RAPD primer screening as a preliminary study to analyze the genetic diversity of Citrus spp. in South Sulawesi, Indonesia

Abstract The typical citrus germplasm collection in South Sulawesi has not been thoroughly characterized, especially in several citrus development centers, which have begun to be promoted again after the decline in productivity due to CVPD infection. The study of citrus diversity is very important to support future citrus breeding programs. Random amplified polymorphic DNA (RAPD) has been widely used for the analysis of genetic diversity among species in populations. In this study, 23 RAPD primers were used on Citrus cultivated in Selayar and Pangkep Regencies, which are citrus development areas in South Sulawesi. A total of 19 primers (OPA-05, OPA-09, OPA-17, OPC-09, OPC-17, OPE-04, OPH-04, OPH-15, OPN-14, 0PN-16, OPR-08, OPR-20, OPW-06, OPW-09, OPX-07, OPX-11, OPX-17, UBC-18, and UBC-51) can form polymorphic bands in randomly selected DNA samples. Monomorphic bands were formed by OPA-12 and OPD-07 primer in 12 samples. The primers OPX-13 and OPX-16 produced unclear bands. These 19 primers can be used to amplify DNA and determine the genetic diversity of Citrus in further analysis.

Download Full-text

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Download Full-text

Genetic diversity of table grape based on morphoagronomic traits

Scientia Agricola ◽

10.1590/s0103-90162011000100007 ◽

2011 ◽

Vol 68 (1) ◽

pp. 42-49 ◽

Cited By ~ 14

Author(s):

Patrícia Coelho de Souza Leão ◽

Cosme Damião Cruz ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Clustering Analysis ◽

Germplasm Collection ◽

Table Grape ◽

Cluster Method ◽

Breeding Programs ◽

Method Analysis ◽

Vitis Spp ◽

Grape Cultivars

The conservation and characterization of grape (Vitis spp) genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits), and 9 clusters (taking into consideration multicategorical traits). There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.

Download Full-text

Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)

Theoretical and Applied Genetics ◽

10.1007/s00122-006-0255-9 ◽

2006 ◽

Vol 112 (8) ◽

pp. 1519-1531 ◽

Cited By ~ 218

Author(s):

Noelle A. Barkley ◽

Mikeal L. Roose ◽

Robert R. Krueger ◽

Claire T. Federici

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Citrus Germplasm ◽

Simple Sequence

Download Full-text

Evaluation of genetic diversity in 19 Glycine max (L.) Merr. accessions included in the Czech National Collection of soybean genotypes

Czech Journal of Genetics and Plant Breeding ◽

10.17221/6114-cjgpb ◽

2012 ◽

Vol 38 (No. 2) ◽

pp. 69-74 ◽

Cited By ~ 2

Author(s):

M. Baránek ◽

M. Kadlec ◽

J. Raddová ◽

M. Vachůn ◽

M. Pidra

Keyword(s):

Genetic Diversity ◽

Glycine Max ◽

Random Amplified Polymorphic Dna ◽

Breeding Programs ◽

Low Level ◽

Low Degree ◽

Soybean Genotypes ◽

Glycine Max L ◽

Rapd Polymorphism ◽

Selection Of

The random amplified polymorphic DNA (RAPD) technique was used to evaluate both genetic diversity among 19 soybean accessions included in the Czech National Collection of Soybean Genotypes and their potential as a new source of genetic variations for soybean breeding programs. Only 22 of all the 40 random primers used in RAPD reactions showed polymorphism acceptable for an effective characterisation of these accessions. Altogether 122 highly reproducible RAPD fragments were generated, 55 of them were polymorphic (46%). However, because of the previously observed low degree of RAPD polymorphism in the case of Glycine max, fragments with low level of informativeness were evaluated, too. Presented results enable the selection of genetically distinct individuals. Such information may be useful to breeders willing to use genetically diverse introductions in soybean improvement process. 

Download Full-text

Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

Australian Journal of Agricultural Research ◽

10.1071/ar01178 ◽

2002 ◽

Vol 53 (6) ◽

pp. 629 ◽

Cited By ~ 17

Author(s):

J. M. Musial ◽

K. E. Basford ◽

J. A. G. Irwin

Keyword(s):

Genetic Diversity ◽

Population Genetic ◽

Random Amplified Polymorphic Dna ◽

Population Diversity ◽

Breeding Programs ◽

Population Genetic Diversity ◽

Medicago Sativa L ◽

Components Analysis ◽

High Level ◽

Selection Of

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

Download Full-text

Genetic diversity in sunflower (Helianthus annuus L.) as revealed by random amplified polymorphic DNA analysis

Australian Journal of Agricultural Research ◽

10.1071/ar9941319 ◽

1994 ◽

Vol 45 (7) ◽

pp. 1319 ◽

Cited By ~ 23

Author(s):

WR Lawson ◽

RJ Henry ◽

JK Kochman ◽

GA Kong

Keyword(s):

