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CROP BREEDING, GENETICS & CYTOLOGY

Allelic Diversity Changes in 96 Canadian Oat Cultivars Released from 1886 to 2001

^a Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada S7N 0X2
^b Dep. of Plant Sciences, Univ. of Saskatchewan, 51 Campus Dr., Saskatoon, SK, Canada S7N 5A8
^c Dep. of Biology, McGill Univ., Montreal, QC, Canada H3A 1B1

^* Corresponding author (fuy{at}agr.gc.ca).

	ABSTRACT

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There is longstanding concern that modern plant breeding reduces crop genetic diversity. Such reduction may have consequences both for the vulnerability of crops to changes in their pests and diseases and for their ability to respond to changes in climate and agricultural practices. This concern, however, has not been well validated in recent molecular studies of genetic diversity of several crop species. The objective of this study was to assess allelic diversity changes in 96 Canadian oat (Avena sativa L.) cultivars released from 1886 to 2001 by means of 30 simple sequence repeats (SSRs). A total of 62 alleles were found from 11 informative SSR loci. Thirty-nine alleles were detected infrequently (frequency 0.15) among the cultivars and only two alleles were observed frequently (frequency 0.95). Analyses of the dynamics of SSR alleles over time in these oat cultivars revealed random patterns of allelic change at three loci, shifting patterns of change at one locus, increasing patterns of change at two loci, and decreasing patterns of change at five loci. Significant decrease of alleles was detected in cultivars released after 1970 and also in some specific breeding programs. Three different band-sharing analyses of the genetic diversity of the grouped cultivars, however, failed to detect significant diversity changes among cultivars released from different breeding periods or programs. These findings indicate that allelic diversity at particular loci, rather than average genetic diversity, is sensitive to oat breeding practices. They also indicate the need for attention to be paid to oat germplasm conservation.

Abbreviations: bp, base pair • AFLP, amplified fragment length polymorphism • PCR, polymerase chain reaction • PGRC, Plant Gene Resources of Canada • SSR, simple sequence repeat

	INTRODUCTION

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CONCERN HAS OFTEN BEEN EXPRESSED that modern plant breeding techniques reduce crop genetic diversity (Vellve, 1993; Clunier-Ross, 1995; Tripp, 1996). Such reduction may have consequences both for the vulnerability of crops to their pests and diseases and for their ability to respond to changes in climate or agricultural practice (Clunier-Ross, 1995; FAO, 1998). To address these concerns, data are needed that allow objective quantification of the changes that have occurred in genetic diversity of the major agricultural crop species (Duvick, 1984; Swanson, 1996; Tripp, 1996; Donini et al., 2000). With the advent of molecular genetic techniques, assessments of crop genetic diversity have increased in number (Karp et al., 1997). Many assessments, in fact, suggest that the reduction of the genetic diversity accompanying plant improvement has been negligible (Donini et al., 2000; Russell et al., 2000; Lu and Bernardo, 2001; Christiansen et al., 2002; Fu et al., 2002, 2003). For example, Donini et al. (2000) showed that plant breeding resulted in a qualitative, rather than quantitative, change in genetic diversity of 55 dominant UK winter wheat (Triticum aestivum L.) varieties released from 1934 to 1994. As well, despite a significant (35%) reduction of microsatellite alleles per locus in eight current maize (Zea mays L.) inbreds, Lu and Bernado (2001) still failed to detect a significant difference in genetic diversity between current and historical maize inbreds. While these results appear to refute the concern that modern breeding reduces diversity, they are based on relatively small amounts of data. It would be useful, therefore, to extend studies of allelic dynamics accompanying intensive breeding over longer periods of time and to many varieties.

