A male and hermaphrodite specific RAPD marker for papaya ( Carica papayaL.)

The random amplified polymorphic DNA (RAPD) technique was used to determine the sex of a dioecious species, Carica papaya L., with three sex types, male, female and hermaphrodite. A 450 bp marker fragment, named PSDM(Papaya Sex Determination Marker), exists in all male and hermaphrodite plants but not in the female plants so far analyzed. The DNA sequence of PSDM exhibited no significant similarity to previously reported sequences. A sequence-characterized amplified region (SCAR) marker, SCARps, was developed from PSDM to determine the sex of papaya. Southern hybridization, using PSDM as a probe, showed that PSDM exists in the male and hermaphrodite genomes, but not in the female genome. This result strongly suggests that PSDM is located on the chromosome region that is specific to the male and the hermaphrodite. SCARps is a suitable marker for the precise and rapid diagnosis of sex in papaya. Received: 1 February 2001 / Accepted: 22 May 2001     

Rapid sex identification of papaya (Carica papaya) using multiplex loop-mediated isothermal amplification (mLAMP)

Papaya (Carica papaya L.) is established as a cash crop throughout the tropical and subtropical regions due to its easy adaptation to diverse agricultural conditions, high yields, and prompt returns. The sex types of papaya plants are hermaphrodite, male, and female. Among them, hermaphroditic plants are the major type in papaya production, because the fruit has commercial advantages over that of the other sexes. Sex inheritance in papaya is determined by the M and M ^h dominant alleles in males and hermaphrodites, respectively, and a recessive m allele in females. Currently, all hermaphrodite seeds are not available due to the lethality of dominant homozygosity. Therefore, in this study, six male–hermaphrodite-specific markers were developed for a rapid sex identification using multiplex loop-mediated isothermal amplification (mLAMP) to efficiently and precisely select hermaphroditic individuals in the seedling or early growth stage. The LM1-LAMP assay consisted of two sex-LAMP reactions for amplifying two male-specific markers (T12 and Cpsm90) in one reaction, and showed several advantages in terms of a rapid reaction time (<1 h), isothermal conditions (less equipment required), a high efficiency (0.5 ng of DNA required in the reaction mixture), and an economical reaction system (5 μl in volume). The established method can be easily performed in the field by visual inspection and facilitates the selection of all hermaphroditic individuals in papaya production.     

A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings

Female plants of several dioecious angiosperms are commercially valued for production of fruits or seeds, viz. papaya, nutmeg, pistachio, kiwi fruit and jojoba. To make the cultivation profitable it is necessary to grow more female than male plants. To discriminate between male and female plants, sex-specific molecular markers have been identified in a few dioecious species such as Silene and pistachio. However, accurate and convenient sex diagnostic methods for early sexing of seedlings are not available to date. For the first time, we report here a PCR-based Seedling Sex Diagnostic Assay (SSDA) specially designed for early sexing of papaya seedlings. We have developed a male-specific SCAR marker in papaya by cloning a male-specific RAPD (831 bp) fragment and designing longer primers. The potential of this SCAR marker is further exploited to develop a simplified and highly accurate sex diagnostic assay by (1) including an internal PCR control, (2) following a single-step DNA extraction procedure and (3) optimising the PCR conditions to simultaneously amplify male-specific and control bands from the crude leaf extract. This diagnostic approach would be of great commercial significance to papaya growers as well as to seed companies and plant nurseries for early identification of female seedlings of dioecious species. In principle, this experimental design could be easily applied to molecular analysis of any agriculturally important trait for which specific DNA probes could be identified and hence opens new avenues of research in the field of genetic diagnostics of plants.     

Genome of papaya, a fast growing tropical fruit tree

Papaya is a major fruit crop in tropical and subtropical regions worldwide. It has long been recognized as a nutritious and healthy fruit rich in vitamins A and C. Its small genome, unique aspects of nascent sex chromosomes, and agricultural importance are justifications for sequencing the genome. A female plant of the transgenic variety SunUp was selected for sequencing its genome to avoid the complication of assembling the XY chromosomes in a male or hermaphrodite plant. The draft genome revealed fewer genes than sequenced genomes of flowering plants, partly due to its lack of genome wide duplication since the ancient triplication event shared by eudicots. Most gene families have fewer members in papaya, including significantly fewer disease resistance genes. However, striking amplifications in gene number were found in some functional groups, including MADS-box genes, starch synthases, and volatiles that might affect the speciation and adaptation of papaya. The draft genome was used to clone a gene controlling fruit flesh color and to accelerate the construction of physical maps of sex chromosomes in papaya. Finishing the papaya genome and re-sequencing selected genomes in the family will further facilitate papaya improvement and the study of genome and sex chromosome evolution in angiosperms, particularly in Caricaceae.     

