Genetic relationship and structure of Mediterranean durum wheat
Moragues M., Royo C., Sorrells M.E.
in
Molina-Cano J.L. (ed.), Christou P. (ed.), Graner A. (ed.), Hammer K. (ed.), Jouve N. (ed.), Keller B. (ed.), Lasa J.M. (ed.), Powell W. (ed.), Royo C. (ed.), Shewry P. (ed.), Stanca A.M. (ed.).
Cereal science and technology for feeding ten billion people: genomics era and beyond Zaragoza : CIHEAM / IRTA
Options Méditerranéennes : Série A. Séminaires Méditerranéens; n. 81 2008
pages 71-73
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Cereal science and technology for feeding ten billion people: genomics era and beyond. Zaragoza : CIHEAM / IRTA, 2008. p. 71-73 (Options Méditerranéennes : Série A. Séminaires Méditerranéens; n.
81)
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Genetic relationship and structure of Mediterranean durum wheat
M. Moraguees*,1, C. Royo** and M.E. Sorrells*
*Department of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, New York 14953, USA
**Area de Conreus Extensius, Centre UdL-IRTA, Rovira Roure 191, 25198 Lleida, Spain.
1MEC/Fulbright Post-doctoral Scholar
SUMMARY – Twenty four unlinked SSR markers were used to genotype 192 durum wheat accessions from the Mediterranean region, consisting of 172 landraces and 20 modern widely grown varieties. Clustering and ordination methods provided a picture of the relationships between individuals, and the program Structure assigned genotypes to different groups using a Bayesian approach. Cluster analysis showed that the accessions tended to group according to their geographical origin. All accessions from Turkey, but one, grouped together.
Modern Spanish and Italian cultivars clustered together excepting cultivar Simeto, which clustered with a group of Italian landraces. Population was structured in three clusters: one formed by landraces from the Middle East, Egypt and the Balcan Peninsula, another formed by landraces from the western Mediterranean countries and a third one consisting in all modern cultivars, excepting Simeto.
Genetic diversity plays a vital role in developing new cultivars. Genetic stocks conserved in genebanks, such as landraces are a valuable source of diversity. Landraces may have useful alleles for genes responsible for adaptation, but are difficult to use because they often contain several genotypes and it complicates the determination of the allele frequency for large sets of accessions. In this paper, we present an approach to determining the genetic relationships and structure between a set of 192 durum wheat accessions from the Mediterranean region.
Material and methods
Twenty four unlinked SSR markers (Fig. 1) were used to genotype 192 durum wheat accessions from the Mediterranean region, consisting of 172 landraces and 20 modern widely grown varieties.
Diversity indices and LD parameter r2 were calculated with the PowerMarker software (Liu and Muse, 2005). UPGMA cluster analysis based on Nei distance (Nei, 1972) was used to determine the genetic relationships between accessions and origins.
0 0.08 0.68 11 Mean
0.01 0.1 0.81 12 7AL16-0.86-0.90
100 7A Xgwm282
0 0.06 0.89 15 89
7A XBarc151
0 0.03 0.82 11 0
6B Xwmc494
0 0.01 0.68 7 3
6B Xwmc486
0 0.03 0.92 18 131
6B XBarc354
0 0.04 0.88 16 91
6A Xwmc580
0 0.06 0.78 10 C-6AL4-0.90*
20 6A XBarc107
0.01 0.16 0.5 10 6AS1-0.35-1.00
0 6A XBarc003
0.05 0.09 0.51 5 5BL1-0.55-0.75
127 5B XBarc140
0.01 0.05 0.25 6 5BL1-0.55-0.75
35 5B XBarc1032
0 0.04 0.84 10 55
5A Xwmc150b
0 0.07 0.38 8 5AS3-0.75-0.98
32 5A Xgwm205
0.02 0.24 0.86 11 C-5AL12-0.35/5AL12-0.35-0.57 72
5A Xgwm156
0 0.09 0.55 6 C-4BS4-0.37
0 4B XBarc1045
0 0.03 0.6 9 7
4A Xwmc420
0 0.15 0.78 11 C-3BS1-0.33
60 3B Xgwm566
0.01 0.14 0.85 12 C-3AL3-0.42
118 3A Xgwm155
0 0.06 0.92 22 51
3A Xcfa2134
0 0.05 0.66 10 25
2B Xwmc25
0 0.1 0.83 16 2BL4-0.50-0.89
87 2B Xwmc175
0.02 0.25 0.91 18 41
2A Xwmc453
0 0.08 0.27 5 1BL3-0.83-1.00
86 1B Xbarc080
0.01 0.08 0.57 6 1AS3-0.86-1.00
27 1A Xbarc263
0 0.01 0.29 4 1AL1-0.17-0.61
114 1A Xbarc158
Two alleles Three alleles Frequency of PIC
Allele No Bin
Distance Chr.
Marker
P<0.01 P<0.001 P<0.0001
Fig. 1. p-values of LD across 24 unlinked SSR for the 192 durum wheat accessions and description and summary statistics of these SSR.
Structure (Pritchard et al., 2000) was used to infer the genetic structure of the population and
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determine the optimum number of subpopulations (K) and the probability of each individual to belong to each group.
Results and discussion
The average frequency of multiple alleles for all loci was 0.08 when two alleles were detected, but close to 0 for detecting 3 alleles (Fig. 1). We were not able to estimate the within accession allele frequency because we bulked the
DNA from 10 plants. In this first step, we ignored the presence of the third allele, which was designated as the weakest band, and thus, was the lowest frequency allele in the accession or possibly a PCR artifact. The subsequent analyses were performed considering multiple alleles as genotype data with unkown gametic phase.