Oat breeding in Canada began in the late 1800s to meet the demand of the growing Canadian livestock industry (Welsh et al., 1953; McKenzie and Harder, 1995). Selection and hybridization from the 1900s to the 1930s at Agriculture and Agri-Food Canada (AAFC) experimental farms and several Canadian agricultural colleges generated several highly productive cultivars such as Liberty and Legacy. Backcrossing of rust resistant genes into ‘Rodney’ and ‘Pendek’ in the 1960s produced several highly successful cultivars such as Harmon, Dumont, and Robert. Introduction of wild oat (A. sterilis L.) germplasm in the 1970s further enhanced the development of many cultivars with genes for resistance to both stem rust (cause by Puccinia graminis f. sp. avenae Eriks. & E. Henn) and crown rust (caused by P. coronata Corda var. avenae Eriks.). So far, the breeding programs have developed and released as many as 130 registered cultivars, most of which have made significant impacts on the economy of western Canada (McKinnon, 1998). In spite of impressive achievements in yield and disease resistance, concern about narrowing of the oat gene pool is warranted, as cultivar development in Canada since 1930 has been largely based on a genetic foundation of fewer than 10 parental lines. This situation is also likely true for the oat breeding programs in the USA, as most USA oat germplasm utilized for cultivar development before 1970 traced back to only seven landrace varieties introduced from Europe (Coffman, 1977).

We conducted a molecular assessment of the genetic diversity in 96 oat cultivars released in Canada from 1886 to 2001. These cultivars represent the majority of the oat cultivars registered in Canada since 1886 and typify the core germplasm used in the major Canadian oat breeding programs. Analyses of these 96 oat cultivars using 442 amplified fragment length polymorphism (AFLP) markers (Vos et al., 1995) confirmed the narrowness of the Canadian oat gene pool and detected a nonsignificant trend of reduction in variable AFLP loci since 1886 (Fu et al., unpublished results). These findings were encouraging, but how applicable they are with respect to the whole oat genome remains unclear. The objective of this study was to assess allelic diversity changes in 96 Canadian oat cultivars released from 1886 to 2001 by means of 30 SSRs.

	MATERIALS AND METHODS

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Plant Materials
Ninety-six Canadian oat cultivars (Table 1) were selected from a panel of 129 cultivars maintained at Plant Gene Resources of Canada (PGRC). The selection was based on pedigree analyses, agronomic and economic importance, and representation of different eras of oat breeding in Canada. Consultation was made with several oat breeders and researchers in the selection of the cultivars. The reliability of the information collected for each cultivar was verified by comparison with data from the literature (Welsh et al., 1953; Baum, 1969; McKenzie and Harder, 1995) and from the related online information resource on oat pedigree (N. Tinker, 2002, personal communication).

SSR Analysis
On the basis of reported polymorphism, 30 SSR primer pairs were selected and assayed in this study: AM1, AM2, AM3, AM4, AM5, AM6, AM15, AM19, AM21, AM23, AM25, AM26, AM27, AM28, AM30, AM31, AM38, AM40, AM41, AM42, AM83, AM87, AM91, AM102, AM112, AM115, HVM3, HVM4, HVM34, and HVM44. The AM-SSRs were isolated from A. sativa (Li et al., 2000; Pal et al., 2002) and the HV-SSRs from barley (Hordeum vulgare L.) (Liu et al., 1996). The polymerase chain reaction (PCR) contained 50 ng template DNA, 1x buffer (Promega, Madison, WI, USA), 1.5 mM MgCl₂, 200 µM each of dNTP, 10 pmol of each primer, and 1 unit of Taq polymerase (Invitrogen, Carlsbad, CA, USA). Different "Touchdown" PCR programs were used for different primers depending on their melting temperatures (Liu et al., 1996; Li et al., 2000; Pal et al., 2002). PCR products were separated on a sequencing gel containing 6% (w/v) polyacrylamide, 7 M urea and 1x TBE at 85-W constant power for 3 h (BioRad sequencing system, Hercules, CA, USA). The gel was fixed, stained, and dried with a DNA silver staining kit (Promega, Madison, WI, USA).