Identification of RAPD markers linked to sex determination in guggal [<Emphasis Type="Italic">Commiphora wightii</Emphasis> (Arnott.)] Bhandari

Decamer RAPD primers were tested on dioeceious and hermaphrodite plants of Commiphora wightii to identify sex-specific molecular markers. Sixty different random decamer primers were screened out of which only three primers were found to be associated with sex expression. A ~1,280-bp fragment from the primer OPN06 was found to be present in all the female individuals. Another primer OPN 16 produced a unique ~400-bp amplification product in only hermaphrodite individuals. The third marker, OPA20 amplified a ~1,140-bp fragment from female and hermaphrodite DNAs, but failed to do so from the male plant DNAs.     

Males are cheaper,or the extreme consequence of size/age‐dependent sex allocation: sexist gender diphasy in Fritillaria montana (Liliaceae)

The bulbous geophyte Fritillaria montana is partially self‐compatible and capable of switching gender. Small flowering plants produce only single male flowers, but larger plants produce hermaphrodite or, rarely, male and hermaphrodite flowers. Eight populations in peninsular Italy were sampled to determine the frequency and size distributions of male and hermaphrodite plants, and to determine the relationship of plant size to male and hermaphrodite flower production. Male plants were significantly smaller than hermaphrodites and made up 14.5–47.8% (100% in one small population) of flowering plants within populations. There were no significant differences in male fitness among female‐sterile and hermaphrodite flowers, as they both possessed full and comparable fertilizing power. Therefore, the gender variation observed in F. montana is likely to depend on resource‐dependent sex allocation. From an evolutionary perspective, we highlight the occurrence of similar mechanisms of gender variation in other representatives of the order Liliales. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 323–333.     

Microsatellite (GATA)n reveals sex-specific differences in Papaya

Papaya, an economically important fruit plant, is polygamous in nature. The sex of dioecious papaya plants can be deduced only after they attain reproductive maturity (6–8 months). Normally, 50% of the population in a field is composed of unfruitful male plants and almost 45% of these have to be uprooted at the flowering stage. This unnecessary cultivation of unwanted males leads to wastage of resources, which can be avoided if the sex of the plant is determined at juvenile stage. Morphological and cytological studies conducted so far have failed to differentiate between the various sex forms of papaya. Its dioecious nature, occasional sex-reversal of male flowers and the absence of a heteromorphic pair of sex chromosomes make papaya an interesting system to study sex determination at the molecular level. In the present study, highly informative microsatellite and minisatellite probes were employed to identify sex-specific differences in papaya. Among these, only the microsatellite probe (GATA)₄ demonstrated sex-specific differences in all the cultivars analysed. The diagnostic potential of this microsatellite marker was exploited to sex papaya plants at the seedling stage. This study also indicates that the genetic material of the X and Y chromosomes of papaya is diverging in a sex-specific manner and hence they are in the process of differentiation. Received: 26 February 1999 / Accepted: 25 March 1999     

Yield improvement through female homosexual hybrids and sex genetics of sweet gourd (<Emphasis Type="Italic">Momordica cochinchinensis</Emphasis> Spreng.)

