A proposed framework for identifying, quantifying, and utilizing plant germplasm resources

Field Crops Research, 29 ( 1992 ) 261-272 Elsevier Science Publishers B.V., Amsterdam

261

A proposed framework for identifying, quantifying, and utilizing plant

germplasm resources

P.R. Beuselinck a and J.J. Steiner b ~USDA-Agricultural Research Service Plant Genetics Research Unit, Columbia, MO, US~i

bNational Forage Seed Production Research Center, Corvallis. OR, USA

ABSTRACT

Beuselinck, P.R. and Steiner, J.J., 1992. A proposed framework for identifying, qaantifying, and utilizing plant germplasm resources. Field Crops Res., 29:261-272.

Efficient utilization of the genetic potential held in germplasm col]ections requires detailed knowledge about the accessions. Information on available accessions may be so scant that the accessions are of little in',erest to potential users. Users of gc.-~..p!asm are inconsistent in their uses and evaluations of germplasm resources and data collection. The large size and heterogeneous structure of some cob lections hinder efforts to increase the use of germplasm resources in crop improvement. O~,~aming more than rudimentary information will not be accomplished unless efforts and dialogue belween curators and users are coordinated. This review proposes a practical framework to aid ~he evaluation and utilization of the germplasm collections. The authors have chosen to exemplify germplasm of clovers (Trifolium spp. ) and special purpose legumes (Lotus, Vicia, Lespedeza, a~d ¢,.~hcrs) because of their familiarity with the species that comprise thi~ group. A ~pecified, we!!~de~c:bed se'ection of accessions from a large germplasm collection can serve both preservation and utilization pu~oses. In this proposed framework, a standard range collection (SRC) is one that will be defined by high- priority descriptive characters, serve as a genetic standard, and represent the genetic di-'crsity of accessions within the larger germplasm collection. The term SRC has been used throughout this man, uscript for clarity, but is not a recommendation for new terminology.

INTRODUCTION

Conserved wild Flant species ca~'~ be important sources of major g, ties for resists.nee to pests and environmental stresses (Astley, 1987 ). However, such wild species cannot be utilized unless their beneficial genes are recognized. Identif~ ing, quantifying, and utilizing genetic diversity in plant collections is essential ~ meet future demands for improved crop cuitivars (Strauss et a!., 1988). Obviously, conservation of germplasm is a paramount concern, but

Correspondence to: P.R. Beuseiinck, USDA-Agricultural Research Service Plant Genetics Re- search Unit, Columbia, MO 65211, USA.

0378-4290/92/$05.00 © i992 Elsevier Science Publishers B.V. All fights reserved.

262 P.R. BEUSELINCK AND J.J. STEINER

the purpose of preservation cannot be the sole goal; utilization by crop devel- opers and other scientists is the purpose for germplasm collection, maintenance, and preservation. Efficient utilizatio,.~, of the genetic potential held in collections requires detailed knowledge of accessions. Description of accessions and recording of information in databases are vital aspects of preservation and utilization of plant genetic resources. Th,e objective of this review is to propose a practical framework to aid in the evaluation and documentation of our plant germplasm resources in a manner that serves the many objectives and needs of those who utilize and maintain this natural resource. We are proposing the framework to aid the evaluation ~md utilization of germplasm collections of clovers and special purpose legumes. These genera are re- searched in the United States by a relatively small cadre of scientists, although the plant species contribute to many aspects of plant and animal ag- riculture, conservation, and landscape uses. W!lth the exception of Trifolium, taxonomic structures of these genera are not highly refiacd and accessions within the germplasm collections have receiw.'d little taxonomic study since their inclusion in the collection.

Most herbage legume cu!tivars and germplasms have arisen from pre-e~:ist- ing cultivars (Rumbaugh, 1991 ) and it is improbable that the germpiasm base of these cu!tivars has been exploited to the extent of necessitating the use of wild germplasm to make filrther genetic improvement. Thus, without a defi- nite need for specific genetic diversity in the gcrmplasm collection, a situation common for the listed gene~ra, tL'ere is little interest in evaluation. Lack of interest in germplasm leads'~o poor maintenance and lack of appreciation for this important resource. Tt:te framework presented here recognizes the perceived different needs of tbe curators and users of this germplasm and seeks to increase information exchange with a strengthened interface; the need for increased information exchange is a general need for all genera.

