Displaying publications 1 - 20 of 712 in total

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  1. Muftah Eltariki FE, Tiwari K, Alhoot MA
    F1000Res, 2021;10:895.
    PMID: 34745563 DOI: 10.12688/f1000research.70644.1
    Background: A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. Mortierella is one of the significant genera in this field and contains about hundred species. Moreover, M. alpina is the main single cell oil producer at commercial scale under this genus. Methods: Soil samples from four unique locations of North-East Libya were collected for the isolation of oleaginous Mortierella alpina strains by a serial dilution method. Morphological identification was carried out using light microscopy (Olympus, Japan) and genetic diversity of the isolated Mortierella alpina strains was assessed using conserved internal transcribed spacer (ITS) gene sequences available on the NCBI GenBank database for the confirmation of novelty. The nucleotide sequences reported in this study have been deposited at GenBank (accession no. MZ298831:MZ298835). The MultAlin program was used to align the sequences of closely related strains. The DNA sequences were analyzed for phylogenetic relationships by molecular evolutionary genetic analysis using MEGA X software consisting of Clustal_X v.2.1 for multiple sequence alignment. The neighbour-joining tree was constructed using the Kimura 2-parameter substitution model. Results: The present research study confirms four oleaginous fungal isolates from Libyan soil. These isolates (barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) were discovered and reported for the first time from diverse soil samples of district Aljabal Al-Akhdar in North-East Libya and fall in the class: Zygomycetes; order: Mortierellales. Conclusions: Four oleaginous fungal isolates barcoded as MSU-101, MSU-201, MSU-401 and MSU-501 were identified and confirmed by morphological and molecular analysis. These fungal isolates showed highest similarity with Mortierella alpina species and can be potentialistic single cell oil producers. Thus, the present research study provides insight to the unseen fungal diversity and contributes to more comprehensive Mortierella alpina reference collections worldwide.
    Matched MeSH terms: Genetic Variation
  2. Seri Masran SNA, Ab Majid AH
    J Med Entomol, 2017 11 07;54(6):1453-1462.
    PMID: 28981881 DOI: 10.1093/jme/tjx137
    Matched MeSH terms: Genetic Variation*
  3. Ismail NA, Rafii MY, Mahmud TMM, Hanafi MM, Miah G
    Biomed Res Int, 2019;2019:5904804.
    PMID: 31198786 DOI: 10.1155/2019/5904804
    Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.
    Matched MeSH terms: Genetic Variation*
  4. Nikzad S, Tan SG, Yong Seok Yien C, Ng J, Alitheen NB, Khan R, et al.
    J Med Primatol, 2014 Dec;43(6):433-44.
    PMID: 24930735 DOI: 10.1111/jmp.12130
    The genetic diversity and structure of long-tailed macaques (Macaca fascicularis) in Peninsular Malaysia, a widely used non-human primate species in biomedical research, have not been thoroughly characterized.
    Matched MeSH terms: Genetic Variation*
  5. Noh A, Rafii MY, Saleh G, Kushairi A, Latif MA
    ScientificWorldJournal, 2012;2012:792601.
    PMID: 22701095 DOI: 10.1100/2012/792601
    The performance of 11 oil palm AVROS (Algemene Vereniging van Rubberplanters ter Oostkust van Sumatra) pisiferas was evaluated based on their 40 dura x pisifera (DxP) progenies tested on inland soils, predominantly of Serdang Series. Fresh fruit bunch (FFB) yield of each pisiferas ranged from 121.93 to 143.9 kg palm⁻¹ yr⁻¹ with trial mean of 131.62 kg palm⁻¹ yr⁻¹. Analysis of variance (ANOVA) showed low genetic variability among pisifera parents for most of the characters indicating uniformity of the pisifera population. This was anticipated as the AVROS pisiferas were derived from small population and were inbred materials. However, some of the pisiferas have shown good general combining ability (GCA) for certain important economic traits. Three pisiferas (P1 (0.174/247), P3 (0.174/498), P11 (0.182/308)) were identified of having good GCA for FFB yield while pisiferas P1 (0.174/247), P10 (0.182/348), and P11 (0.182/308) were good combiners for oil-to-bunch ratio (O/B). The narrow genetic base of these materials was the main obstacle in breeding and population improvement. However, efforts have been made to introgress this material with the vast oil palm germplasm collections of MPOB for rectifying the problem.
    Matched MeSH terms: Genetic Variation/genetics*
  6. Sohrabi M, Rafii MY, Hanafi MM, Siti Nor Akmar A, Latif MA
    ScientificWorldJournal, 2012;2012:416291.
    PMID: 22654604 DOI: 10.1100/2012/416291
    Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.
    Matched MeSH terms: Genetic Variation/genetics*
  7. Mostafa N, Omar H, Tan SG, Napis S
    Molecules, 2011 Mar 22;16(3):2599-608.
    PMID: 21441863 DOI: 10.3390/molecules16032599
    Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination.
    Matched MeSH terms: Genetic Variation*
  8. Rogatcheva MB, Borodin PM, Oda SI, Searle JB
    Genome, 1997 Feb;40(1):18-24.
    PMID: 9061910
    A high-resolution G-banding technique was used to identify five metacentrics that characterize Suncus murinus from Sri Lanka. These metacentrics were shown to be the product of Robertsonian fusion of acrocentric chromosomes identical to those in the standard karyotype defined by M.B. Rogatcheva et al. Two of the metacentrics in the Sri Lankan shrews (Rb(10.12) and Rb(14.15)) were the same as those reported by C.H. Sam et al. in Malayan populations of S. murinus. This finding provides strong support for the suggestion of T.H. Yosida that metacentric-carrying shrews colonized Malaya from Sri Lanka and hybridized with individuals of standard karyotype, generating the Robertsonian polymorphism now observed. In addition to the Robertsonian variation in S. murinus, we have used our high resolution technique (G- and C-banding) to characterize variants on chromosome 7, the X chromosome, and the Y chromosome.
    Matched MeSH terms: Genetic Variation*
  9. Ithnin M, Teh CK, Ratnam W
    BMC Genet, 2017 04 19;18(1):37.
    PMID: 28420332 DOI: 10.1186/s12863-017-0505-7
    BACKGROUND: The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia.

