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Detection of Genetic Variation in Wild Populations of Three Allium

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Detection of Genetic Variation in Wild Populations of Three Allium JOBNAME: horts 43#3 2008 PAGE: 1 OUTPUT: April 23 14:50:41 2008 tsp/horts/163067/02508 HORTSCIENCE 43(3):637–643. 2008. information useful in strategies for identify- ing sources of intermountain Allium germ- plasm rich in genetic diversity. Detection of Genetic Variation The genus Allium has a worldwide distri- bution consisting of 700 species, including in Wild Populations of Three Allium 80 species in North America (Brewster and Rabinowitch, 1990; Hanelt, 2001; Kamenetsky Species Using Amplified Fragment and Rabinowitch, 2006; McNeal and Ownbey, 1973; McNeal and Jacobsen, 2001). The genus includes economically important Length Polymorphisms crop species such as onions, garlic, chives, Nathan C. Phillips1 leeks, and other minor crops. Allium species Middle Tennessee State University, School of Agribusiness and Agriscience, have also been traditionally used in the or- namental industry with occasional new spe- Campus Box 5, Murfreesboro, TN 37132 cies derived from natural populations being Steven R. Larson introduced into the trade (Kamenetsky and Rabinowitch, 2006). Virtually all cultivated USDA-ARS, Forage and Range Research Laboratory, Utah State University, Alliums are derived from old world species, Logan, UT 84322-6300 and little is known about many North Amer- ican species. Considering the economic and Daniel T. Drost cultural importance of Alliums throughout Utah State University, Plants Soils and Climate, Logan, UT 84322-4820 history, and the wealth of biodiversity in the genus, it would be prudent to use genetically Additional index words. genetic diversity, germplasm, divergence, Allium acuminatum, Allium sound strategies for the collection of cur- brandegei, Allium passeyi rently unexploited Allium germplasm. Abstract. Three wild onion species native to the intermountain west in the United Rising interest in the preservation of in- States—Allium acuminatum, A. brandegei, and A. passeyi—show horticultural potential, termountain Allium germplasm has encour- but little is known about patterns of genetic diversity among localized populations and aged research to further our understanding of geographical regions. We examined amplified fragment length polymorphisms (AFLP) the genetic diversity found within and among within and among five Allium acuminatum, four A. brandegei, and three A. passeyi species (Adair et al., 2006; Hellier, 2000). collection sites in Utah. These three congeners with contrasting abundance and dis- Growers depending on wild seed collection tribution patterns provide an opportunity to investigate the role of geographic distance, would benefit from understanding genetic altitude, and rarity in patterns of genetic divergence. The collection sites were selected variation in wild populations across the along an altitudinal gradient to reflect ecogeographic variation. Individual plants from natural landscape. Knowing the extent of each of the 12 sites were genotyped using six AFLP primer combinations detecting DNA genetic diversity within and among popula- variation within and among all three species. Genetic differences between species were tions provides information that might be high enough to render comparisons among species impractical, so each species was useful in the selection of a seed collection analyzed separately for differences between populations and variability within popula- site. Intermountain Allium species can vary tions. Similarity coefficients were significantly greater within collection sites versus considerably in their distribution, occurrence, among collection sites indicating divergence between populations. Within-population and habitat. Although among-population genetic diversity was not correlated with elevation for any of the three species. Analysis of genetic variation is often known to be a result molecular variance revealed that 66% (A. acuminatum), 83% (A. passeyi), and 64% (A. of isolation by distance, the significance of brandegei) of observed variation is found within populations. Genetic divergence among correlations between geographic distribution and genetic diversity has been a topic of populations (VST) was higher in the widely distributed species, suggesting that inter- population gene flow may be negatively correlated with range size. Allium acuminatum debate among biologists (Gitzendanner and and A. brandegei individuals cluster into groups corresponding strictly to collection sites Soltis, 2000; Hamrick and Godt, 1989; Karron, based on neighbor-joining analysis of the total number of DNA polymorphisms between 1987). Recent studies have cast doubt on individual plants. Allium passeyi populations, however, had less overall genetic variation the theory that narrowly