Evaluation of Genetic Diversity of QPM, Provit-A, and Elite Maize Inbreds Resistant to Downy Mildew Disease Using Simple Sequence Repeats

<p>Functional maize tends to be more susceptible to major maize diseases, particularly Downy mildew. Among the functional maize are Quality Protein Maize (QPM) and Provit A maize. The presence of higher amino acid and beta carotene in functional maize might have caused these types of maize more susceptible to Downy mildew disease. The objective of the research was to identify the heterotic pairs among maize inbreds i.e. QPM, Provit A, and local maize varieties resistant to Downy mildew disease using Simple Sequence Repeats (SSR) marker. The research was conducted from April to July 2017 at the Molecular Biology Laboratory of Indonesian Cereals Research Institute. A total of five QPM inbreds, 15 Provit A inbreds, and 11 Downy mildew resistant local varieties of maize were used in the experiment using 34 SSR markers. Results indicated that among 34 SSR locus analysed, variation of allele lengths ranged from 74 bp to 500 bp. A total of 125 alleles ranging from two to nine alleles per locus with an average of 3.68 alleles were generated. The data indicated wide genetic variations among characters. DNA band profile showed that nc130 marker produced the highest PIC (over 0.83) and allele value (8.00). Genetic distance analysis found a total of 21 heterotic genotypes with genetic distance exceeds 0.65. </p>

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Keragaman Genetik Inbrida Jagung QPM dan Provit-A Berdasarkan Marka SSRs (Simple Sequence Repeats)

Jurnal Penelitian Pertanian Tanaman Pangan ◽

10.21082/jpptp.v35n2.2016.p133-140 ◽

2016 ◽

Vol 35 (2) ◽

pp. 133

Author(s):

Nining Nurini Andayani ◽

M. Yasin H.G ◽

Marcia B. Pabendon

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeats ◽

Genetic Similarity ◽

Genetic Distances ◽

Large Variability ◽

Maize Germplasm ◽

High Level ◽

Biology Laboratory ◽

Simple Sequence

Information on genetic diversity of QPM and Provit-A maize germplasm is important to support breeding program, in order to form a high yielding maize hybrid. Simple sequence repeats (SSR) have been extensively utilized as genetic markers to study the genetic diversity, cultivar identification, and gene mapping. The objectives of this research were to investigate the genetic diversity and to obtain information the genetic relationship among 20 maize accessions using 29 SSRs. The research was carried out at the Moleculer Biology Laboratory of Indonesian Cereals Research Institute (ICERI) in Maros, South Sulawesi. Twenty nine polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the genotype of the lines, detecting 83 allels, with an average allel number of 3 allels per locus, ranging from 2 to 6 alleles per locus. The results indicated that polymorphism information content (PIC) ranged from 0.10 (nc133 and phi072) to 0.74 (phi064) with the average of 0.45. Genetic distance based on genetic similarity estimate ranged from 0.39 to 0.92. The high level of PIC values and wide genetic distances indicated the large variability among maize germplasm. Cluster analysis divided the 20 maize accessions into three groups. Coefficient cofenetic value (r) was 0.85 indicated a good fit based on the genetic similarity value. As many as 30 inbred heterotic recombinants were derived by incorporating 20 QPM and Provit-A with genetic distance of ≤0.65. The SSRs proved to be reliable and is practical technique for revealing the relationship among specialty maize genotypes.

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Analysis of Genetic Diversity Between Eriobotrya japonica (Thunb.) Lindl. (Rosaceae) Populations Growing in the Aegean Region of Turkey

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Horticulture ◽

10.15835/buasvmcn-hort:2020.0012 ◽

2020 ◽

Vol 77 (2) ◽

pp. 71

Author(s):

Emre SEVİNDİK ◽

Kemalcan OKAN ◽

Fadime EFE

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Distance ◽

Simple Sequence Repeats ◽

Random Amplified Polymorphic Dna ◽

Eriobotrya Japonica ◽

Analysis Program ◽

Aegean Region ◽

Inter Simple Sequence Repeats ◽

Simple Sequence

In this study, we performed a genetic diversity using RAPD (Random amplified polymorphic DNA) and ISSR (Inter-simple sequence repeats) markers for some Eriobotrya japonica populations grown in the Aegean region of Turkey. PCR was performed with all DNA samples and primers with ability of scoring band. Phylogenetic analysis and pairwise genetic distance between the populations were calculated by using the PAUP analysis program. According to the RAPD data, a total of 33 bands were obtained and 21 of them were polymorphic. The closest genetic distance (0.09677) was found between Aydın and Nazilli populations, while the most distant value was found 0.44000 between Salihli and Nazilli populations. According to the ISSR data, a total of 43 bands were obtained and 18 of them were polymorphic. The closest genetic distance (0.09302) was found between İzmir and Aydın populations, while the most distant values (0.48276) were found between Denizli and Nazilli populations. As a result of this study, the rate of polymorphism obtained in ISSR technique was found to be lower than the RAPD technique.