The present research aimed to evaluate the effect of silver nitrate (AgNO₃) on sex modification in sweet gourd (Momordica cochinchinensis Spreng.), and to explore the possibility of sexual crossing between two genetically female plants. Spray applications of AgNO₃ on 30 days’ old female plants induced hermaphrodite flowers. Male plants were insensitive to the AgNO₃ sprays. Application of 500 mg/l AgNO₃ on female plants produced the maximum proportion of induced hermaphrodite flowers. Hermaphrodite flowers appeared 17–21 days after AgNO₃ spray and continued up to 8–17 days, depending upon the concentration of AgNO₃. Pollen grain viability of induced hermaphrodite flowers (93.5%) was similar to pollen grain viability of normal male (95.0%) flowers. Because of higher fruit weight, progenies from female homosexual cross recorded higher yield. The hybrids from such crosses produced only female plants while the hybrids between female and normal male segregated into male and female in an equal proportion, indicating that sex in sweet gourd is controlled by a single factor, male being heterozygous and female being homozygous recessive. Through this technique, elite characters of female genotypes could be combined into a single plant.     

番木瓜性别决定及其鉴定研究新进展

番木瓜有3种基本性别类型,性别遗传较为复杂.就其植株的多型性表现、性别决定及其鉴定研究、连锁遗传图的构建、分子标记辅助选择技术和花器的发育等方面的研究进展进行了综述,并对番木瓜性别鉴定的应用前景做了展望.     

Chromosomal location and gene paucity of the male specific region on papaya Y chromosome

Sex chromosomes in flowering plants evolved recently and many of them remain homomorphic, including those in papaya. We investigated the chromosomal location of papaya’s small male specific region of the hermaphrodite Y (Y^h) chromosome (MSY) and its genomic features. We conducted chromosome fluorescence in situ hybridization mapping of Y^h-specific bacterial artificial chromosomes (BACs) and placed the MSY near the centromere of the papaya Y chromosome. Then we sequenced five MSY BACs to examine the genomic features of this specialized region, which resulted in the largest collection of contiguous genomic DNA sequences of a Y chromosome in flowering plants. Extreme gene paucity was observed in the papaya MSY with no functional gene identified in 715 kb MSY sequences. A high density of retroelements and local sequence duplications were detected in the MSY that is suppressed for recombination. Location of the papaya MSY near the centromere might have provided recombination suppression and fostered paucity of genes in the male specific region of the Y chromosome. Our findings provide critical information for deciphering the sex chromosomes in papaya and reference information for comparative studies of other sex chromosomes in animals and plants. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sex specific expression and distribution of small RNAs in papaya

Background

Regulatory function of small non-coding RNAs (sRNA) in response to environmental and developmental cues has been established. Additionally, sRNA, also plays an important role in maintaining the heterochromatin and centromere structures of the chromosome. Papaya, a trioecious species with recently evolved sex chromosomes, has emerged as an excellent model system to study sex determination and sex chromosome evolution in plants. However, role of small RNA in papaya sex determination is yet to be explored.

Results

We analyzed the high throughput sRNAs reads in the Illumina libraries prepared from male, female, and hermaphrodite flowers of papaya. Using the sRNA reads, we identified 29 miRNAs that were not previously reported from papaya. Including this and two previous studies, a total of 90 miRNAs has been identified in papaya. We analyzed the expression of these miRNAs in each sex types. A total of 65 miRNAs, including 31 conserved and 34 novel mirNA, were detected in at least one library. Fourteen of the 65 miRNAs were differentially expressed among different sex types. Most of the miRNA expressed higher in male flowers were related to the auxin signaling pathways, whereas the miRNAs expressed higher in female flowers were the potential regulators of the apical meristem identity genes. Aligning the sRNA reads identified the sRNA hotspots adjacent to the gaps of the X and Y chromosomes. The X and Y chromosomes sRNA hotspots has a 7.8 and 4.4 folds higher expression of sRNA, respectively, relative to the chromosome wide average. Approximately 75% of the reads aligned to the X chromosome hotspot was identical to that of the Y chromosome hotspot.

Conclusion

By analyzing the large-scale sRNA sequences from three sex types, we identified the sRNA hotspots flanking the gaps of papaya X, Y, and Y^h chromosome. The sRNAs expression patterns in these regions were reminiscent of the pericentromeric region indicating that the only remaining gap in each of these chromosomes is likely the centromere. We also identified 14 differentially expressed miRNAs in male, female and hermaphrodite flowers of papaya. Our results provide valuable information toward understanding the papaya sex determination.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-20) contains supplementary material, which is available to authorized users.     

Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya

The homologous genes FLORICAULA （FLO） in Antirrhinum and LEAFY （LFY） in Arabidopsis are known to regulate the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFY homologs of the two woody tree species： California sycamore （Platanus racemosa） and black cottonwood （Populus trichocarpa）. Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia, but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation in papaya.     

Gender in plants: sex chromosomes are emerging from the fog

Although most plants have flowers with both male and female sex organs, there are several thousands of plant species where male or female flowers form on different individuals. Surprisingly, the presence of well-established sex chromosomes in these dioecious plants is rare. The best-described example is white campion, for which large sex chromosomes have been identified and mapped partially. A recent study presented a comprehensive genetic and physical mapping of the genome of dioecious papaya. It revealed a short male specific region on the Y chromosome (MSY) that does not recombine with the X chromosome, providing strong evidence that the sex chromosomes originated from a regular pair of autosomes. The primitive papaya Y chromosome thus represents an early event in sex chromosome evolution. In this article, we review the current status of plant sex-chromosome research and discuss the advantages of different dioecious models.     

Male‐biased hermaphrodites in a gynodioecious shrub,Daphne jezoensis

Gynodioecy, a state where female and hermaphrodite plants coexist in populations, has been widely proposed an intermediate stage in the evolutionary pathway from hermaphroditism to dioecy. In the gynodioecy–dioecy pathway, hermaphrodites may gain most of their fitness through male function once females invade populations. To test this prediction, comprehensive studies on sex ratio variation across populations and reproductive characteristics of hermaphrodite and female phenotypes are necessary. This study examined the variation in sex ratio, sex expression, flower and fruit production and sexual dimorphism of morphological traits in a gynodioecious shrub, Daphne jezoensis, over multiple populations and years. Population sex ratio (hermaphrodite:female) was close to 1:1 or slightly hermaphrodite‐biased. Sex type of individual plants was largely fixed, but 15% of plants changed their sex during a 6‐year census. Hermaphrodite plants produced larger flowers and invested 2.5 times more resources in flower production than female plants, but they exhibited remarkably low fruit set (proportion of flowers setting fruits). Female plants produced six times more fruits than hermaphrodite plants. Low fruiting ability of hermaphrodite plants was retained even when hand‐pollination was performed. Fruit production of female plants was restricted by pollen limitation under natural conditions, irrespective of high potential fecundity, and this minimised the difference in resources allocated to reproduction between the sexes. Negative effects of previous flower and fruit production on current reproduction were not apparent in both sexes. This study suggests that gynodioecy in this species is functionally close to a dioecious mating system: smaller flower production with larger fruiting ability in female plants, and larger flower production with little fruiting ability in hermaphrodite plants.     

xol-1: a gene that controls the male modes of both sex determination and X chromosome dosage compensation in C. elegans

Loss-of-function mutations in the X-linked gene xol-1 cause the feminization and death of XO animals (normally males) by shifting the sex determination and dosage compensation pathways toward their hermaphrodite modes. XO-specific lethality most likely results from the reduction in X chromosome expression caused by xol-1 mutations. Mutations in genes required for the hermaphrodite mode of dosage compensation suppress lethality but not feminization, and restore X chromosome expression to nearly wild-type levels. Mutations in genes that control the hermaphrodite modes of both sex determination and dosage compensation fully suppress both defects. These interactions suggest that xol-1 is the earliest-acting gene in the known hierarchy controlling the male/hermaphrodite decision and is perhaps the gene nearest the primary sex-determining signal. We propose that the wild-type xol-1 gene product promotes male development by ensuring that genes (or gene products) directing hermaphrodite sex determination and dosage compensation are inactive in XO animals. Interestingly, in addition to feminizing XO animals, xol-1 mutations further masculinize XX animals already partially masculinized.     

