Genetic Vulnerability

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7.1. CENTERS OF ORIGIN

7.2. CONCEPT OF GENE POOL

7.3. THE GENETIC VULNERABILITY OF FOOD CROPS

by Eric Elsner


The genetic vulnerability of food crops can be defined as the susceptibility of food crops to catastrophic losses from pests or pathogens due to the narrowing of their genetic base. One of the most frequently accused culprits responsible for the genetic vulnerability of the world’s food crops is the science of modern plant breeding. Other possible causes of genetic vulnerability include the loss of traditional agricultural lands caused by development, political instability, etc… This review will focus primarily on the genetic vulnerability of food crops as viewed from a plant breeding standpoint. According to Poehlman and Sleper (1995), “Plant Breeding is the art and science of improving the heredity of plants for the benefit of mankind.” As we examine the genetic vulnerability of the world’s food crops, we will discuss what is currently being done to address the issue and assess the status of the world’s plant genetic resources.

Before modern plant breeding is vilified as an evil that is quickly destroying plant genetic resources, it is important that two very important points are made. First, one must realize that the world’s population cannot be fed effectively using landrace or wild type plants alone. The science of modern plant breeding, including genetically modified organisms (GMOs) has allowed farmers to feed the world’s population except in cases of extreme climatic occurrences or political strife. Second, it is unclear how much responsibility modern plant breeding should shoulder for a reduction in the genetic variability of food crops. A review of the available literature on the subject will not lead to a clear answer. For example, Fu et al., (2005) reported that obvious genetic shift and allelic reduction was observed in cultivars of Canadian hard red spring wheat released over a span of 59 years from 1845 to 2004 and that these shifts coincided with six distinct breeding efforts that were undertaken. Christiansen et al., (2002) reported an increase in the genetic diversity of 75 Nordic spring wheat cultivars during the period ranging from 1900 – 1940. However, they further identify a loss of diversity in the same 75 cultivars occurring from 1940-1960 and another increase in diversity from 1960-2000. Lastly, Donini et al., (2000) investigated the genetic diversity of the dominant winter wheat varieties utilized in the UK from 1934-1994 and found little evidence pointing towards a significant narrowing of genetic diversity in the cultivars studied. They indicated that breeding resulted in a qualitative rather than quantitative shift in diversity (Donini et al., 2000). From these examples it is clear that when viewed from the perspective of the plant breeder, the issue of declining crop genetic diversity is by no means clear cut but must be an important consideration in order to protect the world’s food supply.


7.3.1. A HINT OF A PROBLEM

For at least the last 10,000 years humans have been selecting plants that performed better for them across a wide range of criteria including fruit size, number of fruit per plant, adaptation to specific environments, resistance to certain pests, and many other characteristics. It is reasonable to assume that thousands of plants were utilized and therefore a tremendous range of genetic diversity existed. Even as late as the middle of the 20th century, approximately 30,000 different cultivars of rice were grown in India (Kotschi, 2010). Mankind has shifted from relying on many species rich in genetic diversity to the place where we find ourselves today; with approximately 150 species in cultivation and 60% of the world’s food production coming from three species: rice, maize, and wheat (Kotschi, 2010). Simply put, fewer and fewer species are being used to feed an ever expanding population and the cultivars are becoming more genetically uniform (Harlan, 1975).

One may speculate that the current interest in the genetic diversity and vulnerability of crop plants was brought about by the United States’ experience with corn leaf blight in 1969 – 1970 (Brown, 1983). During 1970, a previously unknown race of Helminthosporium maydis destroyed approximately 15% of the U.S. corn crop. This widespread destruction was due to the disease susceptibility of the T cytoplasm used by a majority of the hybrid corn seed companies during this time (Brown, 1983). Following this outbreak, the National Academy of Sciences commissioned a survey that resulted in a statement of the genetic vulnerability of food crops. From the survey, it became evident that the genetic base of every major crop grown in the United States was very narrow. For example, in 1975, the U.S. soybean industry could trace its heritage to 6 introductions from the same region in China (Harlan, 1975).


7.3.2. HOW AND WHY BREEDING CAN CAUSE VULNERABILITY

Plant breeding by definition is the selection of superior genotypes and/or phenotypes over a period of time. This selection naturally results in a narrowing of the genetic base of the plant in question. Even if the breeder has introduced alleles from wild types or landraces to his target crop, he/she must then begin the process of “weeding out” the alleles that are undesirable. This weeding out of undesirable alleles is once again narrowing the genetic base of the line. If a breeder is working with a species that has previously been a target of breeding research, the breeding materials will likely be elite varieties that are currently in use (Brown, 1983). A breeder typically intermates the best varieties available and selects superior progeny from the mating. The continual use of the best varieties as parents naturally narrows the gene pool to only those alleles that are available from the elite parents and therefore tends to decrease the genetic variation of the population (Brown, 1983). It is not hard to understand the breeder’s reasons for following this path. Farming is a business and a farmer needs to produce maximum yield for the least amount of input in order to run a profitable business. In order to attain this goal and be able to farm for multiple years, farmers must have access to crops that have favorable qualitative traits such as disease or pest resistance and favorable quantitative traits such as high yield, resistance to environmental stresses, favorable grain moisture at harvest, favorable test weight, and a crop that matures uniformly in order to allow for mechanical harvest (Khoury et al., 2010). In response to this need, plant breeders work to produce high yielding, elite cultivars that are tailored to the farmer’s needs.

