Management Regulatory Agency, 2720 Riverside Drive, Ottawa, ON, K1A 0K9 Canada

* Corresponding author (diane.mather{at}mcgill.ca)


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
In the development of barley (Hordeum vulgare L.) cultivars for malting purposes, it is usually not possible to select for malt quality characteristics in early generations because of the high cost associated with micromalting large numbers of grain samples and assessing quality traits on the resulting malt samples and because of the sensitivity of quantitative malt quality traits to environmental variation. Thus, barley malting quality may be a good candidate for marker-assisted selection. Here, the objective was to use marker-based selection to manipulate a malt quality characteristic, {alpha}-amylase activity, in a barley breeding population. Marker-based selection was applied among F2:3 lines from the cross ‘Morex’/‘Labelle’, targeting Morex alleles in a region of chromosome 7(5H) that had previously been found to affect {alpha}-amylase activity in the cross ‘Steptoe’/Morex. The target region was represented by two polymerase chain reaction (PCR) markers. Selected lines were grown in field plots in two years. Agronomic and grain quality data were measured. Grain samples were micromalted and assessed for malt quality traits. Selection for the Morex allele at two PCR markers on chromosome 7(5H) was effective in increasing {alpha}-amylase activity. It was concluded that marker-based selection for a quantitative trait locus could be effective even when applied in a population other than the mapping population.

Abbreviations: D.U., dextrinizing units • oL, o Lintner • MAS, marker-assisted selection • PCR, polymerase chain reaction • QTL, quantitative trait locus


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
GENETIC LINKAGE MAPS have been developed in various barley crosses (e.g., Heun et al., 1991; Graner et al., 1991; Kleinhofs et al., 1993) and used to detect and map quantitative trait loci (QTLs) contributing to various traits, including grain and malt quality (e.g., Hayes et al., 1993; Thomas et al., 1995; Mather et al., 1997; Marquez-Cedillo et al., 2000; Ayoub et al., 2002). Information on the position of QTLs relative to marker loci provides a basis for marker-assisted selection (MAS) for quantitative traits. In barley, MAS is of particular interest for the development of genotypes with superior malting quality because (i) thorough assessment of grain and malt quality traits is expensive and requires larger grain samples than are normally available in the early stages of a breeding program and (ii) grain and malt quality traits are subject to considerable environmental variation and genotype x environment interaction. With MAS for QTLs that affect grain and malt quality, barley breeders could limit breeding populations to those progeny with the highest probability of having superior malting quality.

Marker-assisted selection may follow one of several strategies. One involves the genotyping of additional progeny from the mapping population (i.e., progeny that were not used for QTL detection). Application of this approach in barley has been used for QTLs affecting malting quality (e.g., Han et al., 1997; Romagosa et al., 1999; Igartua et al., 2000). Another MAS strategy involves backcrossing mapping progeny to one of the parents. In barley, this has been used for QTLs affecting yield (Larson et al., 1996; Kandemir et al., 2000a) and head shattering (Kandemir et al., 2000b). A third MAS strategy involves intercrossing of selected progeny from mapping populations. For example, Zhu et al. (1999) selected two doubled haploid lines from the Steptoe/Morex mapping population on the basis of their molecular marker genotypes in regions of the genome where QTLs had been detected for grain yield, and crossed them with the expectation of producing progeny with superior grain yield.

All of the strategies referred to above are restricted to materials derived directly from parents that had been used in QTL detection experiments. For MAS to be widely applicable in plant breeding programs, it would be desirable to transfer favorable QTL alleles into other materials. In barley, Toojinda et al. (1998) have succeeded in introgressing QTL alleles that confer adult plant resistance to stripe rust (Puccinia striiformis Westend. f. sp. hordei) into a genetic background unrelated to the mapping population. Here, we employed a similar strategy for a QTL region affecting grain and malt quality in barley. We crossed a malting barley cultivar (Morex) with an unrelated but adapted feed barley cultivar (Labelle) and selected among the progeny based on genotypes at marker loci near a QTL region that had been mapped in a population derived from a cross between Morex and another feed barley cultivar (Steptoe). Our objective was to assess whether marker-based selection could be effective in manipulating a QTL region in a barley breeding population that shared only one parent with the population in which the QTL region had originally been detected and mapped.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
QTL Analysis and PCR Markers
QTL positions for {alpha}-amylase activity were estimated from data from the North American Barley Genome Project (available on Graingenes http://wheat.pw.usda.gov/ggpages/; verified 25 Sept. 2002). The data were analyzed by simple interval mapping using the software MQTL (Tinker and Mather, 1995) with significance thresholds set by permutation to obtain a per-genome Type-I error rate of 0.05. The marker map was the same as that used by Borém et al. (1999). The phenotypic data used were means across nine environments, four in which the population was grown in 1991 [Aberdeen, ID; Bozeman, MT; Klamath Fall, OR; and Pullman, WA (Hayes et al., 1993)], and five in which the population was grown in 1992 [Tetonia, ID; Crookston, MN; Bozeman, MT (irrigated); Bozeman, MT (dryland); and Pullman, WA]. We targeted a region of the genome, between the RFLP markers ABC302 and ABC717 on the minus arm of chromosome 7(5H), in which Morex contributed a favorable allele or alleles for {alpha}-amylase activity in Steptoe/Morex (Fig. 1). We used two pairs of PCR primers (Blake et al., 1996) to represent it, primer pair ABC302.3 (5'-ATAAAGGAGAAGATTGAGTC-3' and 5'-ATAAGGAACAGGAACAGAGT-3') and primer pair ABC717 (5'-CAATACGGCAACAAATAACA-3' and 5'-CCCCACCAAAATTACCAGTC-3').



