Francis Zee

A primitive Y chromosome in papaya marks incipient sex chromosome evolution

Many diverse systems for sex determination have evolved in plants and animals. One involves physically distinct (heteromorphic) sex chromosomes (X and Y, or Z and W) that are homozygous in one sex (usually female) and heterozygous in the other (usually male). Sex chromosome evolution is thought to involve suppression of recombination around the sex determination genes, rendering permanently heterozygous a chromosomal region that may then accumulate deleterious recessive mutations by Mullers ratchet, and fix deleterious mutations by hitchhiking as nearby favourable mutations are selected on the Y chromosome. Over time, these processes may cause the Y chromosome to degenerate and to diverge from the X chromosome over much of its length; for example, only 5% of the human Y chromosome still shows X–Y recombination. Here we show that papaya contains a primitive Y chromosome, with a male-specific region that accounts for only about 10% of the chromosome but has undergone severe recombination suppression and DNA sequence degeneration. This finding provides direct evidence for the origin of sex chromosomes from autosomes.

The pineapple genome and the evolution of CAM photosynthesis

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

A phylogenetic analysis of the genus Carica L. (Caricaceae) based on restriction fragment length variation in a cpDNA intergenic spacer region

The phylogenetic relationships among twelve wild and cultivated species of Carica (Caricaceae) were analyzed using restriction fragment length variation in a 3.2-kb PCR amplified intergenic spacer region of the chloroplast DNA. A total of 138 fragments representing 137 restriction sites accounting for 5.8% of the amplified region were examined. Both parsimony and neighbor joining cluster analyses confirmed the close association among South American wild Carica species. However, cpDNA data did not support the traditional monophyly hypothesis for the evolution of Carica. Further, cpDNA analyses showed two basic evolutionary lineages within the genus Carica, one defined by cultivated C. papaya and another consisting of the remaining wild species from South America in a well resolved but poorly supported monophyletic assemblage. This evolutionary split in Carica strongly suggests that C. papaya diverged from the rest of the species early in the evolution of the genus and evolved in isolation, probably in Central America.

Molecular Diversity of Ralstonia solanacearum Isolated from Ginger in Hawaii

ABSTRACT The genetic diversity of Ralstonia solanacearum strains isolated from ginger (Zingiber officinale) growing on the island of Hawaii was determined by analysis of amplified fragment length polymorphisms (AFLPs). Initially 28 strains of R. solanacearum collected from five host plant species worldwide were analyzed by AFLP. A second analysis was conducted on 55 R. solanacearum strains collected from three ginger farms along the Hamakua Coast of Hawaii, the principle area of ginger cultivation in the state. From the initial analysis, R. solanacearum strains from ginger in Hawaii showed a high degree of similarity at 0.853. In contrast, the average genetic similarity between R. solanacearum strains from heliconia and ginger was only 0.165, and strains from ginger showed little similarity with strains from all other hosts. The second analysis of 55 strains from ginger on different Hawaiian farms confirmed that they were distinct from race 1 strains from tomato. Strains from ginger also showed greater diversity among themselves in the second analysis, and the greatest diversity occurred among strains from a farm where ginger is frequently imported and maintained. Our results provide evidence that R. solanacearum strains from ginger in Hawaii are genetically distinct from local strains from tomato (race 1) and heliconia (race 2).

The origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea

Carica and Vasconcellea are two closely related sister genera in the family Caricaceae, and were once classified as two sections under Carica. Sex chromosomes have been found in papaya and originated approximately 2-3 million years ago. The objectives of this study were to determine whether sex chromosomes have evolved in Vasconcellea. Six X/Y gene pairs were cloned, sequenced and analyzed from three dioecious, one trioecious and one monoecious species of Vasconcellea. The isolation of distinctive X and Y alleles in dioecious and trioecious species of Vasconcellea demonstrated that sex chromosomes have evolved in this genus. Phylogenetic analyses indicated a monophyletic relationship between the X/Y alleles of Carica and those of Vasconcellea. Distinctive clusters of X/Y alleles were documented in V. parviflora and V. pulchra for all available gene sequences, and in V. goudatinana and V. cardinamarcensis for some X/Y alleles. The X and Y alleles within each species shared most single nucleotide polymorphism haplotypes that differed from other species. Limited evidence of gene conversion was documented among the X/Y alleles of some species, but was not sufficient to cause the evolutionary patterns reported herein. The Carica and Vasconcellea sex chromosomes may have originated from the same autosomes bearing the X allelic form that still exist in the monoecious species V. monoica, and have evolved independently after the speciation event that separated Carica from Vasconcellea. Within Vasconcellea, sex chromosomes have evolved at the species level, at least for some species.

