Yong-Bi Fu

Current molecular characterization of ex situ plant germplasm has placed more emphasis on cultivated gene pools and less on exotic gene pools representing wild relative species. This study attempted to characterize a selected set of germplasm accessions representing various Avena species with the hope to establish a reference set of exotic oat germplasm for oat breeding and research. The amplified fragment length polymorphism (AFLP) technique was applied to screen 163 accessions of 25 Avena species with diverse geographic origins. For each accession, 413 AFLP polymorphic bands detected by five AFLP primer pairs were scored. The frequencies of polymorphic bands ranged from 0.006 to 0.994 and averaged 0.468. Analysis of molecular variance revealed 59.5% of the total AFLP variation resided among 25 oat species, 45.9% among six assessed sections of the genus, 36.1% among three existing ploidy levels, and 50.8% among eight defined genome types. All the species were clustered together according to their ploidy levels. The C genome diploids appeared to be the most distinct, followed by the Ac genome diploid A. canariensis. The Ac genome seemed to be the oldest in all the A genomes, followed by the As, Al and Ad genomes. The AC genome tetraploids were more related to the ACD genome hexaploids than the AB genome tetraploids. Analysis of AFLP similarity suggested that the AC genome tetraploid A. maroccana was likely derived from the Cp genome diploid A. eriantha and the As genome diploid A. wiestii, and might be the progenitor of the ACD genome hexaploids. These AFLP patterns are significant for our understanding of the evolutionary pathways of Avena species and genomes, for establishing reference sets of exotic oat germplasm, and for exploring new exotic sources of genes for oat improvement.

Genetic diversity assessment of improved crop germplasm can facilitate the expansion of the genetic base in a plant breeding program, but little effort has been made to assess the Canadian soybean [Glycine max (L.) Merr.] gene pool established over the past century. Simple sequence repeat (SSR) markers were applied to assess the genetic diversity of 45 Canadian soybean cultivars released from 1934 to 2001 and 37 exotic germplasm accessions. Thirty‐seven SSR primer pairs were applied and 234 polymorphic bands were scored for each accession. The frequencies of the scored bands ranged from 0.01 to 0.90 and averaged 0.17. The proportion of total SSR variation occurring between exotic and Canadian germplasm was 9%; among the Canadian cultivars of three breeding periods 10%; and between the cultivars of maturity groups 0 and 00 4%. More diversity was found for exotic germplasm than the Canadian. More diversity was observed in the cultivars of the recent breeding period than the early. The Canadian cultivars were clustered into seven major groups, partially congruent to the known pedigrees, and they were more related to germplasm from Russia, Sweden, and Ukraine and less to the Asian germplasm. The six genetically most distinct cultivars were PS86 RR, Gaillard, Manitoba Brown, Beechwood, Maple Isle, and 92B91. These findings are useful for the selection of genetically distinct or less related soybean materials to improve the genetic background of the soybean gene pool.

The Avena sterilis L. collection in the Plant Gene Resources of Canada (PGRC) consists of 11,235 accessions originating from 27 countries and is an invaluable source of genetic variation for genetic improvement of oats, but it has been inadequately characterized, particularly using molecular techniques. More than 35 accessions have been identified with genes for resistance to oat crown and stem rusts, but little is known about their comparative genetic diversity. This study attempted to characterize a structured sample of 369 accessions representing 26 countries and two specific groups with Puccinia coronata avenae (Pc) and Puccinia graminis avenae (Pg) resistance genes using microsatellite (SSR) markers. Screening of 230 SSR primer pairs developed from other major crop species yielded 26 informative primer pairs for this characterization. These 26 primer pairs were applied to screen all the samples and 125 detected alleles were scored for each accession. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.01 to 0.99 and averaged 0.28. More than 90% of the SSR variation resided within accessions of a country. Accessions from Greece, Liberia, and Italy were genetically most diverse, while accessions from Egypt, Georgia, Ethiopia, Gibraltar, and Kenya were most distinct. Seven major clusters were identified, each consisting of accessions from multiple countries and specific groups, and these clusters were not well congruent with geographic origins. Accessions with Pc and Pg genes had similar levels of SSR variation, did not appear to cluster together, and were not associated with the other representative accessions. These SSR patterns are significant for understanding the progenitor species of cultivated oat, managing A. sterilis germplasm, and exploring new sources of genes for oat improvement.

