A. G. Abbott

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

Multiple Models for Rosaceae Genomics

The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.

Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation

Buds are specialized structures that protect fragile meristematic regions during dormancy and are part of the mechanism that plants use to survive unfavorable environmental conditions such as low temperature or dessication stress. The evergrowing (evg) mutant of peach [Prunus persica (L.) Batsch] does not form terminal vegetative buds in response to dormancy-inducing conditions such as short days and low temperatures, and the terminal meristems maintain constant growth (leaf addition and internode elongation). We genetically mapped the evg trait and identified the corresponding genomic region in a wild-type genome. We sequenced and annotated the 132-kb region. Nineteen genes were predicted to be in the sequenced region. Ten of the predicted genes were demonstrated to be expressed in the wild-type germplasm but six of these were not expressed in mutant tissues. These six genes are a cluster of MIKC-type MADS-box transcription factors similar to genes from Ipomoea batatas and Solanum tuberosum MADS-box, which also regulate meristem growth in vegetative tissues. A 41,746-bp deletion is present in this region of the mutant genome which results in the loss of all or part of four of the six MADS-box genes. The six MADS-box genes that are not expressed in the mutant are candidates for the regulation of growth cessation and terminal bud formation in peach in response to dormancy-inducing conditions and have been named dormancy-associated MADS-box (DAM) genes.

Mapping With a Few Plants: Using Selective Mapping for Microsatellite Saturation of the Prunus Reference Map

The concept of selective (or bin) mapping is used here for the first time, using as an example the Prunus reference map constructed with an almond × peach F2 population. On the basis of this map, a set of six plants that jointly defined 65 possible different genotypes for the codominant markers mapped on it was selected. Sixty-three of these joint genotypes corresponded to a single chromosomal region (a bin) of the Prunus genome, and the two remaining corresponded to two bins each. The 67 bins defined by these six plants had a 7.8-cM average length and a maximum individual length of 24.7 cM. Using a unit of analysis composed of these six plants, their F1 hybrid parent, and one of the parents of the hybrid, we mapped 264 microsatellite (or simple-sequence repeat, SSR) markers from 401 different microsatellite primer pairs. Bin mapping proved to be a fast and economic strategy that could be used for further map saturation, the addition of valuable markers (such as those based on microsatellites or ESTs), and giving a wider scope to, and a more efficient use of, reference mapping populations.

Dormancy-associated MADS genes from the EVG locus of peach [Prunus persica (L.) Batsch] have distinct seasonal and photoperiodic expression patterns

Mapping and sequencing of the non-dormant evg mutant in peach [Prunus persica (L.) Batsch] identified six tandem-arrayed DAM (dormancy-associated MADS-box) genes as candidates for regulating growth cessation and terminal bud formation. To narrow the list of candidate genes, an attempt was made to associate bud phenology with the seasonal and environmental patterns of expression of the candidates in wild-type trees. The expression of the six peach DAM genes at the EVG locus of peach was characterized throughout an annual growing cycle in the field, and under controlled conditions in response to a long day–short day photoperiod transition. DAM1, 2, 4, 5, and 6 were responsive to a reduction in photoperiod in controlled conditions and the direction of response correlated with the seasonal timing of expression in field-grown trees. DAM3 did not respond to photoperiod and may be regulated by chilling temperatures. The DAM genes in peach appear to have at least four distinct patterns of expression. DAM1, 2, and 4 are temporally associated with seasonal elongation cessation and bud formation and are the most likely candidates for control of the evg phenotype.

Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica).