    RESULTS: In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity.

    CONCLUSION: The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.

    Matched MeSH terms: Genetic Variation*
  10. Fix AG
    Ann. Hum. Genet., 1978 Jan;41(3):329-39.
    PMID: 626477
    Most current models of human population structure view migration solely as a deterministic force reducing the variance in gene frequencies among the local colonies of a subdivided population. By an empirical example and through simulation experiments, it is shown that migration structured along kinship lines (by analogy to the lineal or 'kinship' effect) does not always reduce the variances of gene frequencies arising through intergenerational random genetic drift. Thus populations experiencing high rates of migration may not be genetically homogenous.
    Matched MeSH terms: Genetic Variation*
  11. Wang MMH, Gardner EM, Chung RCK, Chew MY, Milan AR, Pereira JT, et al.
    Am J Bot, 2018 05;105(5):898-914.
    PMID: 29874392 DOI: 10.1002/ajb2.1094
    PREMISE OF THE STUDY: Underutilized crops and their wild relatives are important resources for crop improvement and food security. Cempedak [Artocarpus integer (Thunb). Merr.] is a significant crop in Malaysia but underutilized elsewhere. Here we performed molecular characterization of cempedak and its putative wild relative bangkong (Artocarpus integer (Thunb). Merr. var. silvestris Corner) to address questions regarding the origin and diversity of cempedak.

    METHODS: Using data from 12 microsatellite loci, we assessed the genetic diversity and genetic/geographic structure for 353 cempedak and 175 bangkong accessions from Malaysia and neighboring countries and employed clonal analysis to characterize cempedak cultivars. We conducted haplotype network analyses on the trnH-psbA region in a subset of these samples. We also analyzed key vegetative characters that reportedly differentiate cempedak and bangkong.

    KEY RESULTS: We show that cempedak and bangkong are sister taxa and distinct genetically and morphologically, but the directionality of domestication origin is unclear. Genetic diversity was generally higher in bangkong than in cempedak. We found a distinct genetic cluster for cempedak from Borneo as compared to cempedak from Peninsular Malaysia. Finally, cempedak cultivars with the same names did not always share the same genetic fingerprint.