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  		Fig. 1. Chromosome-7(5H) test-statistic scan from simple interval mapping in the barley population Steptoe/Morex based on means of {alpha}-amylase activity across none environments. The chromosome is oriented with the "plus" arm on the left. A horizontal scale shows centimorgan positions (tick mark every 25 cM). Horizontal solid lines show significance thresholds estimated from 1000 permutations of the data to maintain the per-genome Type I error rate below 0.05.

 
To obtain DNA for PCR, samples of frozen leaf tissue were ground in 500 µL of CTAB (hexadecyltrimethylammonium bromide) buffer [2% (w/v) CTAB, 1.4 M NaCl, 100 mM Tris/HCl, 20 mM EDTA, 0.2% (v/v) 2-mercaptoethanol), incubated for 45 min at 60°C then mixed with 500 µL of 24:1 chloroform/isoamyl alcohol and centrifuged at 11 750 g for 5 min. The aqueous top phase was transferred to a new tube and reextracted two or three times. The DNA was precipitated in 500 µL of cold isopropanol, then centrifuged at 16 000 g at 4°C for 15 min. The supernatant was removed and the pellet washed three times with 70% (v/v) cold ethanol and dried. The pellet was resuspended in 50 µL of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and stored at -70°C. Optical density was measured at 260 and 280 nm and DNA concentration was adjusted to 5 ng µL-1.

PCR amplifications were conducted with approximately 20 ng of genomic DNA in a volume of 25 µL containing 5 mM of each dNTP, 0.156 µM of each primer, 1.25 units of Taq polymerase and 1x PCR-buffer. The reaction was overlaid with 25 µL of heavy mineral oil and thermocycling was performed with one step at 94°C for 1 min, then 35 cycles of 94°C for 1 min, 52°C for 1 min 12 sec, 72°C for 1 min, and one final step at 72°C for 5 min. Products amplified with the ABC302.3 primers were restricted for 2 h at 37°C with two units of MseI restriction enzyme, and fragments were separated on 1.4% (w/v) agarose gels and stained with ethidium bromide. Products amplified with the ABC717 primers were separated on 1.8% (w/v) agarose gel and stained with ethidium bromide for scoring.

Population Development and Marker-Based Selection
A cross was made between Morex and Labelle. Morex is a six-rowed, spring-habit malting barley cultivar developed in Minnesota (Rasmusson and Wilcoxson, 1979). Labelle is a six-rowed, spring-habit cultivar developed in Québec (Mather and Klinck, 1992). Kernels of Morex barley have white aleurone whereas those of Labelle barley have distinctly blue aleurone. Morex/Labelle F1 plants were grown in a controlled-environment plant growth cabinet. In May 1995, several thousand F2 seeds with white aleurone were space planted in the field at Ste-Anne-de-Bellevue, QC. Blue-aleurone seeds were not used because blue aleurone color is generally considered undesirable for malting. Among barley cultivars, differences in aleurone color are usually conditioned by the blx1 locus on the minus arm of chromosome 4(4H) (Finch and Simpson, 1978), in a region where no QTL had been detected for {alpha}-amylase activity in Steptoe/Morex (Hayes et al., 1993). At maturity (early August 1995), 804 F2 plants on which all seeds had white aleurone were harvested and threshed. A random sample of 8 to 10 seeds of each of the 804 F2:3 lines was sown in a Cyg seed growth pouch (Mega International, Minneapolis, MN). After 7 d, a bulk sample of 0.1 g of fresh leaf tissue from each line was harvested, cut into pieces and stored in Eppendorf tubes at -20°C. DNA was extracted as described above. Using DNA extracted from a random sample of 50 F2:3 lines, we verified that polymorphisms detected with the ABC302.3 and ABC717 primer pairs corresponded with those of their RFLP counterparts (as analyzed for us by Linkage Genetics Inc., Salt Lake City, UT, using DNA extracted from the same 50 lines). Both markers were codominant. The remaining 754 F2:3 lines were then genotyped by means of the ABC717 primer pair. Lines were classified as being fixed for the Morex genotype (M lines, derived from F2 plants homozygous for the Morex allele) or the Labelle genotype (L lines, derived from F2 plants homozygous for the Labelle allele) or segregating (derived from heterozygous F2 plants). All segregating lines were eliminated from further consideration, whereas 202 M lines and a random sample of 50 L lines were retained for generation advance and for genotyping with the ABC302.3 primer pair.

