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Published online 7 November 2007
Published in Crop Sci 47:2372-2378 (2007)
© 2007 Crop Science Society of America
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PLANT GENETIC RESOURCES

Frequency of a Loss-of-Function Mutation in Oleoyl-PC Desaturase (ahFAD2A) in the Mini-Core of the U.S. Peanut Germplasm Collection

Y. Chua, L. Ramosa, C. C. Holbrookb and P. Ozias-Akinsa,*

a Dep. of Horticulture, Univ. of Georgia Tifton Campus, Tifton GA 31793
b Research Geneticist, USDA ARS, P.O. Box 748, Tifton, GA 31793. Funding was provided by the Georgia Seed Development Commission and the University of Georgia Research Foundation Cultivar Development Program

* Corresponding author (pozias{at}uga.edu).


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
High oleic acid to linoleic acid ratios (high O/L) in tetraploid peanut (Arachis hypogaea L.) are controlled by the activity of oleoyl-PC desaturase, which is encoded by two homeologous genes (ahFAD2A and ahFAD2B). In a naturally occurring high O/L peanut, a spontaneous mutation (G-to-A at position 448 resulting in a D150N amino acid substitution) has been found in ahFAD2A, which resulted in a dysfunctional desaturase. In normal x high O/L crosses, segregation ratios for high:normal O/L are either 1:3 or 1:15 suggesting that one gene in some normal O/L lines may be mutated. We designed a cleaved amplified polymorphic sequence (CAPS) marker to differentiate the mutant and wild-type ahFAD2A alleles at the critical point mutation. The mutant allele was present in 31.6% of the accessions from the mini-core collection of peanut germplasm and was confirmed by DNA sequence analysis. The mutant allele was frequent among subspecies hypogaea accessions but absent from subspecies fastigiata accessions and the putative diploid, A-genome progenitor of peanut, Arachis duranensis. These data will be useful to breeders who would like to transfer disease resistance traits from mini-core accessions to high oleic acid cultivars.

Abbreviations: AFLP, amplified fragment polymorphism • CAPS, cleaved amplified polymorphic sequence • O/L, oleic acid to linoleic acid ratio • ORF, open reading frame • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • SSR, simple sequence repeat

Frequency of a Loss-of-Function Mutation in Oleoyl-PC Desaturase (ahFAD2A) in the Mini-Core of the U.S. Peanut Germplasm Collection

Y. Chua, L. Ramosa, C. C. Holbrookb and P. Ozias-Akinsa,*

a Dep. of Horticulture, Univ. of Georgia Tifton Campus, Tifton GA 31793
b Research Geneticist, USDA ARS, P.O. Box 748, Tifton, GA 31793. Funding was provided by the Georgia Seed Development Commission and the University of Georgia Research Foundation Cultivar Development Program

* Corresponding author (pozias{at}uga.edu).

High oleic acid to linoleic acid ratios (high O/L) in tetraploid peanut (Arachis hypogaea L.) are controlled by the activity of oleoyl-PC desaturase, which is encoded by two homeologous genes (ahFAD2A and ahFAD2B). In a naturally occurring high O/L peanut, a spontaneous mutation (G-to-A at position 448 resulting in a D150N amino acid substitution) has been found in ahFAD2A, which resulted in a dysfunctional desaturase. In normal x high O/L crosses, segregation ratios for high:normal O/L are either 1:3 or 1:15 suggesting that one gene in some normal O/L lines may be mutated. We designed a cleaved amplified polymorphic sequence (CAPS) marker to differentiate the mutant and wild-type ahFAD2A alleles at the critical point mutation. The mutant allele was present in 31.6% of the accessions from the mini-core collection of peanut germplasm and was confirmed by DNA sequence analysis. The mutant allele was frequent among subspecies hypogaea accessions but absent from subspecies fastigiata accessions and the putative diploid, A-genome progenitor of peanut, Arachis duranensis. These data will be useful to breeders who would like to transfer disease resistance traits from mini-core accessions to high oleic acid cultivars.