Until recently, plant germplasm evaluation in the United States consisted of limited information obtained at the time of plant introduction plus data obtained by numerour; germp!asm users. Users of plant germplasm resources are principally sel.e_ntists representing many disciplines. Mass screenings of collections by breeders for specific traits of interest often end with elimina- tion of all germplasm!; that are not of interest, and the retention of only those ~Lccessions, or genotypes within accessions, judged to be of some value Germ- Iflasm evaluation should have a larger role than simply characterizing pres- ently held accessions for immediate use in breeding programs. Yet, the community is inconsistent in their needs and evaluations of germplasm, giving little uniformity to the manner of evaluation or data collection. Al thou~ the, return of evaluation data to the curator is requested, it is not mandato~ and datz on g e ~ p l a s m accessions often go unreported. Wh¢:n data are provided for any specific accession, its value often cannot be judged because u~ers con- duct evaluations in different environments with no common reference or

IDENTIFYING, QUANTIFYING AND UTILIZING GERMPLASM RESOURCES 263

control that can be used as a standard for comparing new data with that previously collected. Information may be so scant that it is of little interest to potential users. The need to quantify and document genetic diversity of ex situ collections to promote utilization ofthe resources is urgent, but adequate management of the resource must be ensured. Still, the germplasm may be considered to be under-utilized or adequately utilized relative to expectations of individual scientists having specific objectives (Rumbaugh, 1991 ). To re- veal the value of accessions in the collection by critical evaluation, it is necessary to standardize accessior, performance in such a manner as to identify the extent of the genotype × environment influences associated with the evaluation (Westcott, 1985).

The International Board for Plant Genetic Resources (IBPGR) classifies assemblages of genetic resources as base and active collections (Bass, 1984). Base collections are intended for long-term preservation, while active collections are used for multiplication, evaluation, documentation~ distribution, and use by plant breeders. The process of acquiring information about the genetic diversity in collections usually requires distribution of germp!asm to users, which in turn, necessitates the need to increase s~edstocks. There is a risk of introducing genetic change in a germplasm ~esource whenever seedstocks are regenerated, jeopardizing preservation and conservation efforts of germ- olasm curator.,; (Chang et ai., i 979). Factors such as pollination control, dis- ease and insect susceatibJlity, and physical environment-related changes are of great concern. Yet, to meet needs of germplasm users, it is necessary to ensure that adequate sup~lies of a particular accession are available with a minimum amount of genetic change from the original collection.

The large size and heterogeneous composition of collections can hinder efforts to increase the use ofgermplasm resources in crop improvement. Fran- kel (1984) proposed a core collection of accessions to provide efficient access to a larger germplasm collection. Brown (1989a,b) outlined the genetic basis of the core concept and the development of the core collection. Although core collections are representative samples of the genetic diversity of a species, they can also be viewed as a management technique tbr conserving the major- ity of reserve accessions more efficiently.

Seedstock regeneration can jeopardize the genetic integrity of accessions. Bass (1984) prt~posed using a base collection to preserve the integrity of the germplasm resource while Frankel (1986) proposed the core collection of accessior, s to promote increased utilization. We propose that a sl~ecified, well- described selection of accessions from a larger collection can serve both preservation and utilization purposes. We define this collection as the SRC (standard range co!!ectie.,,.) f-.;r t~.c context of our discussion. For a species, the SRC will be defined by high-priority descriptive characters, serve as a genetic standard, and represent the genetic diversity of accessions within a collection.