Data Analysis
To generate a dataset of SSR allele counts for each cultivar, DNA fragments amplified by SSR primer pairs were identified on the basis of their size in base pairs measured with a 10-bp DNA ladder (Invitrogen, Carlsbad, CA, USA), and compared with the size reported in the literature (Liu et al., 1996; Li et al., 2000; Pal et al., 2002). Frequencies of the scored alleles were calculated with respect to primer, breeding period, and breeding program. To identify the patterns of allelic changes for each locus, the numbers of alleles detected in the cultivars were assessed in chronological order from 1886 to 2001. Such assessment was also performed for groups of cultivars on the basis of their release periods and originating programs.

To assess the significance of the observed difference in allelic counts between the cultivars released in different breeding periods or programs, a permutation method was applied. Specifically, an allele was chosen, and on the basis of its observed frequency of occurrence among all 96 cultivars, it was randomly allocated to the 96 cultivars without replacement regardless of cultivar origin or release year. This step was repeated for the other alleles identified in this study, followed by counting the number of alleles for the "artificial" cultivars from a known period or program. The difference in allelic counts between two groups of "artificial" cultivars was calculated and compared with the actual observed difference. This permutation of alleles was repeated 10 000 times. The numbers of alleles in these "artificial" cultivars was averaged over 10000 runs to generate the expected and standard deviation of number of alleles for the cultivars in each group of interest. The proportion of the 10 000 runs, in which the difference in allelic counts was larger than the observed allelic difference, gave the probability of detecting the allelic difference between two cultivar groups. The simulation was done by a SAS program written in SAS IML (SAS Institute, 1996) for the different breeding periods and programs, and it is available from the senior author.

To assess the change in diversity in the cultivars released from different breeding periods or programs, average diversity was measured by three commonly employed similarity (or band-sharing) methods. The simple matching method, first described by Sokal and Michener (1958) and later applied by Apostol et al. (1993), defines the similarity as S_ij = (a + d)/(a + b + c + d), where S_ij is the similarity between two individuals i and j, a is the number of bands present in both i and j, b is the number of bands present in i and absent in j, c is the number of bands present in j and absent in i, and d is the number of bands absent from both i and j. The second method, proposed by Dice (1945) and later applied by Nei and Li (1979), calculates the similarity as S_ij = (2a)/(2a + b + c). The third method, described by Jaccard (1908), estimates the similarity as S_ij = a/(a + b + c). Note that a, b, and c used in the last two methods are the same as in the first method. In this study, dissimilarity (i.e., 1- similarity) was calculated by a SAS program written in SAS IML.

	RESULTS

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Ten out of 30 SSR primer pairs (AM2, AM4, AM6, AM23, AM27, AM30, AM41, AM83, HVM34, and HVM44) displayed unscorable banding patterns, whereas nine (AM15, AM19, AM21, AM26, AM28, AM40, AM91, HVM3, and HVM4) revealed monomorphic bands only. The remaining 11 primer pairs (Table 2) detected a total of 62 alleles, with an average of 5.6 alleles per primer pair. Primer pair AM5 detected 12 alleles (the largest number) and AM25 and AM115 only two alleles each. The frequency distribution of alleles in the 96 cultivars is shown in Fig. 1A. There were two alleles having occurrence frequencies of 0.95 in the cultivars and 39 alleles with frequencies of 0.15. Among the 39 infrequent alleles, there were four and 16 alleles with frequencies of 0.02 and 0.05, respectively. An examination of the oat linkage maps with SSR markers (Pal et al., 2002; Wight et al., 2003) revealed only five of the 11 SSR loci were mapped on five linkage groups (AM3 on the linkage group 36; AM42 on 11; AM87 on 24; AM102 on 22; and AM112 on 2). This implies that the 11 SSR loci assayed here may be widely distributed over oat chromosomes.