Abbreviations: AFLP, amplified fragment polymorphism • CAPS, cleaved amplified polymorphic sequence • O/L, oleic acid to linoleic acid ratio • ORF, open reading frame • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • SSR, simple sequence repeat


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
THE TRAIT FOR high oleic to linoleic acid ratio (high O/L) in peanut (Arachis hypogaea L.) is favored over low O/L because it confers health benefits and oil stability. High oleic acid in the diet can reduce blood cholesterol and aortic cholesterol accumulation thereby decreasing the risk of cardiovascular disease (O'Byrne et al., 1997; Wilson et al., 2006). Oleic acid also can be beneficial in preventing cancer, increasing insulin sensitivity, and ameliorating some inflammatory diseases (Chong et al., 2006; Colomer and Menendez, 2006; Mesa Garcia et al., 2006). Regarding oil stability, high O/L ratios in peanut extend shelf life by delaying the development of rancidity (O'Keefe et al., 1993). The high stability of oleic acid also makes the catalytic hydrogenation of vegetable oil unnecessary. Hydrogenated vegetable oil is the major source of trans fatty acids, compounds that exacerbate heart disease and diabetes (Chong et al., 2006). Replacing partially hydrogenated oil by high oleic acid peanut oil can minimize the consumption of trans fatty acids (Broun et al., 1999).

Normal oleate peanut genotypes have 36 to 70% oleic acid and 15 to 43% linoleic acid, whereas high oleate peanut genotypes have approximately 80% oleic acid and approximately 2% linoleic acid (Norden et al., 1987). The conversion from oleate to linoleate is catalyzed by oleoyl-PC desaturase which introduces the second double bond to oleic acid (Schwartzbeck et al., 2001). Loss-of-function of oleoyl-PC desaturase activity is solely responsible for the high O/L trait in peanut (Ray et al., 1993). Oleoyl-PC desaturase activity is governed by two genes, ahFAD2A and ahFAD2B (Jung et al., 2000a; Jung et al., 2000b). These genes share 99% nucleotide sequence homology in the coding region and both of them code for active desaturases (Bruner et al., 2001). The two genes are homeologous in that ahFAD2A belongs to the A subgenome of A. hypogaea and ahFAD2B to the B subgenome (Jung et al., 2000b). A spontaneous high O/L mutant F435 was discovered by Norden et al. (1987). This line has a nonfunctional ahFAD2A desaturase and the transcription of ahFAD2B is greatly suppressed (Jung et al., 2000a,b). In crosses between F435 and normal oleate peanut, F2 segregation ratios can be either 1:3 (genotype I) or 1:15 (genotype II) for high:normal O/L (Norden et al., 1987). Further molecular analysis showed that in some normal O/L peanut breeding lines, a natural point mutation was present in ahFAD2A which caused a nonsynonymous substitution of asparagine for aspartate at position 150 (D150N). This mutation results in a dysfunctional ahFAD2A desaturase, which explains the 3:1 segregation ratio in genotype I peanut breeding lines. As for genotype II, normal O/L peanut lines, ahFAD2A retains aspartate at position 150 and the ahFAD2A desaturase is functional along with ahFAD2B; therefore, the segregation ratio becomes 15:1 (Jung et al., 2000a). The functional importance of aspartate at position 150 was proved by site specific mutagenesis studies (Bruner et al., 2001). Consequently, the presence or absence of this D150N point mutation in ahFAD2A will control the segregation ratio in crosses with high-oleic acid genotypes.