We perceive the SRC as a core collection of accessions that rece.~ve priority

264 P.R. BEUSELINCK AND J.J. STEINE~,i

evaluation for all traits of interest and the first to be distributed when requests for germplasm are received. The difference between the SRC and previously desciibed core collections (Frankel, 1984; Brown, 1989a,b; Williams, 1989) is manner of selection of core candidates and description of the core. Brown (1989a) proposed that core entries should use available data on geographic origin, genetic characteristics, and value to breeders as selection criteria. Wil- liams (1989) suggested requiring quality passport data (characterization and ecogcographic data) where available to choose entries in the core. Our selection o,' il,e SRC first assumes that passport information is incomplete and often ~mverifiable thus requiring complete re-exaraination and verification of passport information an~ characterizations. Additionally, users of the SRC will be expected to evaluate accessions of this colle,:',t 'o~ for their trait of interest and report their findings before ~r'equesting additional germplasm in the reserve collection (Frankel, 1986; Brc, wn, 1989b). The reported evaluation data will increase the descriptive data ~I:,rofile compiled for ineividual accessions within the SRC. Because the SRC will contain the same access;ons sent to each user, a standardized questio~na:ire can be developed to accommodate uniform reporting from users.

DEVELGP.~,~,ENT OF THE STANDA RD RANGE COLLECTION

Three important judgements must be' made prior to choosing the components of our SRC. Because the SRC must serve as a base collection, it is im- perative that each of the entries have a known, verifiable passport. The lack of documentation and de scription of taxonomic verification or characterization of material held in germplasm banks is a technical constraint to utilization (Marshall, 1989). "l"he IBPGR has stressed the importance of passport data, but t~i~e is a serious void of data in many collections• Many clover and

• t specml purpose legume accessions in the United States collection can be traced to the colrector and origin, but have no additional passport history that can provide the base information for the descriptive data profile of the SRC. Ab- sence of a passport is a major hindrance to cura :.ors in assessing the range of va.riation in their collections, and in identifying gaps that should be filled (Williams, 1989). Many accessions ofunknow~a origin were obtained tiirough intbrmal linkages among diplomats, scientists, missionaries, and wellointend- ing travelers. Altl~ough these accessions may contain valuable genes, information on their native environment or post-collection regeneration is unver- ifiable and should not be considered for inclusion in the SRC. Only accessions with verifiable passport,~ should be eligible for inclusion i~a the SRC. There- fore, the first judgement in identifying accessions for the SRC is to review, all passport data and group available accessions into acceptable and unaccepta- ble classes for consideration of the SRC.

The second judgement on a group of accessions with acceptable passport

IDENTIFYING. QUANTIFYING AND UTILIZING GERMPLASM RESOURCES 265

information is to consider geographic origin as the most delineating component of data in the passport. If there are many accessions that have acceptable passports, an initial rudimentary paring of accessions to a manageable number can be madc by choosing accessions with the most diverse origi~ls. Once the size of the preliminary SRC is decided, all accessions arc su~ q,~<.qed to exteasive morphological, cytological, and reproductive examinations to ver- ify l heir species identity. Cost of these evaluations can be high, but although ¢xp,znsive, time-consuming, and requiring specialized expertise, this verification phase is essential for proper classification. Roath (1989) presents an extensive listing of Crop Advisory Committee (CAC)-defined high-priority agronomic and morphological descriptors for a wide range of crops. But only tile CAC for cotton (Gossypium) lists cytology and taxonomic evaluation as priorities (Nos. 2 and 8, respectively). It appears that other CACs have assumed taxonomic correctncs,~ of their accessions, which may not be justified. Clearly, only evaluations essc.ntial to developing initial databases should be performed due to resource limitations. Polymorphic traits have been used to characterize species and include biochemical characters such as isozymes (Kahler and Allard, 1981; Second, 1982; Goodman and Stuber, 1983; Doe- bley et al., 1985 ), DNA markers (Beckman and Soller, 1986 ) or minisatellite allele patterns ( H illel et al., 1990 ), morphological characters (Jain et al., 1975; McGraw et al., 1989), entomological characters (Nielson aad Schonhorst, 1967; Dickson and Eck :nrode, 1975) and plant secondary product composition (Davis, 1982, 1986 ). It is also i:~lportant that relationships between different traits be studied, particularly to determine whether there are molecular or other biochemical markers which are congruent or exclusive to useful agronomic traits. Such diverse complexity needs to be described and utilized when an SRC is developed. Associations among different kinds of traits within germplasm collections might prc~e valuable, but there is a general absence in the literature (Brown, 1989a)~ Such studies are complex and require stand- ardization in the choice of accessions which are evaluated within the same species. Organized groups of specialists, likc those constituting the CACs, could conceive an agenda for generating descriptive data needed to develop the SRC for each species. Final selection of components of the SRC would be based on the iterative analysis of verified data. Like the core collection conceived by Frankel (1984), development of SRC will differ markedly between species.