restricted or rare between populations. Genetic isolation by distance appeared responsible for much of the species necessarily exhibit lower levels of variability among populations, although there was one notable exception showing sig- among-population genetic variation in com- nificant differences between two geographically close populations in A. acuminatum. parison with widespread species (Bjerregaard, 2004). In comparing genetic variation in rare and widespread congeners compiled from the existing literature, there was no universal Efficient propagation of native inter- genetic diversity among localized popula- trend in levels of among-population genetic mountain plant species for rangeland resto- tions and geographical regions needs to be diversity in response to range size (Gitzen- ration and other commercial uses requires better understood to help identify collections danner and Soltis, 2000). The authors did some basic knowledge about natural genetic crucial for conservation and suitable for note high congeneric correlations for genetic diversity in the landscape (Adair et al., 2006; breeding efforts (Adair et al., 2006; Rio and measures, suggesting that it is useful to assess Monsen and Shaw, 2001). The patterns of Bamberg, 2002). Ideally, a crop gene bank genetic variation in relation to range size collection would contain a representative within species of the same genus. Doing so core of a species germplasm, providing stor- allows one to investigate genera-specific re- age and access to the widest range of genetic lationships between range size and genetic Received for publication 8 Aug. 2007. Accepted traits. In conjunction with evaluations of life variation within and among populations. for publication 13 Nov. 2007. history, growth characteristics, demograph- Like range size, habitat variation may also This research was supported by grants from the ics, and habitat of three intermountain Allium play a role in the partitioning of genetic vari- Utah Botanical Center, the Utah Native Plant Society, and by the Utah Agricultural Experiment species native to Utah, we used the amplified ation. Genetic differentiation in some species Station, Utah State University, Logan, UT (journal fragment length polymorphism (AFLP) tech- has also been shown to be closely related paper no. 7909). nique in investigating patterns of genetic to altitude (Wen and Hsiao, 2001), whereas 1To whom reprint requests should be addressed; diversity within and among the study pop- in other species, no such correlation was e-mail [email protected] ulations. The description of our study offers found (Bingham and Ranker, 2000). Ecotypic HORTSCIENCE VOL. 43(3) JUNE 2008 637 JOBNAME: horts 43#3 2008 PAGE: 2 OUTPUT: April 23 14:50:43 2008 tsp/horts/163067/02508 genetic variation may be detected within a understand the genetic variation that exists Data analyses. Hypothesis testing using species by sampling along an altitudinal gra- within and among common and rare Allium the similarity index (Leonard et al., 1999), dient (Clausen et al., 1940). Understanding populations. analyses of molecular variance (Excoffier how genetic diversity is partitioned within et al., 1992), and neighbor-joining genetic and among intermountain Allium populations distance analysis (Saitou and Nei, 1987) were can give insight into the mechanisms that Materials and Methods used to investigate genetic diversity within have influenced their current habitats as well and among populations. as aid in the development of propagation Plant materials and DNA extraction. Genetic distances between individual protocol, seed transfer guidelines, and con- Fresh leaf material was collected in the wild plants were determined by the numbers of servation management plans. at multiple locations for each species (Table AFLPs (Euclidean distance) and similarity Previous studies of genetic diversity in 1) in the spring of 2005. Five A. acuminatum, coefficients computed as 2Nm/(Nx +Ny)in several North American Allium species have four A. passeyi, and three A. brandegei sites which Nm is the number of pairs of bands provided information useful for germplasm were sampled. Samples were collected along matching between individuals and Nx and Ny conservation strategies. In a study examining a line transect to minimize potential clonal are the total number of bands amplified from the genetic diversity existing in three popu- influence with distances between individuals the individuals (Dice, 1945; Lynch, 1990; lations each of Allium columbianum and A. varying according to the density of individ- Nei and Li, 1979). Neither of these Euclidean fibillum, over 90% of the diversity was found uals at the site. Genomic DNA was extracted distances nor similarity coefficients relies on within-population for each species (Hellier, from leaf tissue of 192 individuals using the shared null alleles. Analyses
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