Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins

Aligning a New Reference Genetic Map of Lupinus angustifolius with the Genome Sequence of the Model Legume, Lotus japonicus

We have developed a dense reference genetic map of Lupinus angustifolius (2n = 40) based on a set of 106 publicly available recombinant inbred lines derived from a cross between domesticated and wild parental lines. The map comprised 1090 loci in 20 linkage groups and three small clusters, drawing together data from several previous mapping publications plus almost 200 new markers, of which 63 were gene-based markers. A total of 171 mainly gene-based, sequence-tagged site loci served as bridging points for comparing the Lu. angustifolius genome with the genome sequence of the model legume, Lotus japonicus via BLASTn homology searching. Comparative analysis indicated that the genomes of Lu. angustifolius and Lo. japonicus are highly diverged structurally but with significant regions of conserved synteny including the region of the Lu. angustifolius genome containing the pod-shatter resistance gene, lentus. We discuss the potential of synteny analysis for identifying candidate genes for domestication traits in Lu. angustifolius and in improving our understanding of Fabaceae genome evolution

Crop Updates 2006 - Lupins and Pulses

This session covers sixty six papers from different authors: 2005 LUPIN AND PULSE INDUSTRY HIGHLIGHTS 1. Lupin Peter White, Department of Agriculture 2. Pulses Mark Seymour, Department of Agriculture 3. Monthly rainfall at experimental sites in 2005 4. Acknowledgements Amelia McLarty EDITOR 5. Contributors 6. Background Peter White, Department of Agriculture 2005 REGIONAL ROUNDUP 7. Northern agricultural region Wayne Parker, Department of Agriculture 8. Central agricultural region Ian Pritchard and Bob French, Department of Agriculture 9. Great southern and lakes Rodger Beermier, Department of Agriculture 10. South east region Mark Seymour, Department of Agriculture LUPIN AND PULSE PRODUCTION AGRONOMY AND GENETIC IMPROVEMENT 11. Lupin Peter White, Department of Agriculture 12. Narrow-leafed lupin breeding Bevan Buirchell, Department of Agriculture 13. Progress in the development of pearl lupin (Lupinus mutabilis) for Australian agriculture, Mark Sweetingham1,2, Jon Clements1, Geoff Thomas2, Roger Jones1, Sofia Sipsas1, John Quealy2, Leigh Smith1 and Gordon Francis1 1CLIMA, The University of Western Australia 2Department of Agriculture 14. Molecular genetic markers and lupin breeding, Huaan Yang, Jeffrey Boersma, Bevan Buirchell, Department of Agriculture 15. Construction of a genetic linkage map using MFLP, and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus augustiflolius L) Jeffrey Boersma1,2, Margaret Pallotta3, Bevan Buirchell1, Chengdao Li1, Krishnapillai Sivasithamparam2 and Huaan Yang1 1Department of Agriculture, 2The University of Western Australia, 3Australian Centre for Plant Functional Genomics, South Australia 16. The first gene-based map of narrow-leafed lupin – location of domestication genes and conserved synteny with Medicago truncatula, M. Nelson1, H. Phan2, S. Ellwood2, P. Moolhuijzen3, M. Bellgard3, J. Hane2, A. Williams2, J. Fos‑Nyarko4, B. Wolko5, M. Książkiewicz5, M. Cakir4, M. Jones4, M. Scobie4, C. O’Lone1, S.J. Barker1, R. Oliver2, and W. Cowling1 1School of Plant Biology, The University of Western Australia, 2Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, 3Centre for Bioinformatics and Biological Computing, Murdoch University, 4School of Biological Sciences and Biotechnology, SABC, Murdoch University,5Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland 17. How does lupin optimum density change row spacing? Bob French and Laurie Maiolo, Department of Agriculture 18. Wide row spacing and seeding rate of lupins with conventional and precision seeding machines Martin Harries, Jo Walker and Murray Blyth, Department of Agriculture 19. Influence of row spacing and plant density on lupin competition with annual