Isozyme variation in cultivated and wild pineapple

SummaryIsozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs. Considerable variation exists within and between species of Ananas. Sixty-six distinct zymotypes were identified. Multivariate analyses of isozyme variation indicated that A. comosus contains five genetically diverse groups that do not match perfectly with the traditional varietal groups. Isozyme evidence also suggests that A. erectifolius is a conspecific variant of A. comosus, and that among other wild species, A. ananassoides is more closely related to A. comosus than A. bracteatus. Pseudananas is genetically distinct from all species of Ananas. It is evident from our study that differentiation among the species of Ananas may be due to ecological isolation rather than genetic divergence with breeding barriers and therefore may represent a species complex.

Intra-specific DNA polymorphism in pineapple (Ananas comosus (L.) Merr.) assessed by AFLP markers

Pineapple (Ananas comosus (L.) Merr.) cultivars, often derived from somatic mutations, are propagated vegetatively. It has been suggested by isozyme data that there is little genetic variation among Smooth Cayenne cultivars. A thorough investigation of the genetic variation within the cultivated speciesAnanas comosus, particularly among commercial cultivars, will provide critical information needed for crop improvement and cultivar protection. One-hundred and forty-eight accessions ofA. comosus and 14 accessions of related species were evaluated with AFLP markers. The average genetic similarity ofA. comosus was 0.735 ranging from 0.549 to 0.972, suggesting a high degree of genetic variation within this species. With AFLP markers, discrete DNA fingerprints were detected for each commercial cultivar, breeding line, and intra-specific hybrid. Self-incompatibility, high levels of somatic mutation, and intraspecific hybridization may account for this high degree of variation. However, major cultivar groups of pineapple, such as Cayenne, Spanish, and Queen, could not be distinctively separated. These cultivar groups are based on morphological similarity, and the similar appearance can be caused by a few mutations that occurred on different genetic background. Our results suggest that there is abundant genetic variation within existing pineapple germplasm for selection, and discrete DNA fingerprinting patterns for commercial cultivars can be detected for cultivar protection. The genetic diversity and relationships of fourAnanas species are also discussed.

Genetic relationships of macadamia cultivars and species revealed by AFLP markers

World production of macadamia nuts is based on two species, the smooth shell Macadamia integrifolia Maiden and Betche, and the rough shell Macadamiatetraphylla L.A.S. Johnson, and their hybrids. One hundred and five AFLP markers were used to analyze 26 macadamia accessions representing four species: M. integrifolia, M. tetraphylla,M. ternifolia, and M. hildebrandii as well as a wild relative,Hicksbeachia pinnatifolia (rose nut).Each macadamia accession showed distinct AFLP fingerprints indicating a significant level of genetic variation in this macadamia germplasm collection. The fourMacadamia species included in this study were clearly separated using cluster analysis with AFLP marker data. Based on a single accession, the separation of M. ternifolia from M. integrifoliasuggested the relatively distant genetic relationship between these two species and casts doubts on the notion that the M. ternifolia may be a variant of M. integrifolia. Within the major cluster ofM. integrifolia, nine established smooth shell cultivars were separated into two sub-clusters, suggesting the heterozygous nature of the original gene pool that had contributed to macadamia variety improvement programs. M. hildebrandii and H. pinnatifoliaformed a distinct cluster and share dramatically less genetic similarity with the other Macadamia species. Additional data would be needed to clarify the phylogenetic nature and status of M. hildebrandii in the genus Macadamia.

Emerging Fruit Crops

Hundreds of fruit species with commercial potential are currently in a status of low economic importance. Some, such as quince, pomegranate, and figs, have been cultivated for thousands of years. Others have only been locally collected and consumed from wild populations of the fruit. The development of these underappreciated crops depends on a range of factors including the cultivation limitations, yields, uses of the fruit, and marketing potential. Although initially many crops are developed using selections from the wild, as they are developed, breeding programs work toward improving the crop for both production and quality. This chapter examines nine emerging crops chosen among hundreds of potential crops which are currently showing much promise as commercial crops. These include five tree fruits, namely, pawpaw, quince, mayhaw, pomegranate, and fig, and four berry crops, namely, blue honeysuckle, elder, goji, and ‘ōhelo.

Development of Microsatellite Loci in Artocarpus altilis (Moraceae) and Cross-Amplification in Congeneric Species

Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.