Organelle DNA accumulation in the recently evolved papaya sex chromosomes

Sex chromosomes are a pair of specialized chromosomes containing a sex determination region that is suppressed for recombination. Without recombination, Y chromosomes are thought to accumulate repetitive DNA sequences which contribute to their degeneration. A pair of primitive sex chromosomes controls sex type in papaya with male and hermaphrodite determined by the slightly different male-specific region of the Y (MSY) and hermaphrodite-specific region of Y^h (HSY) chromosomes, respectively. Here, we show that the papaya HSY and MSY in the absence of recombination have accumulated nearly 12 times the amount of chloroplast-derived DNA than the corresponding region of the X chromosome and 4 times the papaya genome-wide average. Furthermore, a chloroplast genome fragment containing the rsp15 gene has been amplified 23 times in the HSY, evidence of retrotransposon-mediated duplication. Surprisingly, mitochondria-derived sequences are less abundant in the X and HSY compared to the whole genome. Shared organelle integrations are sparse between X and HSY, with only 11 % of chloroplast and 12 % of mitochondria fragments conserved, respectively, suggesting that the accelerated accumulation of organelle DNA occurred after the HSY was suppressed for recombination. Most of the organelle-derived sequences have divergence times of <7 MYA, reinforcing this notion. The accumulated chloroplast DNA is evidence of the slow degeneration of the HSY.     

How pollinator-mediated mating varies with population size in plants

In most higher plants sexual interactions are mediated by animal pollinators that affect the number and differential reproductive success of mates. The number and sex of breeding individuals in populations are central factors in evolutionary theory, but the quantitative effect of plant population size on pollinator-mediated mating is understudied. We investigated variation in pollen removal (male function) and fruit set (female function) among flowering populations of different size of two bumblebee-and one butterfly-pollinated, rewardless, pollen-limited, hermaphroditic orchid species in Sweden. As the amount of pollen removed from plants by insects (either absolute or proportional) increased, so did the number of pollinations, whereas the proportions of plants with different pollinator-designated functional sex (male, female, hermaphrodite) depended primarily on the ratio between the amount of fruit set and pollen removed within populations. A larger population size was found to have several effects: (1) the total numbers of pollinia removed and fruits set increased; (2) the proportion of pollen removed from plants decreased; (3) the proportion of flowers pollinated decreased in the butterfly-but was not affected in the bumblebee-pollinated species; (4) the ratio between fruits set and pollinia removed increased linearly in the bumblebee-pollinated species but reached a maximum at c. 80 individuals in the butterfly-pollinated species; (5) the numbers of pollinator-designated pure male and hermaphrodite individuals increased; and (6) the variance in pollinium removal, but not fruit set, increased among individuals. These findings empirically verify the basic importance of population size for the mating structure of outcrossing plants, and indicate that selection for female sexual traits is reinforced when population size is smaller while selection for male sexual traits is reinforced when population size is larger.     

CHARACTERIZATION OF GENETIC MARKERS LINKED TO SEX DETERMINATION IN THE HAPLOID‐DIPLOID RED ALGA GRACILARIA CHILENSIS1

Bulk segregant analysis, random amplified polymorphic DNA (RAPD), and sequence characterized amplified region (SCAR) methods were used to identify sex‐linked molecular markers in the haploid‐diploid rhodophyte Gracilaria chilensis C. J. Bird, McLachlan et E. C. Oliveira. One hundred and eighty 10 bp primers were tested on three bulks of DNA: haploid males, haploid females, and diploid tetrasporophytes. Three RAPD primers (OPD15, OPG16, and OPN20) produced male‐specific bands; and one RAPD primer (OPD12), a female‐specific band. The sequences of the cloned putative sex‐specific PCR fragments were used to design specific primers for the female marker SCAR‐D12‐386 and the male marker SCAR‐G16‐486. Both SCAR markers gave unequivocal band patterns that allowed sex and phase to be determined in G. chilensis. Thus, all the females presented only the female band, and all the males only the male band, while all the tetrasporophytes amplified both male and female bands. Despite this sex‐specific association, we were able to amplify SCAR‐D12‐386 and SCAR‐G16‐486 in both sexes at low melting temperature. The differences between male and female sequences were of 8%–9% nucleotide divergence for SCAR‐D12‐386 and SCAR‐G16‐486, respectively. SCAR‐D12‐386 and SCAR‐G16‐486 could represent degenerated or diverged sequences located in the nonrecombining region of incipient sex chromosomes or heteromorphic sex chromosomes with sequence differences at the DNA level such that PCR primers amplify only one allele and not the other in highly specific PCR conditions. Seven gametic progenies composed of 19 males, 19 females, and the seven parental tetrasporophytes were analyzed. In all of them, the two SCAR markers segregated perfectly with sexual phenotypes.