Modern plant breeding is a business as well and Gepts and Hancock (2006), report that approximately 75% of plant breeders are employed by private industry. Multi-national seed companies employ thousands of breeders who are tasked with creating new and improved varieties on an almost yearly basis in order for their parent companies to compete for market share and to please company shareholders. In the private sector, each company is in a race of sorts with its competitors to introduce improved varieties to the marketplace in order to compete for market share. Essentially the same is true in the public sector where funding for many plant breeding projects is received from outside sources and progress towards improved cultivars via genetic gain is expected in order for continued funding to occur.

Given the time constraints often placed on breeders, and when we take into account that a typical breeding cycle for many agronomic crops may take up to seven to ten years from cross to cultivar, it is not hard to understand why breeders rely on elite lines for their parental stock. For instance, if a corn breeder in the mid-western United States would like to develop a cultivar with resistance to a certain pathogen, the logical step would be for the breeder to take an existing elite line that already contains a suite of traits that are adapted to the mid-west and introgress resistance for the pathogen of interest into the elite line. This method would be much more efficient and streamlined as opposed to starting with a wild-type or landrace with a broader genetic base and breeding for the suite of traits that already exist in the elite line. In most instances, the elite lines will already contain most of the desired alleles and it is only necessary for the breeder to introgress a few specific alleles into the elite line or to further the breeding program of the elite line and make further phenotypic selections. Elite lines are the product of extensive research from both private and public funds. To expect a breeder to ignore these lines is to expect that breeder to not use all of the tools at his/her disposal.


7.3.3. TOWARDS DECREASING VULNERABILITY

If it is logical to assume that the plant breeder can increase genetic vulnerability by decreasing genetic variability then that same breeder can also reverse the trend and decrease genetic vulnerability by increasing genetic variability. One method used by breeders to increase the genetic variability of crop plants is to use crop wild relatives (CWR). Crop wild relatives have been enormously useful to plant breeders and to modern agriculture by allowing breeders to tap into a broad pool of genetic diversity (Hajjar and Hodgkin, 2007). Generally speaking, wild relatives have poor agronomic performance and are not typically used as the foundation for any breeding program (Hajjar and Hodgkin, 2007). However, plant breeders have had significant success using the CWR of modern crops to introgress favorable alleles into elite lines with the most common use being using CWR as a source of disease and pest resistance (Hajjar and Hodgkin, 2007). Hajjar and Hodgkin (2007) conducted a survey of the introduction of genes from CWR into cultivars of crops of major importance to the world food supply. The crops surveyed were: rice, wheat, maize, barley, sorghum, millet, cassava, potato, chickpea, cowpea, lentil, soybean, bean, pigeon pea, banana, tomato, sunflower, lettuce, and peanut (Hajjar and Hodgkin, 2007). Examples of wild genes being included in a released cultivar were found in every crop surveyed with the exception of soybean, pigeon pea, sorghum, and lentil with over 60 wild species identified as having been used to derive over 100 beneficial traits (Hajjar and Hodgkin, 2007). Current examples of CWR genes being used in cultivars include genes that convey resistance to leaf and stem rust, powdery mildew, and wheat streak mosaic virus in wheat, and resistance in sunflower to imidazolinone and sulfonylurea chemicals resulting in cultivated hybrids sold under the “Clearfield” trade name (Hajjar and Hodgkin, 2007). In 2010, three soybean plant introductions were found to have unique resistance to peanut root-knot nematode and it is hoped that these plant introductions can be used to improve the current resistance levels in elite lines (Yates et al., 2010).

Typically, a breeder identifies a trait that he/she would like to introgress into an elite line and then screens available germplasm for the trait of interest and selects potential parents based on the phenotype of the CWR. This type of system works well for traits controlled by one or a few genes with disease resistance being an important example. For traits controlled by multiple alleles, the situation is more complex. Breeders who are using CWRs as donors of favorable alleles contributing to quantitative traits such as yield or stress tolerance are almost certainly leaving behind some desirable alleles if they select parents based purely on phenotype. Recent advances in genomics and genome mapping are allowing breeders to shift from selection based solely on phenotype to selection based on the presence of useful genes (genotypic selection) (Tanksley and McCouch, 1997). One would assume that a high yielding parent would contain most of the genes for high yield and that a low yielding parent would not make a substantial contribution to the yield of the progeny of a cross. However, when molecular markers are used to identify loci controlling yield for a population derived from this type of cross, the results are contrary to what is expected. DeVicente and Tanksley (1993) found that while most of the “high yield contribution” comes from the high yielding parent, there are almost always some loci with alleles contributed by the inferior parent. One implication of this discovery is that assessing the breeding value of an accession based solely on its phenotype is likely to be misleading when one is dealing with quantitative traits and that potential parents should be evaluated using molecular markers and quantitative trait loci (QTL) analysis to identify useful genes/loci (Tanksley and McCouch, 1997). Tanksley and McCouch (1997) further report that using this technique and a breeding technique referred to as the advanced backcross QTL method in tomato led to the creation of lines that contain specific loci from the wild species Lycopersicon hirsutum and that these lines outperform the original elite cultivar by 48% when grown in different environments around the world. It is clear that the technology exists to confer alleles from CWR into modern elite lines either through phenotypic or genotypic selection. The obvious conclusion is that genetic diversity is important and plant breeders must have access to CWR in order to introduce new genes and characteristics into new cultivars. Therefore it is important to briefly review the state of the world’s plant genetic resources.