    CONCLUSIONS: Cempedak origins are complex, with likely admixture and hybridization with bangkong, warranting further investigation. We provide a baseline of genetic diversity of cempedak and bangkong in Malaysia and found that germplasm collections in Malaysia represent diverse coverage of the four cempedak genetic clusters detected.

    Matched MeSH terms: Genetic Variation*
  12. Freeman MA, Kristmundsson Á
    Parasit Vectors, 2018 Oct 22;11(1):551.
    PMID: 30348210 DOI: 10.1186/s13071-018-3087-y
    BACKGROUND: The myxosporean Myxidium giardi Cépède, 1906 was described infecting the kidney of the European eel, Anguilla anguilla (L.), having spindle-shaped myxospores and terminal sub-spherical polar capsules. Since then, numerous anguillid eels globally have been documented to have similar Myxidium infections. Many of these have been identified using the morphological features of myxospores or by the location of infection in the host, and some have been subsequently synonymised with M. giardi. Therefore, it is not clear whether M. giardi is a widely distributed parasite, infecting numerous species of eels, in multiple organs, or whether some infections represent other, morphologically similar but different species of myxosporeans. The aim of the present study was to assess the status of M. giardi infections in Icelandic eels, and related fish hosts in Malaysia and to use spore morphology and molecular techniques to evaluate the diversity of myxosporeans present.

    RESULTS: The morphologies of the myxospores from Icelandic eels were very similar but the overall dimensions were significantly different from the various tissue locations. Myxospores from the kidney of the Malaysian tarpon, Megalops cyprinoides (Broussonet), were noticeably smaller. However, the SSU rDNA sequences from the different tissues locations in eels, were all very distinct, with percentage similarities ranging from 92.93% to as low as 89.8%, with the sequence from Malaysia being even more dissimilar. Molecular phylogenies consistently placed these sequences together in a clade that we refer to as the Paramyxidium clade that is strongly associated with the Myxidium clade (sensu stricto). We erect the genus Paramyxidium n. g. (Myxidiidae) to accommodate these histozoic taxa, and transfer Myxidium giardi as Paramyxidium giardi Cépède, 1906 n. comb. as the type-species.

    CONCLUSIONS: There is not a single species of Myxidium (M. giardi) causing systemic infections in eels in Iceland. There are three species, confirmed with a robust phylogeny, one of which represents Paramyxidium giardi n. comb. Additional species probably exist that infect different tissues in the eel and the site of infection in the host fish is an important diagnostic feature for this group (Paramyxidium n. g. clade). Myxospore morphology is generally conserved in the Paramyxidium clade, although actual spore dimensions can vary between some species. Paramyxidium spp. are currently only known to infect fishes from the Elopomorpha.