Genetic Diversity ◽

Ribosomal Rna ◽

Dna Analysis ◽

Random Amplified Polymorphic Dna ◽

Efficient Tool ◽

Breeding Programs ◽

Breeding Lines ◽

Sunflower Genome ◽

Pair Wise Comparison ◽

Selection Of

A cross-section of sunflower genotypes grown in Australia including commercial cultivars (Suncross 40R, Hysun 33, Hysun 45CQ, Advance, DK3873), breeding lines (Sunfola, S37- 388, PhRR3, HA-R2, MC29, MC69, S37-388RR), wild sunflower varieties (H. annuus, H. argophyllus), a distantly related species (Tithonia diversifolia), and a hexaploid/diploid cross (H. tuberosus L.x H. annuus L.) were assessed for genetic diversity using RAPD (Random Amplified Polymorphic DNA) analysis. A considerable amount of polymorphism was revealed. Of the total of 158 markers amplified, 133 were polymorphic for at least one pair-wise comparison within the 16 genotypes. Overall, 33% dissimilarity was detected, with an average of 27% dissimilarity revealed among the hybrids and breeding lines, which exhibited 38% dissimilarity to the wild varieties H. annuus and H. tuberosus, and 51% dissimilarity to Tithonia and H. tuberosus x H, annuus. PCR of the 5S ribosomal RNA gene spacer region did not reveal any polymorphisms among the cultivated and breeding lines, but did distinguish between H. tuberosus and the other wild species. This survey of a selection of sunflower genotypes indicates that the genetic base of domesticated sunflower may be quite wide. These results suggest that RAPD methodology will provide an efficient tool for the analysis of the sunflower genome, in particular in breeding programs.

Download Full-text

Genetic characterization of the Moxotó goat breed using RAPD markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2005000300006 ◽

2005 ◽

Vol 40 (3) ◽

pp. 233-239 ◽

Cited By ~ 12

Author(s):

Rejane Rodrigues de Oliveira ◽

Andréa Alves do Egito ◽

Maria Norma Ribeiro ◽

Samuel Rezende Paiva ◽

Maria do Socorro Maués Albuquerque ◽

...

Keyword(s):

Genetic Variability ◽

Rapd Markers ◽

Genetic Characterization ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

Goat Breed ◽

Breeding Programs ◽

Analysis Of Molecular Variance ◽

Polymorphic Bands

The objective of this study was to verify the genetic diversity between and within seven populations of Moxotó goat (n = 264) from the States of Pernambuco, Paraíba and Rio Grande do Norte, using RAPD (Random Amplified Polymorphic DNA). Moxotó, as well as other naturalized breeds, suffers genetic losses due to the indiscriminate miscegenation with breeds raised in the Northeast Region of Brazil. The genetic characterization of these genetic resources is essential to conservation and breeding programs. DNA was extracted from lymphocytes using a non-organic protocol. The 16 primers used were selected from 120 decamer oligonucleotide primers and generated 56 polymorphic bands. The analysis of molecular variance (AMOVA) showed that the greater part of total genetic variability (71.55%) was due to differences between individuals within populations, while 21.21% was among populations. The analysis of variance among the pairs of populations demonstrated that the populations located in Floresta, PE x Angicos, RN presented a smaller value of intrapopulational differentiation (8.9%), indicating low genetic variability among them. Nei's genetic distances varied between 0.0546 and 0.1868 in the populations. The dendrogram generated showed that the Canindé breed, used as outgroup, clustered with the populations of Moxotó, indicating a possible common origin of the naturalized goat breeds.

Download Full-text

Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

Current Agriculture Research Journal ◽

10.12944/carj.5.2.01 ◽

2017 ◽

Vol 5 (2) ◽

pp. 149-159 ◽

Cited By ~ 1

Author(s):

Y. El Kharrassi ◽

M.A. Mazri ◽

M.H. Sedra ◽

A. Mabrouk ◽

B . Nasser ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Morphological Traits ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Group Method ◽

Rapd Primer ◽

Opuntia Spp ◽

Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

Download Full-text

Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers

Horticultura Brasileira ◽

10.1590/s0102-05362012000100019 ◽

2012 ◽

Vol 30 (1) ◽

pp. 112-118 ◽

Cited By ~ 1

Author(s):

Maria do Desterro M dos Santos ◽

Carlos Francisco Ragassi ◽

Maria Esther de N Fonseca ◽

Anne Gizelle R Buzar ◽

Valter R Oliveira ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Germplasm Collection ◽

Rio Grande ◽

Breeding Programs ◽

Tropical Regions ◽

Low Genetic Diversity ◽

Tropical Conditions ◽

Average Similarity ◽

Onion Germplasm

Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7%) were monomorphic and 102 (16.3%) were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical'), for which the genetic origin (with few exceptions) can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in relation to main 'Baia Periforme' group. This germplasm displayed a relatively low genetic diversity, with the predominance of materials originated from the base population 'Baia Periforme'. There are, however, some accessions, which can add genetic diversity to this germplasm and they can be exploited by onion breeding programs aiming to develop cultivars for tropical regions of the world.

Download Full-text