The third judgement which must be made is determination of the number of accessions and number of individuals per accession. If it could be assumed that the genetic variation of all trab~.s were randomly distributed within the collection, then ra~dom sampling could be used. A sensible size for our SRC, like a core collection could then be 5 to 10% of the total collection (Brown, 1989a). However, it is most likely that distribution of traits within most collections is skewed to some degree and that the amount of variation within and between accessions varies (Brown, 1989b). Limited a priori knowledge

266 P.R. BEUSELINCK AND J.J. SFEINER

of the distribution of variation within most populations is likely, so general principles for sampling based on the neutral allele model (Kimura and Crow, 1964) can be used to develop sampling schemes (Ewens, 1972; Nei et al., 1975 ). Brown (1989a) and Roath (1989) reviewed the statistical principles related to sampling the distribution of alleles in populations a.nd their appli- cations to sampling s~rategies. To maintain important non-additive traits in individual accensions, i000 or more individuals may need to be retained (Rowe, 1986). When developing sampling strategies, factors other than variability, such as the cost of evaluations and seed availability, must be considered (Roath, 1989).

MECHANICS OF STANDARD RANGE COLLECTION DEVELOPMENT

Once the initial select.ion of candidate accessions has been completed and specific characteristics to be evaluated determined, it is necessary to quantify and describe the character profile of the SRC for the purpose of establishing discriminant classes. These discriminant classes will be used as standards tbr making all future accession comparisons. This is an iterative process and may require further additions and deletions of entries into and out of the SRC to produce a true range of genetic characteristics representative of the larger collection. Simple random selection of entries is not suitable for producing a SRC because such sampling may result in a dispropo,-tionate representation of certain traits which are redundant in the larger collection.

To begin the process of developing a descriptive data profile for the SRC, fundamen~.a! descriptive statistics which measure central tendency (e.g., mean ) and dispersion (e.g., standard deviation and range) of the candidates can be made for specific characters. For example, proposed characters tbr a TriJblium, Viola, or Lotus SRC should be developed by the CAC for clover and special purpose legumes, evaluated, and used to generate the descriptive data profile. This information allows examination of characters to determine the nature of their distribution throughout the collection. It is likely that mul- tiple trait diversity is unevenly distributed in collections (Brown, 1989a,b), but descriptive statistics provide an initial reference for further comparisons wi~h othe," alternative entries or newly acquired entries. However, it i= necessary to consider a multiplicity of characters to develop descriptive data profiles for the SRC in a unified manner which utilizes the diversity of the germplasm rather than focusing on one or a few specific characters.

Descriptive data profiles are used to describe specific characters of the germplasm collection. Multivariate statistical techniques, readily available in micro-, mini- and mainframe computer software products, are required to readily handle large volumes of data. Howe-,eL multivariate techniques must only be employed when a priori protocols are established, otherwise results


will often be changed greatly with minor modifications of the routine parameters resulting in non-standard comparisons.

Principal component factor analysis (PCFA) can be used to determine relationships between a myriad of different measured geographic, morphological, and biochemical characters of the SRC entry candidates recommended by groups of crop specialists like the CACs. Data analysis by PCFA produces rotated loading factar matrices which present correlations of the individual characters of different entries with created classification factors which describe their associated relationships (Frane and Hill, 1974). The resulting loading factor matrix of PCFA can be used to determine which traits are independent and which are associated. Those factors which are independent of one another can be used to generate classifications of the entries which comprise the SRC.

