Detection of sequence characterized amplified region (SCAR) markers linked to sex expression in <i>Carica papaya</i> L.

Abstract

Carica papaya L. exhibits monoecious and dioecious plants that usually take six months for phenotypic manifestation. Nursery culling aided by sex-specific DNA markers was envisaged to alleviate the unnecessary cost incurred by farmers for maintaining unproductive male plants that contribute to 40-50% of the population. The mechanism of sex determination in papaya has been described as a tri-allelic single gene system with alleles, M 1 -dominant for maleness, M 2 -dominant for hermaphrodism and m-recessive for femaleness with diploid zygotes; M 1 M 1 , M 2 M 2 and M 1 M 2 being inviable. Bulked DNA samples of male, female and hermaphrodite plants were amplified by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) using 100 random primers. Twenty of most promising of these were analyzed among individual sex types. Two sex-specific fragments, OPC09-1.7 and OPE03-0.4 were associated with maleness and hermaphrodism. The segregation of these two markers was analyzed in the F 1 population obtained by selfpollinating a hermaphrodite plant. A linkage was detected between the RAPD markers, OPC09-1.7 and OPE03-0.4 and the male and hermaphrodite sex of papaya plants. These sex-specific RAPD fragments were cloned and sequenced for converting them to more authentic SCAR markers. The Southern blot hybridization of RAPD-PCR products obtained by amplification of female, male and hermaphrodite papaya DNA amplified by OPC09 primer using radio labeled recombinant plasmid detected a polymorphic fragment in male and hermaphrodite papaya sex types. The nucleotide sequence of OPC09-1.7 fragment showed the possibility of developing more authentic SCAR markers to enhance the accurate sex determination of Carica papaya at the nursery stage.

Development of SCAR Marker Linked to Sex Determination Locus in<i> Trichosanthes dioica</i>

“…This may be due to either small size of the fragment obtained during initial characterization or a single base differences or single base mutation at the primer. The result is in agreement with Niroshini et al (2008) in papaya. However, the SCAR marker SCF/R-01 was monomorphic and did not discriminate female from male plants.…”

Molecular characterization of Cuban endemism Carica cubensis Solms using random amplified polymorphic DNA (RAPD) markers

“…Therefore, the availability of an optimized protocol for DNA characterization to estimate the genetic diversity and to ensure genetically representative non-redundant samples is of great interest [41]. In this sense, universal RAPD markers can be a most suitable in the molecular characterization of C. cubensis accessions and to construct efficient core collections as has been described by Bortolini [42] in white clover complementary to the application of more recent developed markers in C. papaya of dominant SPAR (Single primer amplification reaction) [17] and SCAR (sequence characterized amplified region) markers [25], and codominant SSR (Single sequence repeat) markers [43,44].…”

“…This results in differential amplification of regions that vary in primer site sequence resulting in polymorphic amplification products usually analyzed as presence/ absence. These markers have been previously assayed in the molecular characterization of Carica papaya cultivars [15][16][17][18] and some wild related species [14,19,20], the identification of flower sex types [8,[21][22][23][24][25] and development of genetic linkage maps [26]. In addition, to improve the capacity of the molecular characterization assays using these PCR-based markers, multiplex PCR, a variant of the PCR in which more than one target sequence is amplified using more than one pair of primers are being assayed [27][28][29].…”

PCR Detection Assay for Sex Determination in Papaya Using Scar Marker

“…Previous studies have provided preliminary data indicating that random amplifi ed polymorphic DNA (RAPD) markers might be useful for detecting sex expression in papaya (SONDUR et al 1996, SOMSRI et al 1998, NIROSHINI et al 2000, 2008, PARASNIS et al 2000, LEMOS et al 2002, URASAKI et al 2002a, but these reports utilized a relatively small number of plants. However, DEPUTY et al (2002) reported SCAR markers that are specifi c for male and hermaphrodite plants in a large number of plants.…”

“…As the segregation in this case is also 1:1 for female to hermaphrodite, identifi cation at the early stage is desirable. Molecular markers have been studied earlier for sex determination in papaya (SONDUR et al 1996, SOMSRI et al 1998, PARASNIS et al 1999, NIROSHINI et al 2000, 2008, URA-SAKI et al 2002a, b, DEPUTY et al 2002, LEMOS et al 2002. Recently a transcriptomics study has been conducted for sex determination in papaya (URASAKI et al 2012).…”