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Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210348 ◽

2020 ◽

Vol 21 (3) ◽

Author(s):

Uslan Uslan ◽

NUR JANNAH

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Genetic Variation ◽

Genetic Distance ◽

Simple Sequence Repeats ◽

Zea Mays L ◽

Sample Collection ◽

High Genetic Diversity ◽

Inter Simple Sequence Repeats ◽

Simple Sequence

Abstract. Uslan, Jannah N. 2020. Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker. Biodiversitas 21: 1208-1214. Corn (Zea mays L.) is one of the most important food crops in Indonesia. However, the studies described their genetic variation is relatively poor. Therefore, the aim of this study was to analyze the genetic diversity of local corn cultivars from South Amarasi, Kupang District, East Nusa Tenggara (NTT), Indonesia using ISSR markers. The sampling was conducted in 4 different sites in Sub-district of Amarasi, Kupang District. A total of 11 corn cultivars from Sub-district of South Amarasi was collected. DNA isolation was performed by using CTAB Method. Clustering analysis was conducted on MSVP 3.2 software. It was shown that all ISSR-primers used (UBC 811, UBC 814 and UBC 824) were successfully produced polymorphic bands and represents the high genetic diversity of the local corn cultivars. The genetic distance index indicated that several corn cultivars from two different populations were geographically unclustered, although there are samples from several populations that have a low genetic distance. The genetic variation index also showed high genetic diversity among the populations. Further research on the exhaustive sample collection was needed to give an insight into the genetic diversity of local corn cultivars (Zea mays L.) from South Amarasi, Indonesia. Please write implementation of this research

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Identification and Characterization of Simple Sequence Repeats (SSR) Markers Associated with Downy Mildew Resistance Locus “<i>RPV1</i>” in Grapes

Advances in Bioscience and Biotechnology ◽

10.4236/abb.2021.1211024 ◽

2021 ◽

Vol 12 (11) ◽

pp. 371-387

Author(s):

Neetu Goyal ◽

Akshay Nag ◽

Roshni R. Samarth ◽

Anuradha Upadhyay ◽

Kashmir Singh

Keyword(s):

Downy Mildew ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Resistance Locus ◽

Downy Mildew Resistance ◽

Mildew Resistance ◽

Identification And Characterization ◽

Simple Sequence

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KERAGAMAN GENETIK 22 AKSESI PADI LOKAL TORAJA UTARA BERBASIS MARKA SIMPLE SEQUENCE REPEATS (SSR)

Jurnal Bioteknologi & Biosains Indonesia (JBBI) ◽

10.29122/jbbi.v5i2.3031 ◽

2019 ◽

Vol 5 (2) ◽

pp. 230

Author(s):