Specific characters of descriptive data profiles are used for the initial classification of the SRC candidates using a cluster analysis method. Cluster analysis allows verification of distinctness and diversity of entries which have been verified and selected for the S_RC based on characterized traits used in the analysis. Common analysis parameters include using the Euclidean distance (the square root of the sum of squares of the distances between the multidi- mensional space values of the variables for any two entries) to describe the relationship of the entries and a criterion for joining the resulting hierarchical clusters of the entries examined (e.g., Ward's minimum variance method or kth neares~ neighbor) (Romesburg, 1984). The resulting dendrograph can then be examined to determine relatedness of the different candidates which are proposed for inclusion in the SRC. It is important that different characters which are used to generate the classification be independent (no: collin- eat). Inclusion of collinear characters will over-weight the ir portt,~:ce of a particular trait in determining the trait's effect (Romesburg, 1984). Exami- nation of the distribution of entries within specific clusters gives an approxi- mation of diversity 'based on the initial sampling by geographic origin and the choice of prioritize.d descriptive characters. If the dispersion of SRC candidates is deemed adequate, then the final decision of which accessions to include in the SRC can be made. If not, then further iterative accession sampling and testing is required until an acceptable dispersion is obtained.

Once the decision of which accessions to include in the SRC has been made based on the establishment of cluster classes, other entries from the reserve collection or new accessions acquired from collection trips can be assigned to *.h ~,.qc ~' . . . . . : - , ~ J" . . . . . . . . . . ., _. ,_,~-,:r.,:nm~,at an~.iy:.,i~ based on the standard characteristic

A~t..r. . . . . should be given to the traits they most resemble (Manly, 1986). * ~ +:"" nature of the distributions of profile data of the entries used to create the discriminant classes because non-normal distributions may greatly affect the classification (Lachenbruch and Goldstein, 19, ~ ). Many computer software programs make such allowances simple to implement.


USING THE STANDARD RANGE COLLECTION FOR GERMPLASM EVALUATION

One objective of developing a SRC is to provide a representation ofgenetic characteristics which are present in the base collection maintained by germplasm curators. Frequency of requests for any germplasm accession by any user cannot be predicted. Curators of collections are faced with the dilemma of preservation of the collection while needing evaluation of the germplasm. The dilemma arises from the dissemination of germplasm with hcpes of ob- taining valuable data from evaluations by users, but never being able to pre- dict extent of demand for any accession or return of evaluation data. Regen- eration of seedstocks can introduce changes into the germplasm, but with the curator's need for data, seed supplies must be regenerated for dissemination. The SRC can relieve the curator's dilemma yet benefit the user. Implemen- ,~ation of the SRC has the potential of addressing and solving problems identified by Frankel (1989) concerning preliminary evaluation of germplasm prior to utilization. Namely, that gene banks are not being used very exten- sively by plant breeders, the main reason being the scarcity ef useful information (Peeters and Williams, 1984).

A second objective of the SRC is to provide a standard re, fe~ ence for the evaluation ofgermplasm by users. Like the core collection, the SRC becomes the key germplasm resource distributed to users requesting germplasm. The SRC would be characterized by a descriptive data profile that provides: (i) relationships among SRC entries as determined by mtdtivariate statistical analyses and (ii) range of variation for each trait evaluated in the SRC. Users wishing to evaluate germplasm for new traits should also evaluate the SRC for a minimum of one trait already described in the data profile. Roath (1989) addressed the problem of universal comparability of evaluation data for accessions. Concurrent evaluation will provide the user with a reference for comparing a user's evaluation results with t~,ose contained in the descriptive data profile. Users must recognize their responsibility to report evaluation results to the curator to increase the body of knowledge compiled in the descriptive profile. A standardized format can be provided by the curator for the reporting of evaluation results. Users not finding useful germplasm within the SRC would report their evaluation of the SRC before second requests would be cot, o;a'~''~ The ,,,,~.! t,,~ . . . . . . . . . ~,,,,, of requiring reporting of evalua~oils for .... SRC, like a core collection, is to ensure continued definition of the data profile for each entry, not to restrict user access to reserve germplasm (Frankel and Brown, 1984; Frankel, 1987; Strauss et al., 1988 ).