In May 1996, a random sample of 20 F3 seeds from each of the 202 M lines and each of the 50 L lines was sown in a single row in the field at Ste-Anne-de-Bellevue, QC. At maturity (August 1996), all spikes were hand harvested from each row.

Meanwhile, the 252 lines were genotyped at the ABC302 locus, by the methods described above for the ABC717 locus. Lines that were fixed for the Morex allele at both marker loci (MM lines) and those that were fixed for the Labelle allele at both marker loci (LL lines) were selected. In the autumn of 1996, all F4 seeds from one randomly selected spike of each MM or LL line were sown in the greenhouse. Eighty-seven of the resulting F3:4 lines (73 MM lines and 14 LL lines) produced sufficient F5 seed for evaluation in field experiments.

Field Experiments and Evaluation of Grain and Malt Quality
In 1997, the 87 F3:5 lines were grown in single plots in the field at Ste-Anne-de-Bellevue, QC, arranged in a randomized field experiment with the parental lines (Morex and Labelle) grown as repeated controls. Each plot consisted of four 2-m rows spaced 20 cm apart and seeded at 300 seeds m-2. Plots were arranged in blocks of seven, with each block containing five F3:5 lines, bordered by Morex at one end and Labelle at the other end. The experiment was sown on 13 May 1997. At maturity (early August 1997), plots were trimmed to a uniform length of 1.76 m, a random sample of 10 spikes per line was hand harvested, and grain was harvested from the rest of the plot with a plot combine.

On 7 May 1998, a similar experiment was seeded in the field at Ste-Anne-de-Bellevue, QC, to evaluate F3:6 lines corresponding to the F3:5 lines evaluated in 1997, using seed from the spikes that had been hand harvested from the 1997 experiment. Here, each plot consisted of four 3.1-m rows spaced 20 cm apart and seeded at 300 seeds m-2. At maturity (late July 1998), plots were trimmed to a length of 2.6 m and grain was harvested with a plot combine.

Heading and maturity dates, plant height, and final grain yield were recorded for all plots in both years. Grain quality was assessed following the American Society of Brewing Chemists (1992) procedures for measurement of test weight, kernel weight, grain protein, germination of 100 kernels in 4 mL and 8 mL of water, and size grading of kernels (>2.8 mm, 2.4–2.8 mm, 2.0–2.4 mm, <2.0 mm). Water sensitivity was calculated as the difference between the germination percentages in 4 mL and 8 mL of water. Samples were micromalted and malt quality was assessed following the American Society of Brewing Chemists (1992) procedures for measuring malt extract, total malt protein, soluble protein, soluble:total protein ratio, extract viscosity, malt friability, diastatic power, {alpha}-amylase activity, and extract ß-glucan. For 8 of the 73 MM lines, the amounts of grain harvested in 1997 were not sufficient to permit the measurement of grain and malt quality variables.

Data Analysis
For each plot within each block, the grain yield value was divided by the mean grain yield of the two parental plots from the same block and multiplied by the overall mean of the parents across all blocks. There were two values for {alpha}-amylase activity missing from the 1997 data set (two LL lines for which the {alpha}-amylase activity level was below the detection threshold) and one extract ß-glucan value missing from the 1998 data set (an MM line). Data were analyzed with PROC MIXED of SAS (Littel et al., 1996), with statistical tests conducted at the 0.05 level of probability. Parents and genotypic classes (MM and LL) were considered fixed effects, whereas years were considered random effects. Likelihood-ratio statistics were used to test the significance of genotypic-class x year interactions (Littel et al., 1996, p. 44). Contrasts were calculated to compare the genotypic classes with each other and with the parents.