Previously, fatty acid genotypes of five Virginia-type peanuts were screened by measurement of oleic and linoleic acid content in segregating populations and all five were found to be "genotype I" (Isleib et al., 1996). Up to now there has been no systematic study on the frequency of the D150N point mutation in ahFAD2A among peanut germplasm. One method for sampling a germplasm collection is to use a core collection developed for peanut (Holbrook et al., 1993). The peanut core collection of 831 accessions, representing approximately 10% of the total U.S. germplasm collection was selected based on country of origin and available morphological data to maximize genetic diversity. The core collection has been extensively studied for a variety of disease resistances such as nematode, tomato spotted wilt, and leaf spot, among others (Anderson et al., 1996; Franke et al., 1999; Holbrook and Anderson, 1995; Holbrook and Dong, 2005; Holbrook et al., 2000b). Fatty acid composition in this core collection also was examined (Hammond et al., 1997). More recently, a mini-core collection which preserves the majority of genetic variation in the core collection was further developed (Holbrook and Dong, 2005). It is highly possible that the natural D150N mutation in ahFAD2A would be present in the U.S. peanut germplasm collection. Therefore, we designed a cleaved amplified polymorphic sequence (CAPS) marker using the available sequence data for ahFAD2A to screen the mini-core collection as well as 27 accessions of Arachis duranensis, the putative A subgenome progenitor of peanut. The mutant allele frequency between these populations allows one to infer when such a mutation may have occurred, that is, before or after polyploidization. Furthermore, this research will provide important genetic information for peanut breeders engaged in the development of peanut cultivars with the trait for high O/L ratio.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS AND DISCUSSION
 REFERENCES
 
Mini-Core Growth Condition
One hundred twelve accessions for the mini-core collection were planted in field plots in Tift County Georgia on 5 June 2006. Plots consisted of two rows, 2 m long and 0.9 m apart. Standard cultural practices for peanut production were followed.

DNA Extraction
For samples from the mini-core collection, a maximum of 15 leaflets were sampled from each accession with one leaflet per individual plant. A 6 mm leaf disk from each leaflet was excised with a hole-punch. All leaf disks from the same accession were pooled for DNA extraction. The leaf disks were frozen in liquid N and ground into powder by vortexing with three to four 3 mm stainless steel ball-bearings. Subsequently, DNA was extracted according to a CTAB extraction method (Singsit et al., 1997). For samples from Arachis duranensis, individual young leaves were frozen in liquid N and ground with two stainless steel ball-bearings. Genomic DNA was prepared from Qiagen DNeasy 96 plant kit (Qiagen, Valencia, CA). DNA quantification was performed by fluorometry and the concentration was adjusted to 25 ng/µL–1 with TE buffer (10 mM Tris-Cl, pH 7.5; 1 mM EDTA, pH 8.0).

Polymerase Chain Reaction Amplification and Restriction Digestion
The polymerase chain reaction (PCR) performed was with sense primer, 5'-GATTACTGATTATTGACTT-3', and anti-sense primer, 5'-CCAACCCAAACCTTTCAGAG-3'. The sense primer sequence was identical to primer aF19 (Patel et al., 2004), which includes the 19-bp insertion specific to the 5'UTR of the ahFAD2A gene. The anti-sense primer anneals within the coding sequence of ahFAD2A. The expected size of the specific ahFAD2A PCR product is 826 bp. The PCR was performed with 0.8 U of Jumpstart Taq DNA polymerase (Sigma, St. Louis, MO), 1x reaction buffer supplied by the manufacturer, 0.1 mM dNTPs, 0.2 µM each primer, and 40 ng DNA template in a total reaction volume of 40 µL. The PCR reaction conditions were 94°C for 5 min followed by 35 cycles of 94°C for 30 s, 48.5°C for 30 s, and 72°C for 1 min with a final extension step at 72°C for 7 min. All PCR amplifications were performed with the GeneAmp PCR system 9700 (Applied Biosystems, Foster City, CA). Agarose gels (1%) were run with 5 µL of the PCR reaction to confirm the success of amplification. Each PCR reaction was purified with Qiaquick PCR purification kit (Qiagen, Valencia, CA), and PCR products were eluted with 30 µL of water. Purified PCR products (8 µL) were digested with 0.4 U of Hpy99I restriction enzyme (New England Biolabs, Ipswich, MA) at 37°C for 1 h. The digested products were separated on a 2% agarose gel and stained with SYBR Green I (Invitrogen, Carlsbad, CA) for 30 min. Gel images were recorded with a Molecular Imager Gel Doc XR System (Bio-Rad, Hercules, CA). The PCR products from ahFAD2A mutant lines were sequenced directly with the anti-sense primer reported above. Sequencing was performed with a CEQ 8000 Genetic Analysis System (Beckman Coulter, Fullerton, CA). The Vector NTI software program (Invitrogen, Carlsbad, CA) was used for sequence analysis.