ryegrass, Martin Harries, Jo Walker and Murray Blyth, Department of Agriculture 20. Effect of timing and speed of inter-row cultivation on lupins, Martin Harries, Jo Walker and Steve Cosh, Department of Agriculture 21. The interaction of atrazine herbicide rate and row spacing on lupin seedling survival, Martin Harries and Jo Walker Department of Agriculture 22. The banding of herbicides on lupin row crops, Martin Harries, Jo Walker and Murray Blyth, Department of Agriculture 23. Large plot testing of herbicide tolerance of new lupin lines, Wayne Parker, Department of Agriculture 24. Effect of seed source and simazine rate of seedling emergence and growth, Peter White and Greg Shea, Department of Agriculture 25. The effect of lupin row spacing and seeding rate on a following wheat crop, Martin Harries, Jo Walker and Dirranie Kirby, Department of Agriculture 26. Response of crop lupin species to row spacing, Leigh Smith1, Kedar Adhikari1, Jon Clements2 and Patrizia Guantini3, 1Department of Agriculture, 2CLIMA, The University of Western Australia, 3University of Florence, Italy 27. Response of Lupinus mutabilis to lime application and over watering, Peter White, Leigh Smith and Mark Sweetingham, Department of Agriculture 28. Impact of anthracnose on yield of Andromeda lupins, Geoff Thomas, Kedar Adhikari and Katie Bell, Department of Agriculture 29. Survey of lupin root health (in major production areas), Geoff Thomas, Ken Adcock, Katie Bell, Ciara Beard and Anne Smith, Department of Agriculture 30. Development of a generic forecasting and decision support system for diseases in the Western Australian wheatbelt, Tim Maling1, Art Diggle1,2, Debbie Thackray1, Kadambot Siddique1 and Roger Jones1,2 1CLIMA, The University of Western Australia, 2Department of Agriculture 31.Tanjil mutants highly tolerant to metribuzin, Ping Si1, Mark Sweetingham1,2, Bevan Buirchell1,2 and Huaan Yang l,2 1CLIMA, The University of Western Australia, 2Department of Agriculture 32. Precipitation pH vs. yield and functional properties of lupin protein isolate, Vijay Jayasena1, Hui Jun Chih1 and Ken Dods2 1Curtin University of Technology, 2Chemistry Centre 33. Lupin protein isolation with the use of salts, Vijay Jayasena1, Florence Kartawinata1,Ranil Coorey1 and Ken Dods2 1Curtin University of Technology, 2Chemistry Centre 34. Field pea, Mark Seymour, Department of Agriculture 35. Breeding highlights Kerry Regan1,2, Tanveer Khan1,2, Stuart Morgan1 and Phillip Chambers1 1Department of Agriculture, 2CLIMA, The University of Western Australia 36. Variety evaluation, Kerry Regan1,2, Tanveer Khan1,2, Jenny Garlinge1 and Rod Hunter1 1Department of Agriculture, 2CLIMA, The University of Western Australia 37. Days to flowering of field pea varieties throughout WA Mark Seymour1, Ian Pritchard1, Rodger Beermier1, Pam Burgess1 and Dr Eric Armstrong2 Department of Agriculture, 2NSW Department of Primary Industries, Wagga Wagga 38. Semi-leafless field peas yield more, with less ryegrass seed set, in narrow rows, Glen Riethmuller, Department of Agriculture 39. Swathing, stripping and other innovative ways to harvest field peas, Mark Seymour, Ian Pritchard, Rodger Beermier and Pam Burgess, Department of Agriculture 40. Pulse demonstrations, Ian Pritchard, Wayne Parker, Greg Shea, Department of Agriculture 41. Field pea extension – focus on field peas 2005, Ian Pritchard, Department of Agriculture 42. Field pea blackspot disease in 2005: Prediction versus reality, Moin Salam, Jean Galloway, Pip Payne, Bill MacLeod and Art Diggle, Department of Agriculture 43. Pea seed-borne mosaic virus in pulses: Screening for seed quality defects and virus resistance, Rohan Prince, Brenda Coutts and Roger Jones, Department of Agriculture, and CLIMA, The University of Western Australia 44. Yield losses from sowing field peas infected with pea seed-borne mosaic virus, Rohan Prince, Brenda Coutts and Roger Jones, Department of Agriculture, and CLIMA, The University of Western Australia 45. Desi chickpea, Wayne