View larger version (32K): [in this window] [in a new window]   Fig. 1. The distributions of 62 SSR alleles (A) and 18 alleles undetected in the oat cultivars released since 1990 (B) with respect to their occurrence frequencies in all 96 oat cultivars. Fig. 1A also separately illustrates four and 16 SSR alleles of occurrence frequency less than or equal to 0.02 and 0.05, respectively. Note that different scales are presented in the axes of Fig. 1A-B.

View larger version (93K): [in this window] [in a new window]   Fig. 2. Four silver staining gels that illustrate the four allelic change patterns over the 115 years of Canadian oat breading. A, Random (from AM3); B, Shifting (from AM42); C, Increasing (from AM102); and D, Decreasing (from AM31). In each gel, samples from 96 Canadian oat cultivars are arrayed from left to right in a chronological order, from 1886 to 2001. The order parallels that in Table 1. Only the last two digits of the release year are given for each cultivar. M is the DNA ladder.

The average number of new alleles per cultivar was 1.29 for the 1930s, 1.27 for the 1940s, 0.92 for the 1950s, 0.60 for the 1960s, 0.53 for the 1970s, 0.62 for the 1980s, and 0.64 for the 1990s (Table 2). Clearly, the cultivars released before 1960 had one fold more new alleles than those released after 1960. The cultivars with the most number of new alleles are Erban, Brighton hulless, and Shield, each having five new alleles. They were released in 1937 from the University of Guelph, in 1941 from ECORC at Ottawa and in 1956 from ECORC, respectively. Eighteen alleles were undetected in cultivars released after 1990 and their allelic frequencies ranged from 0.0104 to 0.1458 with an average of 0.0544 (Table 2, Fig. 1B). These undetected alleles came from six different SSR loci (i.e., 4 in AM1, 1 AM3, 3 AM5, 5 AM31, 4 AM38, and 1 AM112), indicating the allelic reduction is not restricted to a single chromosomal segment.

Permutation assessments of the detected numbers of alleles in cultivars released from different breeding programs (Table 3) showed that the cultivars generated from the breeding program at Sainte-Foy, QC, had significantly (P = 0.024) fewer alleles than a group of cultivars introduced to Canada from other countries. The permutations also revealed marginally fewer alleles in cultivars released from the breeding programs at Guelph and Ottawa than in the introduced cultivars. These differences are consistent with the relatively small numbers of new alleles detected for the cultivars from each breeding program. For example, the numbers of new alleles versus the total number of alleles detected in cultivars from different breeding programs were 7:33 for Sainte-Foy, 5:20 for Guelph, and 14:45 for Ottawa.

	DISCUSSION

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The SSR analyses conducted in this study reveal the first, clear-cut molecular evidence for the negative impacts of oat breeding on the genetic diversity. Four different patterns of allelic change were identified in the Canadian oat germplasm: random at three loci, shifting at one locus, increasing at two loci, and decreasing at five loci. Most importantly, a significant decrease in SSR allele number was detected in materials from more recent breeding periods and from specific breeding programs. The reduction in SSR allele number is of special concern in terms of genetic resource conservation and plant breeding. If this pattern of allelic reduction is reflective of the genome as a whole, future efforts to improve this species through selective breeding may be hindered by lack of diversity.

The increase in the average genetic diversity of cultivars released from 1930 to 1950 may well reflect the consequences of extensive hybridization performed from 1920 to 1940 (Table 4). This hybridization not only generated impressive increases in oat yields, but also simultaneously broadened the genetic background of the released cultivars by employing genetically diverse lines. The decrease in the average genetic diversity of cultivars released since 1950 (Table 4) may in part be explained by breeding efforts to utilize almost all of the known crown and stem resistance genes, which was accomplished by backcrossing to resistant parental lines (after 1950) and introgression of resistance from three to four wild oat lines to several specific rust races (in the 1970s). This effort may have reduced diversity in some chromosomal segments. This reasoning is supported by the observation of allelic reductions at five SSR loci in cultivars released since 1950 (e.g., Fig. 2D) as well as significant allelic reduction after 1970 (Table 2). Thus, identifying these specific chromosomal regions marked by these SSR loci and determining if these regions are associated with rust-resistant genes would help verify the diversity changes observed in the assessed gene pool. However, only one such locus (AM112) was mapped (Pal et al., 2002) and whether the mapped region harbors any rust-resistant genes remains unknown.