*Chilling requirement, together with heat requirement, determines the bloom date, which has an impact on the climatic distribution of the genotypes of tree species. The molecular basis of floral bud chilling requirement is poorly understood, despite its importance to the adaptation and production of fruit trees. In addition, the genetic nature of heat requirement and the genetic interrelationships among chilling requirement, heat requirement and bloom date remain unclear. *A peach (Prunus persica) F(2) population of 378 genotypes developed from two genotypes with contrasting chilling requirements was used for linkage map construction and quantitative trait loci (QTL) mapping. The floral bud chilling and heat requirements of each genotype were evaluated over 2 yr and the bloom date was scored over 4 yr. *Twenty QTLs with additive effects were identified for three traits, including one major QTL for chilling requirement and two major QTLs for bloom date. The majority of QTLs colocalized with QTLs for other trait(s). In particular, one genomic region of 2 cM, pleiotropic for the three traits, overlapped with the sequenced peach EVG region. *This first report on the QTL mapping of floral bud chilling requirement will facilitate marker-assisted breeding for low chilling requirement cultivars and the map-based cloning of genes controlling chilling requirement. The extensive colocalization of QTLs suggests that there may be one unified temperature sensing and action system regulating chilling requirement, heat requirement and bloom date together.

Genetic linkage mapping in peach using morphological, RFLP and RAPD markers.

We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F2 individuals derived from the self-fertilization of four F1 individuals of a cross between ‘New Jersey Pillar’ and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh color, and flower petal color, size and number. The segregation of 65 markers, comprising 46 RFLP loci, 12 RAPD loci and seven morphological loci, was analyzed. Low-copy genomic and cDNA probes were used in the RFLP analysis. The current genetic map for the WV family contains 47 markers assigned to eight linkage groups covering 332 centi Morgans (cM) of the peach nuclear genome. The average distance between two adjacent markers is 8 cM. Linkage was detected between Pillar (Pi) and double flowers (Dl) RFLP markers linked to Pi and flesh color (γ) loci were also found. Eighteen markers remain unassigned. The individuals analyzed for linkage were not a random sample of all F2 trees, as an excess of pillar trees were chosen for analysis. Because of this, Pi and eight other markers that deviated significantly from the expected Mendelian ratios (e.g., 1∶2∶1 or 3∶1) were not eliminated from the linkage analysis. Genomic clones that detect RFLPs in the WV family also detect significant levels of polymorphism among the 34 peach cultivars examined. Unique fingerprint patterns were created for all the cultivars using only six clones detecting nine RFLP fragments. This suggests that RFLP markers from the WV family have a high probability of being polymorphic in crosses generated with other peach cultivars, making them ideal for anchor loci. This possibility was examined by testing RFLP markers developed with the WV family in three other unrelated peach families. In each of these three peach families respectively 43%, 54% and 36% of RFLP loci detected in the WV family were also polymorphic. This finding supports the possibility that these RFLP markers may serve as anchor loci in many other peach crosses.

The high oleate trait in the cultivated peanut [Arachis hypogaea L.]. I. Isolation and characterization of two genes encoding microsomal oleoyl-PC desaturases.

Abstract Plant oils rich in oleate are considered superior products compared to oils rich in polyunsaturated fatty acids. Peanut (Arachis hypogaea L.) is one of the major oilseed crops, and high oleate mutant varieties with as much as 85% oleate have been reported. We examined the possibility that this mutant phenotype resulted from reduction in the activity or the transcript level of microsomal oleoyl-PC desaturase. Two independently generated high oleate mutants, M2-225 and 8-2122, and their partially isogenic lines with a normal oleate phenotype were used in this study. Two cDNA sequences coding for microsomal oleoyl-PC desaturases, ahFAD2A and ahFAD2B, have been isolated from the developing peanut seed with a normal oleate phenotype. Cultivated peanut is an allotetraploid, and sequence comparisons with the genes from the putative diploid progenitor species suggested that ahFAD2A and ahFAD2B are non-allelic, but homeologous genes originating from two different diploid species. Northern analysis showed that the transcripts of oleoyl-PC desaturases are highly abundant in both normal and high oleate peanut seeds in the second stage of development. Differential digestion of the RT-PCR products revealed a restriction site polymorphism between ahFAD2A and ahFAD2B, and allowed us to examine the level of transcript expressed from each gene. The results indicate that ahFAD2A is expressed in both normal and high oleate peanut seeds, but the steady state level of the ahFAD2B transcript is severely reduced in the high oleate peanut varieties. These data suggested that the reduction in ahFAD2B transcript level in the developing seeds is correlated with the high oleate trait.