Parker, Department of Agriculture 46. Breeding highlights, Tanveer Khan 1,2, Pooran Gaur3, Kadambot Siddique2, Heather Clarke2, Stuart Morgan1and Alan Harris1, 1Department of Agriculture2CLIMA, The University of Western Australia, 3International Crop Research Institute for Semi Arid Tropics (ICRISAT), India 47. National chickpea improvement program, Kerry Regan1, Ted Knights2 and Kristy Hobson3,1Department of Agriculture, 2Agriculture New South Wales 3Department of Primary Industries, Victoria 48. Chickpea breeding lines in CVT exhibit excellent ascochyta blight resistance, Tanveer Khan1,2, Alan Harris1, Stuart Morgan1 and Kerry Regan1,2, 1Department of Agriculture, 2CLIMA, The University of Western Australia 49. Variety evaluation, Kerry Regan1,2, Tanveer Khan1,2, Jenny Garlinge2 and Rod Hunter2, 1CLIMA, The University of Western Australia 2Department of Agriculture 50. Desi chickpeas for the wheatbelt, Wayne Parker and Ian Pritchard, Department of Agriculture 51. Large scale demonstration of new chickpea varieties, Wayne Parker, MurrayBlyth, Steve Cosh, Dirranie Kirby and Chris Matthews, Department of Agriculture 52. Ascochyta management with new chickpeas, Martin Harries, Bill MacLeod, Murray Blyth and Jo Walker, Department of Agriculture 53. Management of ascochyta blight in improved chickpea varieties, Bill MacLeod1, Colin Hanbury2, Pip Payne1, Martin Harries1, Murray Blyth1, Tanveer Khan1,2, Kadambot Siddique2, 1Department of Agriculture, 2CLIMA, The University of Western Australia 54. Botrytis grey mould of chickpea, Bill MacLeod, Department of Agriculture 55. Kabuli chickpea, Kerry Regan, Department of Agriculture, and CLIMA, The University of Western Australia 56. New ascochyta blight resistant, high quality kabuli chickpea varieties, Kerry Regan1,2, Kadambot Siddique2, Tim Pope2 and Mike Baker1, 1Department of Agriculture, 2CLIMA, The University of Western Australia 57. Crop production and disease management of Almaz and Nafice, Kerry Regan and Bill MacLeod, Department of Agriculture, and CLIMA, The University of Western Australia 58. Faba bean,Mark Seymour, Department of Agriculture 59. Germplasm evaluation – faba bean, Mark Seymour1, Tim Pope2, Peter White1, Martin Harries1, Murray Blyth1, Rodger Beermier1, Pam Burgess1 and Leanne Young1,1Department of Agriculture, 2CLIMA, The University of Western Australia 60. Factors affecting seed coat colour of faba bean during storage, Syed Muhammad Nasar-Abbas1, Julie Plummer1, Kadambot Siddique2, Peter White 3, D. Harris4 and Ken Dods4.1The University of Western Australia, 2CLIMA, The University of Western Australia, 3Department of Agriculture, 4Chemistry Centre 61. Lentil,Kerry Regan, Department of Agriculture, and CLIMA, The University of Western Australia 62. Variety and germplasm evaluation, Kerry Regan1,2, Tim Pope2, Leanne Young1, Phill Chambers1, Alan Harris1, Wayne Parker1 and Michael Materne3, 1Department of Agriculture 2CLIMA, The University of Western Australia, 3Department of Primary Industries, Victoria Pulse species 63. Land suitability for production of different crop species in Western Australia, Peter White, Dennis van Gool, and Mike Baker, Department of Agriculture 64. Genomic synteny in legumes: Application to crop breeding, Huyen Phan1, Simon Ellwood1, J. Hane1, Angela Williams1, R. Ford2, S. Thomas3 and Richard Oliver1,1Australian Centre of Necrotrophic Plant Pathogens, Murdoch University 2BioMarka, School of Agriculture and Food Systems, ILFR, University of Melbourne 3NSW Department of Primary Industries 65. ALOSCA – Development of a dry flow legume seed inoculant, Rory Coffey and Chris Poole, ALOSCA Technologies Pty Ltd 66. Genetic dissection of resistance to fungal necrotrophs in Medicago truncatula, Simon Ellwood1, Theo Pfaff1, Judith Lichtenzveig12, Lars Kamphuis1, Nola D\u27Souza1, Angela Williams1, Emma Groves1, Karam Singh2 and Richard Oliver1 1Australian Centre of Necrotrophic Plant Pathogens, Murdoch University, 2CSIRO Plant Industry APPENDIX I: LIST OF COMMON ACRONYM

