Fucheng Shan

Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms

Cicer reticulatum, C. echinospermum, C. bijugum, C. judaicum, C. pinnatifidum, C. cuneatum and C. yamashitae are wild annual Cicer species and potential donors of valuable traits to improve chickpea (C. arietinum). As part of a large project to characterize and evaluate wild annual Cicer collections held in the world gene banks, AFLP markers were used to study genetic variation in these species. The main aim of this study was to characterize geographical patterns of genetic variation in wild annual Cicer germplasm. Phylogenetic analysis of 146 wild annual Cicer accessions (including two accessions in the perennial C. anatolicum and six cultivars of chickpea) revealed four distinct groups corresponding well to primary, secondary and tertiary gene pools of chickpea. Some possible misidentified or mislabelled accessions were identified, and ILWC 242 is proposed as a hybrid between C. reticulatum and C. echinospermum. The extent of genetic diversity varied considerably and was unbalanced between species with greatest genetic diversity found in C. judaicum. For the first time geographic patterns of genetic variation in C. reticulatum, C. echinospermum, C. bijugum, C. judaicum and C. pinnatifidum were established using AFLP markers. Based on the current collections the maximum genetic diversity of C. reticulatum, C. echinospermum, C. bijugum and C. pinnatifidum was found in southeastern Turkey, while Palestine was the centre of maximum genetic variation for C. judaicum. This information provides a solid basis for the design of future collections and in situ conservation programs for wild annual Cicer.

New methods for comparison of chromosomes within and between species

Abstract A new method (called New Relative Length) was developed for comparison of chromosome size when both paired and unpaired chromosomes are present. All chromosomes were used in the calculation. A method of graphical display of karyotype data (called a Karyotype Graph), plotting New Relative Length on the vertical axis and arm ratio on the horizontal axis was used to indicate sampling error, to pair chromosomes and to match similar chromosomes in related species. Terms for Chromosome Size were also defined namely Small, Medium or Large depending on New Relative Length as a proportion of total chromosome length. These terms could also be used to compare chromosomes within species and between related species.

Development of DNA fingerprinting keys for discrimination of Cicer echinospermum (P.H. Davis) accessions using AFLP markers

To test the hypothesis that DNA markers associated with specific genetic make-up can be detected and used to discriminate genotypes, amplified fragment length polymorphism (AFLP) markers were produced for 14 accessions in Cicer echinospermum, a close relative of Cicer arietinum (chickpea). Six selective amplification primer combinations produced high polymorphism with average polymorphic loci of 77.2%. The polymorphism detected in this study enabled fingerprinting keys to be established to discriminate accessions within C. echinospermum. Results showed that molecular analysis using AFLP was a good and reliable technique to differentiate C. echinospermum accessions and to reconstruct phylogenetic relationships between them, which could help parental selection in chickpea improvement programs.

Identification of duplicates and fingerprinting of primary and secondary wild annual cicer gene pools using AFLP markers

Wild annual Cicer gene pools contain valuable germplasm for chickpea improvement programs. Previous research showed that duplication might exist in accessions collected from these gene pools, which would hinder chickpea breeding and related research. AFLP (amplified fragment length polymorphism) markers were used to fingerprint the world collections of the primary and secondary gene pools including C. reticulatum Lad., C. bijugum K.H. Rech., C. judaicum Boiss. and C. pinnatifidum Jaub. et Sp. Duplicates were detected in a total of 24 accessions in both the gene pools, highlighting the necessity to fingerprint the germplasm. Genotypic difference was detected as gene pool specific, species specific and accession specific AFLP markers. These were developed into fingerprinting keys for accession identification between and within species and gene pools. Use of AFLP markers to detect duplicates and to identify accessions is a reliable method which will assist in the characterisation and use of wild annual Cicer germplasm in chickpea improvement programs. We recommend the procedure presented in this paper as a standard approach for the precise genetic identification and characterisation of future world collections of wild Cicer, to keep germplasm integrity and to benefit chickpea breeding and related research programs.

Basic chromosome number in Boronia (Rutaceae)—competing hypotheses examined

Rutaceae have attracted considerable attention because of the wide chromosome-number variation. Cytoevolution of the genus Boronia, with n = 7-36, has been controversial. The critical issue is whether the base chromosome number is x = 18 or x = 9 in this genus and in the family Rutaceae. Phylogenetic analysis based on random amplified polymorphic DNA (RAPD) markers was used to evaluate the hypothesis. Twenty decamer arbitrary primers were used to produce RAPD markers in 25 accessions of 18 Boronia species and a total of 559 DNA fragments was generated. UPGMA distance analysis and Wagner parsimony analysis on the DNA data produced two phylogenetic trees with very similar topology. The two trees generally supported the present classification of Boronia species. The exception was B. tenuis, which may be better treated as a new section or genus. Chromosome numbers of all the genotypes used in the analysis were counted with n = 7, 8, 9, 11, 16-36. Evolutionary distances between species were determined on the basis of branch length of the Wagner cladogram. Regression analysis indicated that Boronia chromosome number has a significant negative relationship with evolutionary distance. Chromosome number in Boronia evolved from higher to lower. The basic chromosome number for Boronia is suggested to be 18.

Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

Highlight Roots in narrow-leafed lupin (Lupinus angustifolius) exhibit large phenotypic and genetic diversity. An association between root traits and DArT markers demonstrates potential for a marker-assisted selection programme for this species.

Genomic relationships within Boronia (Rutaceae) as revealed by karyotype analysis and RAPD molecular markers

Abstract. The genus Boronia Sm. section Boronia series Boronia contains species with n=7 (B. megastigma), n=7 or 8 (B. heterophylla), n=8 (B. molloyae) and n=9 (B. purdieana), representing ideal species with which to examine comparative chromosome morphology. Between species there were few chromosomes with similar morphology, indicating numerous genome re-organisations. Karyotypes between and within species of Boronia could be distinguished and inheritance of some chromosomes was observed. Species and hybrids with 2n = 14 or 15 had at least one large chromosome. Chromosome morphology indicated a closer relationship between B. heterophylla and B. molloyae and between B. purdieana and B. megastigma than between these two groups. Whole genomic DNA was extracted from 9 genotypes of Boronia. RAPD bands were analysed and pairwise distance matrices between genotypes were computed. Dendrograms were generated and analysed using unweighted pair-group method with arithmetic average cluster analysis. Dendograms supported cytological results, indicating B. heterophylla and B. molloyae are closely related and clearly distinct from B. megastigma and B. purdieana. The evolution of boronias is discussed.