A Chi-square test was performed to determine if the number observed was significantly different from the expected number. The expected number was calculated based on the allele frequency in the entire mini-core.


   RESULTS AND DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
REFERENCES
 
The point mutation resulting in the D150N amino acid substitution in ahFAD2A was a natural allelic variant in Arachis hypogaea and this mutation was encoded by a G to A transition at position 448 of the open reading frame (ORF). To search for a restriction enzyme recognition site that would span this nucleotide position, we submitted the ahFAD2A sequence from Arachis duranensis (AF272951) to the New England Biolabs cutter website (http://tools.neb.com/NEBcutter2/index.php). A unique restriction site for Hpy99I (CGWCG W = A/T) was found in the ORF, recognizing the wild-type sequence beginning at position 477 (CGACG). The G in bold and underlined is the key nucleotide position replaced by A in high O/L mutant peanut lines (Bruner et al., 2001; Patel et al., 2004). Therefore, PCR products amplified from a functional ahFAD2A gene should be recognized by Hpy99I and cut into two fragments, 598 and 228 bp in size. In the ahFAD2A mutant lines, the G-to-A transition at position 478 would make the sequence unrecognizable for Hpy99I and no digestion products should be observed. DNA was obtained from 95 out of 112 accessions in the mini-core collection. We could not obtain DNA from the remaining accessions because either the seeds did not germinate in the field or the plants had died. After PCR amplification and digestion with Hpy99I, 30 samples (31.6%) remained undigested, and therefore carried the mutant allele, whereas 65 (68.4%) yielded the two fragments expected for the wild-type allele. Data for each accession along with its country of origin are summarized in Table 1 . A representative gel image of digested and undigested samples is shown in Fig. 1 . The 826-bp PCR-amplified fragment is readily observed in all the samples that were digested by Hpy99I, although the 228-bp fragment could not be easily visualized after staining with ethidium bromide. Use of SYBR Green I, which has 50 to 100 times higher sensitivity than ethidium bromide, allowed the smaller fragment to be observed. A small amount of undigested PCR product routinely was detected by this staining method even when the amount of Hpy99I enzyme per reaction was increased from 0.4 to 2 U. All of the A. duranensis DNAs were extracted from single plants and the undigested PCR products still were detectable; therefore, a mixture of PCR products resulting from a mixture of templates could not account for the incomplete digestion. Incomplete digestion of a PCR product is not unusual. Jung et al. (2000b) also observed incomplete digestion for their CAPS marker that could distinguish between ahFAD2A and ahFAD2B. Incomplete digestion could be caused in part by the low fidelity of the Taq polymerase used for PCR amplification.


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  		Table 1. Presence or absence of the ahFAD2A point mutation as detected by Hpy99I restriction digestion at the site of G448A. "Individuals pooled" column indicates the actual number of leaf disks from individual plants that were pooled for each DNA sample. m, mutant allele; wt, wild-type allele.

 

Figure 1
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  		Figure 1. Hpy99I-digested ahFAD2A fragments from peanut mini-core collection and Arachis duranensis accessions.

 
Germplasm lines that did not show digestion products were confirmed as G448A mutants by DNA sequencing. Twenty-seven out of 30 PCR products from ahFAD2A mutant lines gave quality sequence with the anti-sense primer. All of the sequences contained the nucleotide substitution that would result in an A at position 448. Therefore, the mutation of ahFAD2A detected by restriction digestion in these lines is the G448A point mutation that leads to loss-of-function of the ahFAD2A desaturase.

