Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

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Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200806 ◽

2019 ◽

Vol 20 (8) ◽

Author(s):

Ni Luh Arpiwi ◽

I Gusti Ayu Sugi Wahyuni ◽

I Ketut Muksin

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Pongamia Pinnata ◽

Sequence Repeat ◽

Binary Matrix ◽

Simple Sequence Repeat Markers ◽

Group I ◽

Simple Sequence

Abstract. Arpiwi NL, Wahyuni IGAS, Muksin IK. 2019. Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers. Biodiversitas 20: 2134-2142. Pongamia pinnata (L.) Pierre is a member of family Leguminosae that produces seed oil for biodiesel feedstock. The aim of the present study was to determine genetic diversity of pongamia trees that grow in Bali using Inter Simple Sequence Repeat (ISSR) markers. This study is important to support the breeding program for the improvement of the biodiesel producing species. Leaf samples were taken from 26 pongamia trees grown on northern and southern coastal areas of Bali. Genomic DNA was isolated from fresh leaves sample and was amplified by Polymerase Chain Reaction (PCR) using 9 ISSR primers. The banding patterns of DNA after PCR were scored and tabulated into a binary matrix. Genetic distance was generated by pairwise distance using composite maximum likelihood. A dendrogram was constructed using Unweighted Pair Group Method Arithmetic (UPGMA) method. The binary matrix was further analyzed for Nonmetric Multidimensional Scaling (NMDS) with Primer E V.6 software. DNA concentrations ranged from 98.59-100.55 ng/μL with sufficient quality for PCR. The number of alleles for 9 primers was 43, the number of the polymorphic band was 35, and the number of monomorphic bands was 8. Percentage of polymorphism ranged from 50 to 100%. Cluster analysis of 26 DNA of pongamia trees showed that the trees were grouped into two, namely group I and II. Group I consisted of two trees only, namely Uma Anyar 1 and Penarukan 1. Group II consisted of 24 pongamia trees which were divided into 3 subgroups, namely IIA, IIB, and IIC with close genetic distance. Analysis of NMDS supported cluster analysis that 23 out of 26 pongamia trees had close genetic distance, and possibly they come from a similar source. Genetic diversity of pongamia in Bali needs to be widen possibly by the introduction of new planting materials from across Indonesia or seed procurement from different sources.

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ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

Jurnal Penelitian Tanaman Industri ◽

10.21082/jlittri.v17n4.2011.156-162 ◽

2020 ◽

Vol 17 (4) ◽

pp. 156

Author(s):

Surti Kurniasih ◽

Rubiyo Rubiyo ◽

Asep Setiawan ◽

Agus Purwantara ◽

Sudarsono Sudarsono

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Ssr Markers ◽

Theobroma Cacao ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Gene Diversity ◽

Sequence Repeat ◽

Theobroma Cacao L ◽

Simple Sequence

Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of < 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (<7.50). The rest of the cacao clones were in the third group with diversity coefficient of>7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity AbstrakMarka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman<3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman < 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman > 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas

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Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

Canadian Journal of Plant Science ◽

10.4141/cjps07088 ◽

2008 ◽

Vol 88 (2) ◽

pp. 313-322 ◽

Cited By ~ 22

Author(s):

S. C. Debnath ◽

S. Khanizadeh ◽

A. R. Jamieson ◽

C. Kempler

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Breeding Lines ◽

Pair Group ◽

Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

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Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/17/4/14720 ◽

2020 ◽

Vol 17 (4) ◽

pp. 651-661

Author(s):

Le Ngoc Trieu ◽

Nong Van Duy ◽

Tran Van Tien

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

New Variety ◽

Gene Differentiation ◽

The Stability ◽

Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %). The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

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Microsatellite Markers and Genetic Diversity in Japanese Apricot (Prunus mume)

HortScience ◽

10.21273/hortsci.39.7.1571 ◽

2004 ◽

Vol 39 (7) ◽

pp. 1571-1574 ◽

Cited By ~ 14

Author(s):

