Copyright zyxwvutsrqp 0 1985 by the Genetics Society of America CHLOROPLAST DNA VARIATION AND EVOLUTION IN PISUM: PATTERNS OF CHANGE AND PHYLOGENETIC ANALYSIS zyxw JEFFREY D. PALMER,' RICHARD A. JORGENSEN' AND WILLIAM F. THOMPSON Carnegie Institution zyxwvut of Washington, Department of Plant Biology, Stanford, Cali$ornia zyx 94305 Manuscript received March 3 1, 1984 Revised copy accepted September 17, 1984 ABSTRACT Variation in 30 chloroplast DNAs, representing 22 wild and cultivated acces- sions in the genus Pisum, was analyzed by comparing fragment patterns pro- duced by 16 restriction endonucleases. Three types of mutations were detected. First, an inversion of between 2.2 kilobase pairs (kb) and 5.2 kb distinguished a population of P. humile from all other Pisum accessions examined. Second, deletions and insertions of between 50 and 1200 base pairs produced small restriction fragment length variations in four regions of the 120-kb chloroplast genome. Two of these regions-one of which is located within the sequence that is inverted in zyxwvutsr P. humile-showed a high degree of size polymorphism, to the extent that size differences were detected between individuals from the same accession. Finally, a total of only 11 restriction site mutations were de- tected among the 165 restriction sites sampled in the 30 DNAs. Based on these results and previous data, we conclude that the chloroplast genome is evolving very slowly relative to nuclear and mitochondrial DNAs. The Pisum chloroplast DNA restriction site mutations define two major lineages: One includes all tested accessions of P. fulvum, which is known to be cytogenetically quite dis- tinct from all other Pisum taxa. The second includes 12 of 13 cultivated lines of the garden pea (P. sativum) and a wild population of P. humile from northern Israel. These observations strongly reinforce an earlier conclusion that the cultivated pea was domesticated primarily from northern populations of P. humile. A 13th P. sativum cultivar has a chloroplast genome that is significantly different from those of the aforementioned lines and somewhat more similar to those of P. elatius and southern populations of P. humile. This observation indicates that secondary hybridization may have occurred during the domesti- cation of the garden pea. HE garden pea, Pisum zyxwvu sativum, occupies a central place in the history of T genetics as the experimental organism that Mendel used in formulating his celebrated principles of inheritance. Moreover, the pea has continued as an object of genetic study and remains to this day one of the genetically best known of the plants (BLIXT 1974; MARX 1977). The garden pea also occupies a prominent place in the history of agriculture as one of the founder crops of zy ' Present address: Division of Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109. * Present address: Advanced Genetic Sciences, 6701 San Pablo Avenue, Oakland, California 94608. Genetics 109: 195-21 3 January, 1985.