The high oleate trait in the cultivated peanut [Arachis hypogaea L.]. II. Molecular basis and genetics of the trait

Abstract A peanut variety with high oleate content has previously been described. When this high oleate variety was used in breeding crosses, the F2 segregation ratio of high oleate to normal oleate progeny was 3:1 or 15:1 depending on the normal oleate varieties used in the crosses. These data suggested that the high oleate trait is controlled by two recessive genes, and some peanut varieties differ from the high oleate variety by mutations in one gene, while others differ by mutations in two genes. The objective of this study was to understand the molecular nature of the high oleate trait and the various segregation patterns. In the previous paper in this issue, we reported that the level of transcripts expressed by one (ahFAD2B) of two homoeologous genes for oleoyl-PC desaturases in cultivated peanut is significantly reduced in high oleate varieties. In this report, we examined gene expression by RT-PCR/restriction digestion in a cross that shows a one-gene segregation pattern for the high oleate trait. Our data showed that the severely reduced level of ahFAD2B transcript correlates absolutely with the high oleate phenotype in this cross, suggesting that the single gene difference is correlated with the ahFAD2B transcript level. When we tested the enzyme activity of the proteins encoded by ahFAD2A and ahFAD2B by expression of the cloned sequences in yeast, only the ahFAD2B gene product showed significant oleoyl-PC desaturase activity. These data, combined with the observation that ahFAD2A shows a change (D150N) in a residue that is absolutely conserved among other desaturases, raised the possibility that the ahFAD2A in these normal and high oleate lines is a mutant allele. In support of this hypothesis, we found that another ahFAD2A allele in a normal oleate peanut line does not have the D150N change. This peanut line displays a two-gene-segregation pattern for the high oleate trait. In conclusion, our results suggest that a mutation in ahFAD2A and a significant reduction in levels of the ahFAD2B transcript together cause the high oleate phenotype in peanut varieties, and that one expressed gene encoding a functional enzyme appears to be sufficient for the normal oleate phenotype.

High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.

A high-oleate trait in the cultivated peanut (Arachis hypogaea L.) was reported to rely on the allelic composition of the two homeologous, microsomal oleoyl-PC desaturase genes (ahFAD2A or ahFAD2B). The enzyme activity of either ahFAD2A or ahFAD2B is sufficient for a normal oleate phenotype, and a significant reduction in the levels of ahFAD2B and a mutation in ahFAD2A were reported to be responsible for the high-oleate phenotype in one chemically induced mutant (M2-225) and one derived from a naturally occurring (8-2122) mutant. Here, we report an insertion of the same miniature inverted-repeat transposable element (MITE) in the ahFAD2B gene in another chemically induced mutant (Mycogen-Flavo) and the previously characterized M2-225 mutant. In both cases, this MITE insertion in ahFAD2B causes a frameshift, resulting in a putatively truncated protein sequence in both mutants. The insertion of this MITE in ahFAD2B, in addition to the point mutation in ahFAD2A, appears to be the cause of the high-oleate phenotype in Mycogen-Flavo and M2-225 mutants. Utilizing sequences of the MITE, we developed a DNA marker strategy to differentiate the two insertion-containing mutants from the normal oleate peanut variety (AT-108) and the naturally occurring, high-oleate mutant 8-2122. Reverse transcript-PCR/differential digestion results reveal the expression of both ahFAD2A and ahFAD2B genes in Mycogen-Flavo mutant. This result is in contrast to the observation that ahFAD2B transcripts are greatly reduced in the M2-225 mutant having the MITE insertion further 3′ in ahFAD2B gene.