Holy Ekklesia Ladjao ◽

Rinaldi Sjahril ◽

Muh. Riadi

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Genetic Similarity ◽

Rice Accession ◽

Polymorphism Rate ◽

Simple Sequence

Genetic Diversity of 22 Local Rice Accessions from North Toraja Based on Simple Sequence Repeats (SSR) MarkersABSTRACTOne way to explore the potential of local rice is by the characterization that could obtain genetic diversity of that plants. The aim of this study was to obtain the genetic diversity of 22 local rice accession from North Toraja. Twenty-two of local rice accessions from North Toraja were characterized by 30 SSR markers and using NTSYS pc 2.1 program to analyze genetic diversity. The results showed that twenty-six SSR markers that had been analyzed produced some alelles with a size between 106.75-311 bp, the average number of alleles were 3 and the polymorphism rate was 0.53. On coefficient genetic similarity at 0.38, the population formed three clusters. Cluster I and II were dominated by rice that had no hair on the tip of the grain and cluster III were dominated by rice that had hair on the tip of the grain. There were 105 opportunities to crossing between accessions when the genetic distance was above 0.7.Keywords: genetic diversity, local rice, North Toraja, polymorphism rate, SSR markers ABSTRAKSalah satu cara untuk menggali potensi padi lokal adalah dengan karakterisasi. Dengan adanya kegiatan karakterisasi tersebut maka dapat diketahui bagaimana keragaman genetik dari suatu tanaman. Penelitian ini bertujuan untuk mengetahui keragaman genetik dari 22 aksesi padi lokal Toraja Utara. Duapuluh dua aksesi padi lokal Toraja Utara dikarakterisasi menggunakan 30 marka SSR dan dianalisis keragaman genetiknya menggunakan program NTSYS pc 2.1. Hasil penelitian menunjukkan bahwa duapuluh enam marka SSR yang dianalisis memiliki kisaran ukuran alel antara 106.75-311 bp, dengan jumlah alel rata-rata 3 dan tingkat polimorfisme sebesar 0,53. Koefisien kemiripan genetik 0,38 dan terbentuk 3 klaster. Pada klaster I dan klaster II didominasi oleh padi yang tidak memiliki rambut pada ujung gabahnya, dan pada klaster III didominasi oleh padi yang memiliki rambut pada ujung gabahnya. Selain itu, pada jarak genetik diatas 0,7 terdapat 105 peluang persilangan.Kata Kunci: keragaman genetik, marka SSR, padi lokal, tingkat polimorfisme, Toraja Utara

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GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v16n2.2015.p.79-86 ◽

2016 ◽

Vol 16 (2) ◽

pp. 79

Author(s):

Amran Muis ◽

Nurnina Nonci ◽

Marcia B. Pabendon

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Downy Mildew ◽

Group Method ◽

Cophenetic Correlation ◽

Pair Group ◽

Maize Genotypes ◽

Maize Varieties ◽

Ssr Primers ◽

Ssr Loci

The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI) between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r) at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

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Genetic Distance Based on Simple Sequence Repeats and Heterosis in Tropical Maize Populations

Crop Science ◽

10.2135/cropsci2003.1275 ◽

2003 ◽

Vol 43 (4) ◽

pp. 1275-1282 ◽

Cited By ~ 123

Author(s):

J. C. Reif ◽

A. E. Melchinger ◽

X. C. Xia ◽

M. L. Warburton ◽

D. A. Hoisington ◽

...

Keyword(s):

Genetic Distance ◽

Simple Sequence Repeats ◽

Tropical Maize ◽

Maize Populations ◽

Simple Sequence

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Development of Extra-Early Provitamin A Quality Protein Maize Inbreds with Resistance/Tolerance to Striga hermonthica and Soil Nitrogen Stress

Agronomy ◽

10.3390/agronomy11050891 ◽

2021 ◽

Vol 11 (5) ◽

pp. 891

Author(s):

Solomon A. Oyekale ◽

Baffour Badu-Apraku ◽

Victor O. Adetimirin ◽

Nnanna Unachukwu ◽

Melaku Gedil

Keyword(s):

Soil Nitrogen ◽

Beta Carotene ◽

Sub Saharan Africa ◽

Provitamin A ◽

Striga Hermonthica ◽

Nitrogen Stress ◽

Maize Varieties ◽

Maize Inbreds ◽

Sub Saharan ◽

Nitrogen Conditions

A hemiparasitic plant, Striga hermonthica (Del.) Benth and soil nitrogen stress are the key constraints to maize (Zea mays L.) productivity in sub-Saharan Africa, where commonly cultivated maize is the normal endosperm type that is deficient in provitamin A, tryptophan and lysine (PVATL). Seventy-six extra-early maize inbreds with provitamin A, tryptophan, and lysine qualities (TZEEIORQ) were developed to address these constraints, and four checks were assessed under Striga, low and high nitrogen conditions at three locations in Nigeria. The inbreds were further genotyped with two beta-carotene hydroxylase 1 (crtRB1) markers, and their seeds were quantified for provitamin A content. Significant (P < 0.01) genetic variations were observed for grain yield and other agronomic attributes of the inbreds under varying environmental conditions. Levels of PVATL for the inbreds ranged from 2.21–10.95 µg g−1, 0.04–0.08%, and 0.19–0.39%, respectively. Beta-carotene marker, crtRB1-3′TE, was polymorphic and grouped the inbreds into two. The marker was effective in identifying inbreds with moderate provitamin A content. Inbreds TZEEIORQ 5, TZEEIORQ 52, and TZEEIORQ 55 exhibited resistance to Striga, tolerance to nitrogen stress with moderate levels of PVATL and could be invaluable sources of favorable alleles for breeding nutritionally improved maize varieties with resistance/tolerance to Striga and soil nitrogen stress.

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