The findings presented here, along with those in barley (Russell et al., 2000) and maize (Lu and Bernardo, 2001), appear to indicate that allelic diversity at particular loci, rather than average genetic diversity, is sensitive to plant breeding practices. This seems to be true as selective improvement largely focuses on certain chromosomal regions with the aim of introducing desirable novel alleles. This implies that diversity assessment of the gene pool would be most informative when allelic diversity itself is the target of study. Thus, evaluation of allelic diversity requires proper selection of effective molecular tools such as multiallelic SSR markers and DNA sequencing of individual genes of interest, rather than random amplified polymorphic DNA (RAPD) (Williams et al., 1990) and AFLP markers with limited polymorphism per locus. This reasoning is supported by the comparisons of AFLP and SSR findings on these 96 oat cultivars. For example, analyses of 442 polymorphic AFLP bands did not reveal clear patterns of diversity change (Fu et al., unpublished results) concordant with the breeding efforts over time as did the SSR analyses presented here. Also, AFLP analyses detected only a nonsignificant trend of fixing 1% of variable AFLP loci over the 115 yr of oat breeding, while significant decrease of some SSR alleles was detected in cultivars released after 1970. This reasoning also suggests that analyses of specific chromosomal regions associated with genes for breeding targets would yield more information on the impacts of plant breeding. The linkage and QTL maps of many crop species established in recent years would enhance such analyses.

With the genetic narrowing of the oat germplasm, there is a need for continuous diversification of oat breeding materials for sustainable breeding programs in the future. To facilitate the diversification of germplasm, conservation of genetically diverse germplasm is a prerequisite and is critical for long-term breeding efforts. Eventually, the introgression of new genes or incorporation of new gene complexes will be needed in some breeding programs to overcome a possible "genetic ceiling" in oat improvement, to avoid genetic vulnerability to biotic stresses, and to widen crop adaptation to new environments. Thus, attention needs to be paid to integrated efforts in the conservation of oat germplasm and exploration for new sources of desirable alleles. While it is not clear how general these findings are with respect to other crop species, further studies of other important crop species with effective molecular tools would not only allow us to understand the impacts of plant breeding on plant genomes, but also facilitate the efforts of conserving and diversifying breeding materials for sustainable crop improvements.

	ACKNOWLEDGMENTS

 
We thank Dallas Kessler and David Williams for their assistance in acquiring oat germplasm; Cheng-Dao Li and Peter Eckstein for their assistance with the SSR analysis; Solomon Kibite, Jennifer Mitchell-Fetch, James Chong, Daryl Somers and Steve Molnar for their help with the choice of oat cultivars; Nick Tinker and Jitka Deyl for their support on the use of their oat pedigree program (POOL); and Bruce Coulman and Felicitas Katepa-Mupondwa for their constructive comments on the early version of the manuscript.

Received for publication December 19, 2002.

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This Article Abstract Figures Only Full Text (PDF) Free Alert me when this article is cited Alert me if a correction is posted Services Related articles in Crop Science Similar articles in this journal Similar articles in ISI Web of Science Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (17) Citing Articles via Google Scholar Google Scholar Articles by Fu, Y.-B. Articles by Richards, K. W. Search for Related Content PubMed Articles by Fu, Y.-B. Articles by Richards, K. W. Agricola Articles by Fu, Y.-B. Articles by Richards, K. W. Related Collections Oat Plant Genetic Resources Crop Genetics