7.4. CONSERVATION OF PLANT GENETIC RESOURCES

More than 70 years ago, Vavilov noted the important role that crop relatives play as a source of genes (Vavilov, 1940). The two means of plant genetic resource conservation are in gene banks (ex situ) and in nature (in situ) with ex situ being vitally important for breeders who need ready access to germplasm (Cohen et al., 1991). In situ conservation of genetic resources on a global scale seems to be increasing with the number of protected areas in the world increasing from 56,000 in 1996 to 70,000 in 2007 with an increase in total area from 13 million to 17.5 million km2 (FAO, 2009). In 2009, there were more than 1,750 gene banks around the world with at least 130 of these holding more than 10,000 accessions each (FAO, 2009). Approximately 1.4 million accessions have been added worldwide since 1996 bringing the total number of accessions held to approximately 7.4 million with roughly 30% of these holdings being unique (FAO, 2009). One of the largest ex situ collections is the United States National Plant Germplasm System (US NPGS) which currently holds approximately 450,000 accessions of 10,000 species of the 85 most commonly grown crops (Smale and Day-Rubenstein, 2002). In 1997, the United States dedicated approximately $20 million to germplasm acquisition and preservation (Tanksley and McCouch, 1997). These data are encouraging for the long term as they speak to the world’s growing commitment to conserve plant genetic resources in both in situ and ex situ situations. The plant breeding community is moving in the right direction with respect to plant genetic resource conservation but more work remains. As always, regional and world politics continue to play a role in how resources are collected and shared and, as reported by the Global Crop Diversity Trust, a major constraint affecting resource conservation is the availability of the resources needed for the collection, storage, and regeneration of germplasm (Khoury et al., 2010).


7.5. CONCLUSIONS

In this review, we have discussed the genetic vulnerability of food crops through the lenses of the plant breeder. The plant breeder plays an important role in determining the level of genetic variability that is contained in our food crops. It is clear that by using traditional techniques and cutting edge genomics, plant breeders have the ability to and are currently introgressing wild-type genes and loci into today’s elite cultivars thereby potentially decreasing the vulnerability of some of our food crops. It seems equally clear from the available literature that efforts have been and are continuing to be made to protect the world’s crop plant diversity both in ex situ and in situ settings. As with every other topic of any importance, there are those who would have the reader believe that the situation is dire and possibly hopeless along with those who would say that there is nothing at all to worry about. As is usually the case, the answer lies somewhere in the middle and the case of the genetic vulnerability of food crops is no different. The genetic vulnerability of our food crops is an issue that we must continue to take seriously. We must take steps to minimize the potential impact of a narrow genetic base for our crops and this author believes that we are currently taking those steps.


REFERENCES

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Christiansen, M.J., S.B. Andersen, and R. Ortiz. 2002. Diversity changes in an intensively bred wheat germplasm during the 20th century. Molecular Breeding 9:1-11.

Cohen, J.I., J.T. Williams, D.L. Plucknett, and H. Shands. 1991. Ex situ conservation of plant genetic resources: global development and environmental concerns. Science 253:866-872.

DeVicente, M.C., and S.D. Tanksley. 1993. QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585-596.

Donini, P., J.R. Law, R.M.D. Koebner, J.C. Reeves , and R.J. Cooke. 2000. Temporal trends in the diversity of UK wheat. Theoretical and Applied Genetics 100:912-917.

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Fu, Y.B., G.W. Peterson, K.W. Richards, D. Somers, R.M. DePauw, and J.M. Clarke. 2005. Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004. Theoretical and Applied Genetics 110:1505-1516.

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Smale, M., and K. Day-Rubenstein. 2002. The demand for crop genetic resources: international use of the US National Plant Germplasm System. World Development 30:1639-1655.

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Vavilov, N.I. 1940. The New Systematics. J. Huxley, Ed. Clarendon, Oxford.

Yates, J.L., R.S. Hussey, S.L. Finnerty, and H.R. Boerma. 2010. Three soybean plant introductions possess unique resistance to peanut root-knot nematode. Crop Sci. 50:118-122.