Molecular characterization ofex situplant germplasm, although more attainable than before, has rarely been applied to a whole germplasm collection of 2000 accessions or larger. The benefits of screening large numbers of accessions have not been well recognized for germplasm management and utilization. Challenges also exist in identifying duplicated and genetically related accessions and in validating developed core subsets. Here we show how a new approach using an average marker-based dissimilarity of an accession in a collection can be applied to identify both redundancy and distinctness in a plant germplasm collection. Application of this dissimilarity measure to 2727 flax accessions genotyped by 149 randomly amplified polymorphic DNA (RAPD) markers revealed that up to 22% of accessions could be deemed to be redundant. Up to 500 of the most distinct flax accessions were identified and these can be directly screened for traits of interest to broaden the genetic base in a flax improvement programme. These results demonstrate that molecular screening of a large number of accessions with an informative diversity analysis can facilitate the management and utilization ofex situplant germplasm.

Sinapis alba L. is a major specialty crop grown as a condiment in western Canada, but little is known about its genetic diversity. The objective of this study was to assess the level and pattern of genetic diversity in a collection of 127 S. alba accessions held at Plant Gene Resources of Canada using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were applied, and 134 polymorphic bands were scored for each accession. These scored bands had frequencies of occurrence ranging from 0.02 to 0.99 with an average of 0.69. More AFLP variation was found within single (79.1%) than between (20.9%) S. alba accessions. A small degree of AFLP difference (1.7%) was observed among the accessions of various regions, while relatively large variation (9.2%) existed among the accessions of various countries. A large AFLP difference (15.6%) also existed between the yellow- and brown-seeded accessions, but only 6.2% difference was observed between the cultivar and landrace accessions. Two distinct groups of S. alba germplasm were identified on the basis of the seed colour (yellow or brown), although a few mixtures also existed. No apparent accessions were observed. The most diverse accessions were from Italy, Spain, France and Greece. Among the most genetically distinct accessions were SA97 from Portugal, SA89 and SA88 from France, SA83 from Russia and SA57 from Italy. These findings are significant not only for managing S. alba germplasm, but also for identifying diverse germplasm that can be used by plant breeders to improve S. alba seed yield and quality parameters.

Genetic diversity changes in wheat germplasm have been studied using different molecular markers, but little is known about the impact of plant breeding on the transcribed segments of the wheat genome. The objective of this study was to assess diversity changes in 75 Canadian hard red wheat cultivars released from 1845 to 2004 using 37 EST-derived microsatellite (eSSR) markers. These markers were derived from at least 19 transcribed sequences with putative functions assigned and sampled 17 wheat chromosomes. A total of 138 eSSR alleles was detected, and their allelic frequencies ranged from 0.01 to 0.99 with an average of 0.41. Allelic counts were significantly reduced at three loci for cultivars released after 1990. Sixteen alleles at 14 loci in pre-1910 cultivars were lost in cultivars released after 1990. The lost alleles had frequencies ranging from 0.03 to 0.17 and averaging 0.07. Partitioning the eSSR variation showed the four ancestral families accounted for 14.7% of the variation, followed by the six breeding periods with 12.8% and the eight breeding programs with 5.8%. A genetic shift was observed in the cultivars released over the six breeding periods, reflecting the various breeding efforts. These results illustrate the impact of the Canadian wheat breeding on the transcriptional segments of the wheat genome. These findings, along with those from genomic SSR markers, suggest the Canadian wheat breeding programs have reduced genetic diversity in the hard red spring wheat.

Many core collections have been developed from large collections of crop germplasm, but most of these have not been characterized, particularly using molecular techniques, for germplasm management and utilization. We have attempted to characterize a structured sample representing a world collection of 11,622 cultivated hexaploid oat accessions in the hope of understanding the genetic structure of the world collection. The amplified fragment length polymorphism (AFLP) technique was applied to screen 670 accessions representing 79 countries and one group of uncertain origin. For each accession, 170 AFLP polymorphic bands detected by five AFLP primer pairs were scored. Analyses of the AFLP data showed the effectiveness of the stratified sampling applied in capturing country-wise AFLP variation. The frequencies of polymorphic bands ranged from 0.11 to 0.99, with an average of 0.72. The majority (89.9%) of the AFLP variation resided within accessions of each country, and only 6.2% of the AFLP differences existed among accessions of major geographic regions. Accessions from the Mediterranean region were the most distinct, while those from Russia and the USA were the most diverse. The two distinct groups that were observed were separated largely on the basis of common oat and red oat. Red oat was genetically more diverse than its common and hull-less counterparts, and hull-less oat was more related to common oat than red oat. Landrace and non-landrace accessions displayed similar AFLP variation patterns. These patterns are significant for understanding the domestication of cultivated oat and are useful in classifying the intraspecific diversity of oat germplasm, developing specific core subsets of the oat collection, and exploring new sources of genes for oat improvement.