We perceive two components for the descriptive data profile: (i) 'fixed' and (ii) 'dynamic'. The fixed component is the descriptive data profile used to develop the SRC using multivariate analysis ofimpertant traits defined for a species. This fixed component retains its integrity independent of new data from SRC entry evaluations. Although this component of the SRC is fixed, it


is not necessarily infallible because it does not include all potential traits evaluated under all environmental conditions. However, the fixed component is a definitive description of the relationships among the SRC entries. The dynamic component of the descriptive data profile is equally valuable as it presents known data for all evaluated traits of any entry in the SRC. This component can contain character data not used to develop the SRC and can vary for each entry. New data for the SRC supplied by users can be tested for con- gruency with existing ,data before incorporation into the dynamic component of the descriptive data profile. Both components contribute to the descriptive data profile and provide curators and users with data from their mutual interface.

The continued evolution of the descriptive data profile will make the SRC more valuable to users. Well-documented accessions are essential to mapping distribution of particular traits within a species (Astley, 1987). Users could request specific SRC entries and not be penalized by having to evaluate the entire SRC, but most requests of a general nature can be serviced by the SRC, without acce,;s::ng the reserve collection. User requests for the entire SRC, or any entry (ies) could be requested through on-line computer access systems. Decisions on individual choice of entries can be random or intuitive based on descriptive data profile information. Evaluation data of a specific entry of the SRC can be used to increase the body of data for that entry but it will not alter the fixed component ofthe SRC descriptive data profile. Ifusers cannot find genetic diversity for a trait in the SRC, it is possible that the SRC repre- sents an incomplete sample of the genetic variat::on for the species or the trait is very rare. If the SRC does not satisfactorily meet the needs of the user, the reserve collection can be made available for evaluation. If the desired trait still cannot be found, it is possible that the trait is not expressed in the species and germplasm transformation may be required.

U T I L I Z A T I O N

Clearly the goal of germplasrn conservation and preservation is to provide the user community, traditional~.y plant breeders, with genetic resources for crop improvement. More recently, the study of genetic variation and biochemical and physiological mechanisms, for the purpose of genetic manipulation through novel molecular techniques, enlarges the cadre of potential users. The SRC provides a described data profile to aid users in choosing accessions for specific morphological or biochemical traits. The SRC is more efficient than a random sample of accessions to evaluate a specific trait because of the manner in which the SRC is initially developed and maintained. The key to utilization of traits expressed by germplasm in the SRC lies in the type of enhancement needed. Users reluctant to use germplasm in the SRC because of the perceived 'excess baggage' that accompanies desired traits will

270 P.R. BEUSELINCK AND J.J, STEINER

find the SRC to be an attractive source o f genes for improvement o f existing cultivars. Once a g e n e has been identified in the SRC, it can be moved to an adapted cultivar. Backcrossing appears to be the me thod of choice among plant breeders and geneticists for i ntrogressing genes from exotic sources into domest ic germplasms. Recent examples include wheat (Tri t icum aestivum) (Eaton et al., 1986), corn (Zea mays) (Crossa and Gardner , 1987; Eagles and Hardacre, i990) , pearl millet (Pennisetum americanum) (Bramel-Cox et al., 1986), rice (Oryza officinalis) (Jena and Khush, 1990), and soybean ( Glycine max) (Carpenter and Fehr, 1986). lntrogression through interspe- cific hybridizat ion has also been practiced tbr potato (Solanum tuberosum) (Brown and Adiwilaga, 1990; Brodie et al., 1991 ), phalaris (Phalaris aqua- dca) ( d r a m et al., 1990), sweetpotato (lpomea batatas) (Jones, 1990), cotton (Gossypium hirsutum) (Umbeck and Stewart, 1985; Aitman et ai., 1990), and wheat (Heun and Friebe, 1990). it is sound breeding judgement to use agronomically superior adapted cultivars for the genetic expression o f desired traits. Any appropria te breeding procedure may be used in enhancement and new techniques for the transfer o f individual genes may enable other types o f enhancement . The SRC facilitates the identif ication o f sources o f genetic diversity by rjromoting evaluation of exotic yet defined accessions from germplasm collections.

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A proposed framework for identifying, quantifying, and utilizing plant germplasm resources