    Matched MeSH terms: Genetic Variation*
  13. Nijman V
    Zoo Biol, 2016 Jan-Feb;35(1):1-3.
    PMID: 26661798 DOI: 10.1002/zoo.21256
    Ogata and Seino [Zoo Biol, 2015, 34:76-79] sequenced the mitochondrial D-loop of five proboscis monkeys Nasalis larvatus from Yokahama Zoo, Japan, that were imported from Surabaya Zoo, Indonesia. They compared their sequences with those of 16 proboscis monkeys from Sabah, Malaysia, and on the basis of a haplotype network analysis of 256 base pairs concluded that the northern Malaysian and southern Indonesian populations of proboscis monkeys are genetically differentiated. I provide information on the origin of the Indonesian proboscis monkeys, showing that they were the first-generation offspring of wild-caught individuals from the Pulau Kaget Strict Nature Reserve in the province of South Kalimantan. Using a phylogenetic approach and adding additional sequences from Indonesia and Malaysia, I reanalyzed their data, and found no support for a north-south divide. Instead the resulting tree based on 433 base pairs sequences show two strongly supported clades, both containing individuals from Indonesia and Malaysia. Work on captive individuals, as reported by Ogata and Seino, can aid in developing appropriate markers and techniques, but to obtain a more complete understanding of the genetic diversity and differentiation of wild proboscis monkeys, more detailed geographic sampling from all over Borneo is needed.
    Matched MeSH terms: Genetic Variation*
  14. Pavitra SP, Ya'cob Z, Tan TK, Lim YAL, Low VL
    Acta Trop, 2020 May;205:105415.
    PMID: 32088275 DOI: 10.1016/j.actatropica.2020.105415
    The population genetic structures of S. vanluni, S. cheongi and S. jeffreyi were determined from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) across different states in Peninsular Malaysia. High levels of genetic diversity and genetic differentiation were observed among three species. All three species revealed an intermediate level of gene flow among the populations. Negative values of Fu's Fs and low values of Raggedness index supported the hypothesis of population expansion in S. vanluni, S. cheongi and S. jeffreyi.
    Matched MeSH terms: Genetic Variation*
  15. Redjeki ES, Ho WK, Shah N, Molosiwa OO, Ardiarini NR, Kuswanto, et al.
    Genome, 2020 Jun;63(6):319-327.
    PMID: 32097026 DOI: 10.1139/gen-2019-0137
    A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
    Matched MeSH terms: Genetic Variation/genetics*
  16. Seri Masran SNA, Ab Majid AH
    J Med Entomol, 2019 06 27;56(4):942-952.
    PMID: 30882146 DOI: 10.1093/jme/tjz024
    The surge in tropical bed bug Cimex hemipterus (Fabricius) (Hemiptera: Cimicidae) infestations has led to an increase in genomic studies. In this study, the population genetics and breeding patterns of 22 Malaysian populations were analyzed, including genetic differentiation and genetic distance. For seven microsatellite loci, the number of alleles varied from 6 to 14. The allelels per loci contrasted sharply between the overall population and within the populations. The average observed and expected heterozygosity was 0.280 and 0.828 for the overall population and 0.281 and 0.657 among the populations, respectively. Based on polymorphic information criteria, the markers with a value >0.5 were highly polymorphic. In the Hardy-Weinberg equilibrium, the loci of Ch 09ttn, Ch 01dn, and Ch 13dn of the overall population showed signs of a null allele. The stutter peaks caused no scoring errors; large allele dropouts were not detected for any loci; and a correlation imbalance was not indicated. The genetic differentiation among populations was moderate, with a coefficient of genetic differentiation (FST) of 0.144. The bed bug populations showed strong inbreeding, with highly positive coefficients of inbreeding (FIS). The molecular variation attributed to inbreeding was 83% within the populations, compared with 17% among the populations. The admixture individuals in STRUCTURE and neighbor-joining phylogenetic trees also indicated weak genetic structure in the geographical populations, suggesting moderate gene flows between populations. Thus, moderately active dispersion and human-mediated transport shaped the genetic structure of C. hemipterus populations in Malaysia.
    Matched MeSH terms: Genetic Variation*
  17. Azrizal-Wahid N, Sofian-Azirun M, Low VL
    Vet Parasitol, 2020 May;281:109102.
    PMID: 32289653 DOI: 10.1016/j.vetpar.2020.109102
    The present study investigated the genetic profile of the cosmopolitan cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) from Malaysia and the reference data available in the National Center for Biotechnology Information (NCBI) GenBank. A set of sequences of 100 Malaysian samples aligned as 550 characters of the cytochrome c oxidase subunit I (cox1) and 706 characters of the II (cox2) genes revealed ten haplotypes (A1-A10) and eight haplotypes (B1-B8), respectively. The concatenated sequences of cox1 and cox2 genes with a total of 1256 characters revealed 15 haplotypes (AB1-AB15). Analyses indicated that haplotype AB1 was the most frequent and the most widespread haplotype in Malaysia. Overall haplotype and nucleotide diversities of the concatenated sequences were 0.52909 and 0.00424, respectively, with moderate genetic differentiation (FST = 0.17522) and high gene flow (Nm = 1.18). The western population presented the highest genetic diversity (Hd = 0.78333, Pi = 0.01269, Nh = 9), whereas the southern population demonstrated the lowest diversity (Hd = 0.15667, Pi = 0.00019, Nh = 3). The concatenated sequences showed genetic distances ranged from 0.08 % to 4.39 %. There were three aberrant haplotypes in cox2 sequences that highly divergent, suggesting the presence of cryptic species or occurrence of introgression. In the global point of view, the aligned sequences of C. felis revealed 65 haplotypes (AA1-AA65) by the cox1 gene (n = 586), and 27 haplotypes (BB1-BB27) by the cox2 gene (n = 204). Mapping of the haplotype network showed that Malaysian C. felis possesses seven unique haplotypes in both genes with the common haplotypes demonstrated genetic affinity with C. felis from Southeast Asia for cox1 and South America for cox2. The topologies of cox1 and cox2 phylogenetic trees were concordant with relevant grouping pattern of haplotypes in the network but revealed two major lineages by which Malaysian haplotypes were closely related with haplotypes from the tropical region.
    Matched MeSH terms: Genetic Variation*
  18. Chong ETJ, Neoh JWF, Lau TY, Lim YA, Chai HC, Chua KH, et al.
    Malar J, 2020 Oct 22;19(1):377.
    PMID: 33092594 DOI: 10.1186/s12936-020-03451-x
    BACKGROUND: Understanding the genetic diversity of candidate genes for malaria vaccines such as circumsporozoite protein (csp) may enhance the development of vaccines for treating Plasmodium knowlesi. Hence, the aim of this study is to investigate the genetic diversity of non-repeat regions of csp in P. knowlesi from Malaysian Borneo and Peninsular Malaysia.