   RESULTS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Agronomic Traits
Labelle headed and matured later than Morex and had significantly higher grain yield (Table 1). The two cultivars had similar plant heights. In the combined analysis across years, the parental cultivars and the genotypic classes exhibited significant interactions with years for heading date, maturity date, and grain yield but not for plant height. In 1997, the MM class headed and matured a little earlier than the LL class, both classes headed later than both parents, the MM class matured later than Morex, and the LL class matured later than both parents (Table 1). In 1998, both genotypic classes headed later than Morex but earlier than Labelle, and they both matured later than Morex. There were no large differences in plant height, but the MM class was a little taller than the parents. The mean grain yields of the MM and LL classes were intermediate to those of Morex and Labelle, and were significantly less than Labelle in both years.


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  		Table 1. Mean values for agronomic traits for Morex, Labelle, 73 lines homozygous for Morex alleles at two marker loci on chromosome 7(5H) (the MM genotypic class) and 14 lines homozygous for Labelle alleles at those loci (the LL genotypic class).

 
Grain Quality Traits
Labelle had larger kernels and lower grain protein than Morex (Tables 2 and 3). Among the grain quality traits, the parents and genotypic classes exhibited significant interaction with years only for test weight. For that trait, there were small significant differences in 1997 only, with Labelle having the highest test weight, followed by the MM class and then Morex and the LL class (Table 2). For kernel weight, the two genotypic classes were intermediate to the parents, with the MM class having somewhat larger kernels than the LL class. The kernel size distribution of the LL class was quite similar to that of Morex whereas that of the MM class was more like that of Labelle. The grain protein contents of the two genotypic classes were intermediate to those of the two parents, with the MM class being higher in protein than the LL class.


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  		Table 2. Mean values for grain quality traits for Morex, Labelle, 73 lines homozygous for Morex alleles at two marker loci on chromosome 7(5H) (the MM genotypic class) and 14 lines homozygous for Labelle alleles at those loci (the LL genotypic class).

 

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  		Table 3. Mean values for germination rate and water sensitivity of germination for Morex, Labelle, 73 lines homozygous for Morex alleles at two marker loci on chromosome 7(5H) (the MM genotypic class) and 14 lines homozygous for Labelle alleles at those loci (the LL genotypic class).

 
For both parents and both genotypic classes, the mean germination rate in 4 mL water was >90%. There were some significant differences for this trait in 1997, with the LL class having the highest viability and Morex having the lowest, but none in 1998 (Table 3). The germination of Morex and the MM classes was more water sensitive than that of Labelle and the LL class.

Malt Quality Traits
As expected, Morex exhibited generally better malt quality than Labelle (Table 4). The Labelle malt samples were not fully modified. They had low friability, enzymatic activities, soluble:total protein ratio, and malt extract, and high extract ß-glucan and viscosity. In contrast, the Morex malt samples were highly modified. The only malt quality trait for which the parents and genotypic classes exhibited significant interaction with year was soluble protein, for which there were significant differences in 1997 but not in 1998 (Table 4). For all of the malt quality characteristics (Table 4), the two classes were intermediate between Labelle and Morex. The MM class had higher values than the LL class for all protein traits [total malt protein, soluble protein (1997 only), soluble:total protein ratio], both enzymatic activity traits ({alpha}-amylase activity and diastatic power), and malt extract. The MM and LL classes had similar values for extract ß-glucan, extract viscosity, and malt friability.


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  		Table 4. Mean values for malt quality traits for Morex, Labelle, 73 lines homozygous for Morex alleles at two marker loci on chromosome 7(5H) (the MM genotypic class) and 14 lines homozygous for Labelle alleles at those loci (the LL genotypic class).

 

   DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
In this experiment, the appropriate comparisons to assess the effectiveness of the selection on chromosome 7(5H) are contrasts between the MM genotypic class and the LL genotypic class. Unlike comparisons of MM class means to midparent values, these contrasts would not be confounded by any unintended effects from the selection for white aleurone. All members of both the MM and LL classes are fixed for white aleurone, but the two classes differ in their genotypes at two marker loci (ABC717 and ABC302) in a region of chromosome 7(5H) in which a QTL affecting {alpha}-amylase activity had been detected in Steptoe/Morex (Fig. 1). For this trait, the mean value for the MM class was higher than the mean value for the LL class (Table 4). This result is consistent with the previously detected positive effect of the Morex allele in Steptoe/Morex, indicating that selection based on marker genotypes was effective for the target QTL region on chromosome 7(5H).