Krapovickas and Rigoni (1960) proposed the subdivision of A. hypogaea L. into two subspecies: A. hypogaea L. spp. hypogaea and A. hypogaea L. spp. fastigiata. One of the primary distinctions between the two subspecies is the presence or absence of flowering on the central axis (main stem). Subspecies fastigiata has flowering on the main stem, hypogaea does not. In the United States, peanuts are classified into four market types. Runner and Virginia market types are spp. hypogaea, whereas Spanish and Valencia are spp. fastigiata (Stalker and Simpson, 1995).

Inheritance studies with different market-type cultivars have indicated that the ahFAD2A mutation is frequent in cultivars with no flowering on the main stem but absent in cultivars with flowering on the main stem. Knauft et al. (1993) examined the inheritance of this trait in crosses with 13 cultivars and breeding lines of the runner and Virginia market types (no flowering on the main stem). The trait exhibited monogenic inheritance in 12 of the 13 cross combinations. Isleib et al. (1996) examined five different cultivars of the Virginia-type cultivars and found that four exhibited monogenic inheritance. Lopez et al. (2001) examined the inheritance of the high oleic acid in six Spanish market-type peanut cultivars (flowering on the main stem). When these were crossed with a high oleic parent, all the resulting populations segregated for two major genes. Our molecular data are consistent with these previously observed frequencies. Our investigation of the accessions in the mini-core collection indicated that the ahFAD2A mutation is frequently present in accessions with no flowering on the main stem but absent in accessions with flowering on the main stem (Table 2 ).


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  		Table 2. Comparison of the frequency of mutant ahFAD2A alleles in mini-core accessions with and without flowering on the main stem, a primary distinction between subspecies. No = spp. hypogaea. Yes = spp. fastigiata.

 
The mini-core was developed by randomly selecting 10% of the core accessions after they had been grouped into 26 clusters based on multivariate analysis of data for 16 morphological characteristics. Previous studies have demonstrated that this clustering method can be used to improve the efficiency of identifying desirable traits in the core collection and in the entire collection (Holbrook and Anderson, 1995; Holbrook and Dong, 2005). In 17 clusters with both flowering habits, a reasonable chance to identify the distribution of ahFAD2A mutation among the accessions exists (Table 3 ). All the mini-core accessions in clusters 2, 7, and 18 contain the mutation and do not have flowering on the main stem. At least half of the mini-core accessions in clusters 8, 10, 14, 20, and 25 contain the mutation, and most of the mini-core accessions in these clusters do not have flowering on the main stem. These should be promising clusters for breeders who are looking for spp. hypogaea germplasm that could be crossed with high oleic cultivars to produce progeny that would segregate 3:1 for normal to high oleic. If a particular cluster also contains a disease resistance trait of interest, the disease resistant accessions now can be screened for the dysfunctional desaturase before their introduction into a breeding program.


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  		Table 3. Number and frequency of mini-core accessions carrying mutations of ahFAD2A and exhibiting flowering on the main stem for the representatives from the 26 clusters of the core collection.

 
All the mini-core accessions in clusters 3, 4, 5, 9, 11, 16, 17, 22, and 23 were spp. fastigiata and did not contain the mutation. Breeders using other accessions from these clusters are likely to produce progeny that segregate 15:1 for normal to high oleic. Based on the associations presented in Tables 2 and 3, it appears unlikely that there are naturally occurring spp. fastigiata accessions that contain the ahFAD2A mutation. Plant breeders working to develop high oleic Spanish-type cultivars should use one of the recently released high oleic Spanish cultivars (Baring et al., 2006; Simpson et al., 2003b) as one of the parents in their crosses.

