Genetic diversity of Burmese grape (Baccaurea ramiflora Lour.) cultivars and Ha Chau cultivar identification based on DNA barcodes
26-05-2025

Burmese grape (Baccaurea ramiflora Lour.) belongs to the family of Phyllanthaceae and is a fruit crop that originated in northeastern India to southern China and Peninsula Malaysia (POWO 2022).  As a nutritional fruit, the species is not only rich in vitamin C and minerals, but also produces antioxidant compounds (Padayatty et al. 2003; Sundriyal and Sundriyal 2004).  With a blend of sweet and sour, the pulp could be utilized in the food industry due to its economic efficiency and commercial importance. In the Mekong Delta, an indigenous variety of well-known Burmese grapes are Ha Chau, Green, Yellow, Red, and Xiem cultivars.
Ha Chau Burmese grape has light yellow color, thin skin,  long fruit shapes, fruit has  3-4 segments, sweet and sour taste and specific aroma. Ha Chau Burmese grape was selected from  indigenous cultivars by gardeners in Phong Dien district and developed in neighboring areas (Tran and Le 2012).  The cultivar was recognized by the Intellectual Property Office of  Vietnam as a specialty of Phong Dien district,  Can Tho city in 2006 (Nguyen et al. 2018).  Ha Chau Burmese grape has become a typical plant in Phong Dien district, Can Tho city, Vietnam and their plantation is the main income source for many horticulturists.
The propagation of Ha Chau Burmese  grape  is  often through the intercrossing of selected plants with traits of interest. Nevertheless, long-term intraspecific hybridization could lead to inbreeding depression and thus, diminishing genetic background. On  the other hand, cultivar identification with traditional techniques would be restricted due to the similarity in morphological features (Tran and Le 2012; Kodsara et al. 2021). Two popular molecular identification methods are AFLP (amplified fragment length polymorphism) and RAPD (random amplification of polymorphic DNA). However, each method has its limitations, such as the high cost of the AFLP technique and the accuracy of the RAPD technique (Kostamo et al. 2013).  Therefore, the development of DNA based method for Burmese grape cultivar identification is of great potential.
Species-specific DNA barcodes have been an effective and  reliable  approach  for  genetic diversity  evaluation  as well  as cultivar identification.  This  method  provides  a powerful tool  for  distinguishing  various  organisms, including animals, plants,  and microbes at genus or species levels  due  to  the  comparison  of  a  short  and  standardized genetic region (DeSalle and Goldstein 2019). Kodsara et al. (2021)  reported  that  plastid  loci  and rpoC1  could  be utilized  for discrimination of nine  Phyllanthus  species. The combination of barcoding  and  phylogenetic  analysis  indicated that  P.  acidus  was the most genetically distinct  from  the rest of  the analyzed species in the group. At the same time, this  study also  confirmed  the  close  relationship  between two pairs of species P. emblica  -  P. urinaria and  P. emblica -  P.  reticulatus.  Some  DNA  barcodes commonly applied  in plant taxonomy are known  as  matK,  psbA-trnH,  rpoB , rpoC1 ,  psbK- I ,  atpF -H,  trnL - trnF (Kress 2017) . Therefore, this study aimed to characte rize genetic diversity among the five cultivars of Burmese  grape in the Mekong Delta and to distinguish Ha Chau to other cultivars based on DN A barcodes.

Figure 1. Amplicons of 6 DNA barcode loci on 2% agarose gel. Note; M: 100 bp DNA ladder, 1: DXAHG, 2: DDVX, 3: DXVX, 4: DHCVX, 5: CHCVX, 6: DXAVX, 7: CHCOM, 8: DDXOM1, 9: DDXOM2, 10: DXABT, 11: CHC9H, 12: DV9H, (-): Negative control) 

Data analysis Target  sequences  of  Burmese  grapes  amplified  were analyzed with corresponding data in  the  GenBank database to investigate  barcode  sequences. Sequences  were  aligned by Clustal  W algorithm in Bioedit program. The consensus sequence  for each  cultivar  was  created  from  individual sequences,  and  variable  sites were  enumerated. Phylogenetic tree was constructed by Maximum Likelihood method  in MEGA  X  software  (Kumar  et  al.  2018)  with Kimura-2-Parameter  (K2P)  model  and  1000 bootstrap replicates. Other options were followed as default setting.

Data  from  this  finding  illustrated  that the  combination of  five  loci,  namely  matK,  rbcL, trnL-F,  psbA-trnH,  and ITS  indicated accurate  species  resolution  while  the  single rbcL was less effective. Vu et al. (2020) also suggested that combination  of plastid DNA barcodes increased the species identification in  Vietnamese Paphiopedilum  species.  At the genome level,  phylogenetic  tree generated  by  14 chloroplast genomes elucidated that B. ramiflora showed  a closed  genetic  relationship  with  Phyllanthus, Glochidion, and Flueggea species (Hu et al. 2021).
In conclusion, the Burmese grape cultivars had genetic diversity based on the combination rcbL, rpoC1, ycf1b, and psbK-I sequences. This finding supports the idea that the sequence region at atpF-H could be used to distinguish Ha Chau Burmese grape from other cultivars in the Mekong Delta.  Further studies on larger sample sizes and survey sites or the remaining regions should be carried out to investigate the appropriate sequence for identifying Ha Chau cultivar among others.

Nguồn bài viết: DOI: 10.13057/biodiv/d230726 B I OD I V E R SI T A S Volume 23, Number 7, July 2022 Pages: 3513-3520

Ngày đăng: 26-05-2025

Tác giả: Nguyễn Thị Bích Như

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