The MM and LL genotypic classes differed for several other traits, with the MM class heading a little earlier and having larger kernels with more water-sensitive germination and higher test weight, grain protein, malt protein, soluble:total protein, malt extract, and diastatic power. Some of these differences are consistent with Morex QTL allele effects that have been detected on chromosome 7(5H) in Steptoe/Morex [grain protein and soluble:total protein (Hayes et al., 1993 and Igartua et al., 2002)], ‘Harrington’/Morex [kernel plumpness, test weight, and grain protein (Marquez-Cedillo et al., 2000)] or ‘Dicktoo’/Morex [heading date (Pan et al., 1994), malt extract, and soluble:total protein (Oziel et al., 1996)] while the difference for diastatic power is consistent with the generally expected correlation of that enzymatic trait with {alpha}-amylase activity

Some of the traits measured here had not been measured in any Morex mapping population. For one of these, water sensitivity, the results were consistent with the presence of a QTL in the target region.

Although the target QTL region in this study was expected to affect {alpha}-amylase activity of the malt, it is not the only genomic region contributing to the {alpha}-amylase activity of Morex (Hayes et al., 1993; Igartua et al., 2002; Marquez-Cedillo et al., 2000). Nevertheless, 18 of the 73 MM lines (24.7%) were equal to or above the midparent value, compared with only 1 of the 14 LL lines (7.1%). Most of the MM lines with high {alpha}-amylase activity equaled or exceeded the midparent value for diastatic power and malt extract, and some of them exceeded it for grain yield.

In breeding malting barley, malt extract is considered to be a key indicator of malting quality, just as grain yield is considered to be a key indicator of agronomic performance. Breeders attempt to develop barley genotypes that combine high malt extract and other superior grain and malt quality characteristics with high grain yield and other preferred agronomic characteristics. On the basis of the very limited information collected on the individual lines in this study (i.e., one observation per line in each of two years) none of the 87 lines had both higher grain yield than Labelle and higher malt extract than Morex, but two had grain yield means just below that of Labelle and malt extract values just below that of Morex. Further field evaluation and malt quality assessment would be necessary to assess adequately the potential of these and other individual lines.

Most other experiments involving marker-based selection for QTLs in barley have used materials derived from the same parents as the mapping population in which the QTLs had been detected: previously unevaluated progeny from the mapping cross (e.g., Han et al., 1997; Romagosa et al., 1999; Spaner et al., 1999; Igartua et al., 2000), materials derived by backcrossing to one of the parents (e.g., Larson et al., 1996; Kandemir et al., 2000a, b), or progeny derived by intercrossing members of the mapping population (Zhu et al., 1999). For marker-assisted selection to be more generally useful in improving quantitative traits, breeders would like to be able to apply it to a wider range of materials, such as those derived from crosses between a mapping parent carrying favorable QTL alleles and lines for which QTL experiments have not been conducted but which would not be expected to carry those alleles. This approach involves a risk that the QTL is not effective in the breeding population (in which case the marker genotyping effort is wasted) or even that the QTL has the opposite effect from what was observed in the mapping population (in which case the marker-based selection is detrimental). We attempted this approach here, by selecting a chromosome region of interest on the basis of QTL mapping results from Steptoe/Morex but applying marker-based selection in Morex/Labelle. Like Steptoe, Labelle is a six-rowed feed barley that is not closely related to Morex and that is not suitable for malting. Labelle is not closely related to Steptoe either, and we did not do any mapping in Morex/Labelle to verify whether the QTL of interest were effective in that cross. Nevertheless, divergent selection for two PCR markers in a region of chromosome 7(5H) resulted in genotypic classes with contrasting grain and malt quality characteristics, with those carrying the Morex marker alleles having higher {alpha}-amylase activity than those carrying the Labelle marker alleles.

Although it remains impossible to predict confidently whether QTLs detected in one mapping population can effectively be manipulated by selecting for specific marker genotypes in a different breeding population, the results of this study indicate that this approach was effective for a Steptoe/Morex QTL region when manipulated in a Morex/Labelle breeding population. Furthermore, the selection program described here led to the development of several lines with potentially good malting quality and good agronomic performance in a geographical region in which Morex and other established malting barley cultivars are not well adapted.


   ACKNOWLEDGMENTS
 
Grain and malt quality analyses were conducted in the Technical Centre of Canada Malting Company. We thank Mary de Pauw, Doris Luckert, Thomas Mpoulimpassis, Peter Freeman, and the Canada Malting Company technical staff for their help with this research.


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
This research was supported by grants from Canada Malting Company, Agriculture and Agri-Food Canada, and the Natural Sciences and Engineering Research Council of Canada and by scholarships awarded to the first author by Agriculture and Agri-Food Canada and the Québec Fonds pour la formation de chercheurs et l'aide à la recherche.

Received for publication March 29, 2002.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 




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