Fig. 2. Cluster analysis of the durum wheat accessions based in the allelic composition for 24 unlinked SSR.
PI-174599 PI-48212 BGE012340 Citr-15428 BGE018354 BGE018350 BGE019263 BGE019270 BGE018351 BGE019264 BGE019262 BGE018192 BGE018353 BGE019265 BGE019266 IG-84856 IG-82547 IG-82549 PI-384037 PI-572901 PI-572903 IG-95841 BGE012566 BGE013056 BGE019281 BGE012392 IG-95931 PI-182666 PI-210947 PI-223169 PI-60727 BGE013723 PI-362638 PI-43246 PI-174697 PI-362629 PI-374658 PI-405908 PI-345249 PI-378303 PI-345260 BGE013694 PI-278600 IG-83920 PI-420946 IG-95812 IG-95847 PI-52503 PI-292032 PI-223156 PI-234382 PI-182667 PI-182669 PI-182671 PI-210885 PI-371833 PI-234388 PI-283155 PI-182674 PI-60742 BGE012407 PI-174662 PI-174620 PI-174699 IPGR-1 BGE012485 BGE012487 BGE018618 IG-96851 BGE019279 BGE020909 BGE012379 BGE018274 BGE013687 IG-94009 BGE018605 BGE012247 BGE013053 IG-92895 IG-92967 BGE013064 BGE013685 BGE018282 BGE012346 BGE018304 PI-192487 PI-410922 Citr-6870 PI-191029 PI-585195 PI-372442 PI-210944 PI-410918 BGE012381 BGE012497 BGE013041 IG-83905 BGE020916 BGE020915 BGE012498 BGE012522 Citr-11246 Citr-6874 Svevo Boabdil Bolido Arment Amilcar Ancalei Hispasano Meridiano Ocotillo Senadur Kronos Vitron Vitronero Bolo Claudio Gallareta Sula Astigi Jupare PI-410920 PI-51211 PI-43245 BGE000097 BGE002893 BGE002876 BGE012328 IG-82551 BGE020911 Simeto IG-96802 BGE013610 IPGR-2 IG-82555 IG-93030 IG-93621 BGE020912 citr-6878 citr-6879 PI-192483 PI-192492 Citr-6872 BGE012330 Citr-6871 BGE018598 BGE013611 BGE000119 BGE013617 PI-292034 PI-192638 PI-192639 BGE013699 BGE018337 BGE018298 BGE018651 Citr-3225 BGE012451 BGE012500 BGE000168 PI-435024 PI-435034 PI-435038 PI-435057 PI-345441 PI-435043 PI-345357 PI-345442 BGE013737 PI-54432 Citr-11245 BGE013729 BGE019289 BGE013103 BGE018599 PI-372485 BGE013658 PI-366109 BGE012534 BGE018619 BGE018621 PI-7016 PI-7422 PI-434894 PI-559973 PI-576803 PI-60726 PI-113395 PI-113397 PI-372470 PI-372475 Fr Fr It Tn Tk Tk Tk Tk Tk Tk Tk Tk Tk Tk Tk Lb Cy Cy Is Is Is Sy Po Sp Sp Sp Sy Lb Cy Jd Eg Po Mc Gc Fr Mc Mc Mc Mc Sr Mc Po Sr It Jd Sy Sy Is Is Jd Jd Lb Lb Lb Jd Jd Jd Jd Lb Eg Tk Fr Fr Fr Bg Po It Sp Gc Po Po Po Sp Sp Al Sp Po Sp Al Al Sp Sp Sp Sp Sp Mr Mr Tn Mr Sr Cy Cy Mr Sp Po Sp It Mr Al It Po Cr Tn MD MD MD MD MD MD MD MD MD MD MD MD MD MD MD MD MD MD MD Mr Lb Gc It It It It It It MD Gc Sp Bg It Al Al It Mr Mr Mr Mr Tn It Tn Sp Sp It Sp Is Mr Mr Sp Sp Sp Sp Tn Eg Po Eg Mn Mn Mn Cr Cr Mn Mn Cr Po Li Cr Sp Sp Sp Sp Gc Po Eg Sp Sp Sp Eg Eg Eg Eg Eg Eg Eg Eg Gc Gc
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Cluster analysis (Fig. 2) showed that the accessions tended to group according to their geographical origin. All accessions from Turkey, but one, grouped together. Modern cultivars, originating in Spain and Italy clustered together. They also showed a low average number of alleles and PIC values (3.7 and 0.38, respectively). The exception would be Simeto, which clustered with a group of Italian landraces.
The model-based clustering method was tested for K from 2 to 5. Only when 2 subpopulations were considered, were all accessions classified in one or the other at a p>0.5, and only 8 landraces from different origins were not classified in any of the three groups when K=3. Two of the three groups represented different geographical regions, i.e. one was mainly formed by landraces from the Middle East, Egypt and the Balcan Peninsula, while the other was formed by landraces from the western Mediterranean countries. The modern cultivars, excepting Simeto, were classified in the third group jointly with Turkish landraces. This result did not agree with the results of the distance-based cluster analysis (Fig. 2).
The LD parameter r2 was significant for 39 % of the pairwise estimates (276) and varied from 0.002 to 0.074, with a median of 0.009. These values are lower of those found in elite wheat accessions (Breseghello and Sorrells, 2006), as was expected for a set of landraces.
References
Breseghello, F. and Sorrells, M.E. (2006). Genetics, 172: 1165-1177.
Liu, K. and Muse, S.V. (2005). Bioinformatics, 21: 2128-2129.
Nei, M. (1972). American Naturalist, 106: 283-292.
Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Genetics, 155: 945-959.
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