    METHODS: A total of 46 csp genes were subjected to polymerase chain reaction amplification. The genes were obtained from P. knowlesi isolates collected from different divisions of Sabah, Malaysian Borneo, and Peninsular Malaysia. The targeted gene fragments were cloned into a commercial vector and sequenced, and a phylogenetic tree was constructed while incorporating 168 csp sequences retrieved from the GenBank database. The genetic diversity and natural evolution of the csp sequences were analysed using MEGA6 and DnaSP ver. 5.10.01. A genealogical network of the csp haplotypes was generated using NETWORK ver. 4.6.1.3.

    RESULTS: The phylogenetic analysis revealed indistinguishable clusters of P. knowlesi isolates across different geographic regions, including Malaysian Borneo and Peninsular Malaysia. Nucleotide analysis showed that the csp non-repeat regions of zoonotic P. knowlesi isolates obtained in this study underwent purifying selection with population expansion, which was supported by extensive haplotype sharing observed between humans and macaques. Novel variations were observed in the C-terminal non-repeat region of csp.

    CONCLUSIONS: The csp non-repeat regions are relatively conserved and there is no distinct cluster of P. knowlesi isolates from Malaysian Borneo and Peninsular Malaysia. Distinctive variation data obtained in the C-terminal non-repeat region of csp could be beneficial for the design and development of vaccines to treat P. knowlesi.

    Matched MeSH terms: Genetic Variation*
  19. Mita T, Shaw SR
    Zookeys, 2012.
    PMID: 23378818 DOI: 10.3897/zookeys.254.4182
    Three new species of Ettchellsia Cameron, namely, Ettchellsia ignitasp. n. from Peninsular Malaysia and Borneo, Ettchellsia nigripessp. n. from Sulawesi and Ettchellsia reidisp. n. from Borneo are described and illustrated. A key to the species of Ettchellsia is provided based on females.
    Matched MeSH terms: Genetic Variation
  20. Mak C, Yap TC
    Theor Appl Genet, 1980 Sep;56(5):233-9.
    PMID: 24305859 DOI: 10.1007/BF00295454
    Seven varieties of long bean, which included three local and four exotic, were crossed in a complete diallel. This was an attempt to study the inheritance of crude protein content, protein yield, flowering date, pod yield and yield components.Both additive and non-additive gene effects were responsible for the genetic variation in the diallel population. However, dominance variance was more important than additive variance in crude protein content, number of pods per plant and number of seeds per pod. For seed weight and pod length, additive variance was more important.The crude protein content, protein yield and number of pods per plant appeared to be controlled by overdominance effects. Partial dominance seemed to be the case for flowering date, pod length and seed weight; complete to overdominance for pod yield. High protein appeared to be associated with recessive genes whereas there was a general trend of high yielding parents carrying more dominant genes.
    Matched MeSH terms: Genetic Variation
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