Wykorzystanie zmiennosci markerow izoenzymatycznych do charakterystyki genotypow odmian grochu [Pisum sativum L.]

Analizę polimorfizmu izoenzymów zastosowano do charakterystyki zmienności genetycznej i identyfikacji odmian hodowlanych grochu. Wybrane linie z banku genów Pisum reprezentowały wszystkie aktualnie zarejestrowane odmiany. Przebadano zmienność 10 systemów enzymatycznych w 21 odmianach grochu biało kwitnącego i 12 barwnie kwitnącego. Polimorfizm wewnątrzodmianowy przynajmniej jednego locus obserwowano w 9 odmianach. Wykryty zakres zmienności izoenzymatycznej 11 loci pozwolił na rozróżnienie wszystkich odmian grochu biało kwitnącego, natomiast identyfikacja wszystkich odmian grochu barwnie kwitnącego wymagała obserwacji polimorfizmu 14 loci. Wyznaczone współczynniki podobieństwa pomiędzy odmianami wykorzystano do dyskusji nad ich pokrewieństwem i zakresem zmienności puli genowej stosowanej w hodowli twórczej. Uzyskane wyniki wzbogaciły charakterystykę genotypów odmian stanowiących część materiałów kolekcyjnych. Tego rodzaju informacje mogą być wykorzystane w pracach hodowlanych do identyfikacji i kontroli czystości odmian grochów podczas produkcji i dystrybucji materiałów nasiennych.Isozyme polymorphism analysis was used for genetic variability characterization and identification of pea cultivars. Lines chosen from the Gene Bank of Pisum represented actually registered Polish cultivars. Variability of 10 enzyme systems was examined among 21 white flowering and 12 colour flowering pea cultivars. Intravarietal polymorphism at least of one locus was observed in 9 cultivars. Detected range of isozyme variability of 11 loci enabled to distinguish all white flowering pea cultivars but the identification of all colour flowering pea cultivars required 14 loci polymorphism observation. Calculated coefficients of similarity among the cultivars were used for discussion on their relationship and on the variability range of gene pool applied in creative breeding. Obtained results enriched the cultivars characteristics of cultivar genotypes which are a part of collected materials. This kind of information can be used in breeding projects for identification and pea cultivar purity control during production and distribution of seed materials

Linkages in Pisum L. VII. Locus for the sterile gene calf [cabbage leaf]