Since ahFAD2A is from the A genome and diploid Arachis duranensis is the putative A-genome donor (Jung et al., 2003; Ramos et al., 2006; Seijo et al., 2004), we further tested available Arachis duranensis accessions (Table 4 ) for the same CAPS marker. All 27 accessions could be digested with Hpy99I indicating that all contain the functional wild-type allele. This result implies that the spontaneous G448A point mutation in ahFAD2A occurred after the polyploidization event that gave rise to allotetraploid peanut. The mutant allele appears to have arisen before the global distribution of peanut from its center of origin (South America) since both mutant and wild-type alleles were found in most geographic regions (Table 1).


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  		Table 4. Arachis duranensis accessions that were screened for the point mutation in ahFAD2A. All of them possess the wild-type allele because polymerase chain reaction products were digested by Hpy99I.

 
The U.S. peanut germplasm collection contains a great deal of genetic diversity. It is a valuable resource for peanut breeding programs. In-depth studies on the genetic variation for this collection are warranted. However, due to the time and expense that would be incurred to evaluate the entire collection, a more economical approach is to develop core and minicore collections that are representative of the diversity found in the entire collection (Holbrook and Dong, 2005; Holbrook et al., 1993). Our survey of the mini-core collection for the loss-of-function ahFAD2A allele now allows a breeder to select not only a disease resistant genotype but also one that could facilitate the combination of disease resistance and the high O/L trait.

During the past 10 yr, numerous peanut cultivars with the high O/L trait have been released. Among them, Sunoleic 95R, Sunoleic 97R, Tamrun OL1, Tamrun OL2, Olin, and Georgia 04S are cultivars whose pedigree included F435 as the high O/L trait donor (Branch, 2005; Gorbet and Knauft, 1997, 2000; Simpson et al., 2003a,b, 2006) and would be expected to carry the mutant ahFAD2A allele. Georgia HiO/L peanut was produced using T2636M as the high O/L parent (Branch, 2000). T2636M is a mutant line induced by gamma radiation. The other parents for the high O/L cultivars confer disease resistance, high yield, or other desirable agronomic traits. Continued breeding efforts to produce elite high O/L peanut cultivars are needed to counteract a broad range of disease and abiotic challenges in the United States. Germplasm collections are a rich resource of resistance genes. It has been shown that the germplasm in the U.S. core collection has a varied level of resistance to nematodes, tomato spotted wilt virus, late leaf spot, and other fungi (Anderson et al., 1996; Franke et al., 1999; Holbrook and Anderson, 1995; Holbrook et al., 2000a,b), and some of the disease resistance patterns are preserved in the mini-core collection (Holbrook and Dong, 2005). These genotypes can serve as parents to improve the resistance gene diversity in peanut cultivars. None of the germplasm in the core collection, however, is high O/L (Hammond et al., 1997). PI288178 demonstrated the highest oleic acid content (60.3% oleate, 19.9% linoleate), only a 3:1 ratio. Therefore, it is unlikely that any B-genome alleles are nonfunctional in the core although there is a 30% chance that the A-genome loss-of-function allele is present based on our survey of the mini-core collection.

Previously, peanut genetic polymorphism has been explored using other PCR-based molecular markers including random amplified polymorphic DNA (RAPD) markers, amplified fragment polymorphism (AFLP) markers, and microsatellite DNA (simple sequence repeat, SSR) markers (Halward et al., 1992; He et al., 2003; Krishna et al., 2004; Lanham et al., 1992; Milla et al., 2005; Moretzsohn Mde et al., 2004). The present study is the first report on the genetic polymorphism of a specific gene in the mini-core collection using a CAPS marker. Our study provides information for a breeder to predict the F2 segregation ratio of either 3:1 or 15:1 for high O/L if they were to use a mini-core collection genotype in crosses with a high O/L parent.


   ACKNOWLEDGMENTS
 
We thank Evelyn P. Morgan for technical assistance.


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 MATERIALS AND METHODS
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Received for publication February 28, 2007.


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 MATERIALS AND METHODS
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Y. Chu, C. C. Holbrook, and P. Ozias-Akins
Two Alleles of ahFAD2B Control the High Oleic Acid Trait in Cultivated Peanut
Crop Sci., October 22, 2009; 49(6): 2029 - 2036.
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