Genetical analyses were conducted to find linkages and the locus of the gene calf on the Pisum chromosome map. The recessive, pleiotropic gene calf (enlarged and undulated leaflets, stipules, flowers and pods, plant sterile), artificially induced (the initial line-Large Podded G-20, the mutagene-DES and NMU) was described by Sharma in 1975. An identical mutant gene at the same locus was isolated in our research (the initial line - cv. Pegro, the mutagene - fast neutrons). Two lines were included in the Pisum gene bank - the type line for the gene calf - Wt 15873 and the representative line - Wt 16024. In linkage studies the representative line was crossed with tester lines bearing gene markers. Analyses of dihybrid segregation in F₂ generations revealed linkages of the gene calf with chromosome 2 markers. Two isozymic markers helped to reveal the calf locus on chromosome 2 with the following gene order: Orp - Calf - K - Pgm-p - Fum. This is in agreement with the current Pisum linkage map

Zmiennosc loci izoenzymatycznych w kolekcji podstawowej rodzaju Pisum

Zgromadzone w krajowej kolekcji Pisum w Wiatrowie zasoby obejmują dzikie populacje, odmiany uprawne i miejscowe, wyselekcjonowane mutanty spontaniczne i indukowane oraz linie pochodzące z krzyżowań w programach hodowlanych i badawczych. Utworzono z nich kolekcję podstawową rodzaju Pisum (266 obiektów), reprezentującą dotychczas opisaną zmienność monogeniczną w genotypach typowych dla alleli, liniach testowych z genami - markerami poszczególnych chromosomów oraz z nowymi genami. Dla zwiększenia przydatności kolekcji podstawowej Pisum zgromadzonej w Wiatrowie scharakteryzowano zakres zmienności loci izoenzymatycznych. Analizowano polimorfizm 18 loci izoenzymatycznych metodą rozdziału elektroforetycznego na żelu skrobiowym. Wszystkie badane loci enzymatyczne wykazały obecność 2-4 allozymów. Niektóre z wykrytych allozymów występowały bardzo rzadko, najczęściej w populacjach należących do dzikich gatunków Pisum. Zakres obserwowanej zmienności izoenzymatycznej w poszczególnych grupach obiektów posłużył do obliczenia częstości alleli i oceny polimorfizmu każdej z grup oraz porównania zmienności pomiędzy grupami. Uzyskane wyniki wykorzystano do dyskusji na temat wykorzystania markerów izoenzymatycznych do charakterystyki genotypu obiektów kolekcyjnych.The Pisum national collection at Wiatrowo covers wild populations, culti- vars and land races, selected spontaneous and induced mutants, as well as cross derivatives from breeding and research programs. There has been constituted the core collection of Pisum genus (266 accesions), representing hitherto described monogenic variability in typical genotypes for alleles, tester lines with marker genes for particular chromosomes, and with new genes. To increase the usefulness of Pisum core collection gathered at Wiatrowo, the range of isozyme loci variability was characterized. The polymorphism of 18 isozyme loci was analyzed using electrophoretic separation on starch gel. All tested loci showed the presence of 2-4 allozymes. Some of them occurred very rarely, usually in populations belonging to the wild species of Pisum. The range of observed isozyme variability in particular groups of accesions was used for statistical calculations of allele frequency and for estimating polymorphism in each group as well as for comparison of variability among groups. The results were used for discussion on utility of isozyme markers for genotype characterization of collection accessions

A dense reference map of the Lupinus Angustifolius L. Genome: A foundation for building lupin genome research

A genetic map provides a foundation on which genomic research can be built, linking together otherwise disconnected studies and forming the basis on which to build physical and cytogenetic maps and conduct whole genome sequencing. As part of a wide collaborative effort, we developed a dense genetic map of the narrow-leafed lupin (Lupinus angustifolius L.) comprising 1073 molecular markers, 6 domestication trait loci and an Anthracnose resistance locus distributed across 20 major linkage groups. This map will be used to investigate the extent of genome conservation between narrow-leafed lupin and the model legume species, Medicago truncatula and Lotus japonicus. We discuss the potential applications of this reference map in lupin genetic and genomic research