Zhi-Hong Gao ◽

Zhi-Jun Shen ◽

Zhen-Hai Han ◽

Jing-Gui Fang ◽

Yu-Ming Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Distance ◽

Microsatellite Locus ◽

Simple Sequence Repeat ◽

Prunus Mume ◽

Sequence Repeat ◽

Microsatellite Sequence ◽

Japanese Apricot ◽

Simple Sequence

Sequencing amplification fragments produced using simple-sequence repeat (SSR) primer pairs pchgms2 and UDP96008 in `Dayezhugan' japanese apricot showed that SSRs obtained included a microsatellite locus originally identified in peach. The microsatellite sequence homogeneity between UDP96008 in japanese apricot in this study and UDP96008 in the peach in GenBank was 98%. Twenty-four japanese apricot genotypes originating in diverse geographic areas had been identified with 14 SSR primer pairs developed in different species of Prunus. In total, 129 alleles were obtained and per primer pairs detected 2.5 alleles on the average. The results from cluster analysis showed that the genetic distance between `Nanhong' and `Zhonghong' was the closest, and cultivars from China and from Japan could not be separated completely.

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Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb2006102 ◽

2006 ◽

Vol 3 (2) ◽

pp. 119-126 ◽

Cited By ~ 8

Author(s):

Liu Yong ◽

Liu De-Chun ◽

Wu Bo ◽

Sun Zhong-Hai

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Similarity Coefficient ◽

Group Method ◽

Allelic Polymorphism ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Arithmetic Average ◽

Pair Group ◽

Simple Sequence

AbstractGenetic diversity in 122 accessions of pummelo (Citrus grandis Osbeck) and its related varieties was assessed using simple sequence repeat (SSR) markers. Thirty-one pairs of SSR informative primers generated a total of 335 alleles. The average number of alleles per locus was 9.85. The value of allelic polymorphism information content (PIC) ranged from 0.1939 to 0.9073, with an average of 0.7085 per primer. The 122 accessions of pummelo and its related varieties could be clustered into seven groups by the unweighted pair-group method arithmetic average (UPGMA), in which the 110 pummelo accessions could be divided into 18 subgroups at similarity coefficient of 0.712. These subgroups were mainly composed of the Shatian pummelo variety group, the Wendan variety group and many of the hybrid pummelo groups. The classification method can be used in targeting many varieties in order to widen the genetic background of pummelo.

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Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Scientific Reports ◽

10.1038/s41598-021-04264-x ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Zhao Zheng ◽

Nannan Zhang ◽

Zhenghui Huang ◽

Qiaoying Zeng ◽

Yonghong Huang ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Genetic Improvement ◽

Similarity Coefficient ◽

Sequence Repeat ◽

Genome Survey ◽

Simple Sequence ◽

Genome Survey Sequencing

AbstractPlatostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

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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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Characterization and Identification of Indigenous Olive Germplasm from Cyprus Using Morphological and Simple Sequence Repeat Markers

HortScience ◽

10.21273/hortsci13192-18 ◽

2018 ◽

Vol 53 (9) ◽

pp. 1306-1313 ◽

Cited By ~ 1

Author(s):

Maria G. Emmanouilidou ◽

Marios C. Kyriacou ◽

Isabel Trujillo

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Agricultural Research ◽

Morphological Variability ◽

Ex Situ ◽

Phenotypic Characterization ◽

Sequence Repeat ◽

Germplasm Collections ◽

Simple Sequence

Implementation of the recently developed Cyprus National Register of Commercial Varieties mandates proper cataloguing of the material conserved in the ex situ Olive Collection at the Agricultural Research Institute of Cyprus. A total of 125 trees belonging to 32 accessions were analyzed using 11 morphological endocarp traits and 14 microsatellite [simple sequence repeat (SSR)] markers. The SSR variability allowed segregation of 16 genotypes among accessions, which were clustered into three main groups based on genetic similarity. Similarity indexes among groups ranged from 0.63 to 0.65 and within groups were ≥0.9. Lower morphological variability was detected among accessions, which conformed to three morphological profiles; moreover, the three morphological profiles corresponded to the three groups of genetic similarity obtained by SSR markers. The identification, based on the unique combination of SSR genotypes and endocarp morphologies, revealed the presence of three cultivars and 15 molecular variants that presented limited molecular differences but morphological profiles identical to their catalogued cultivars. Two cultivars, ‘Ladoelia’ and ‘Kato Drys’, demonstrated molecular variation. The current study underpins the efficient management of olive germplasm collections based on combined molecular and phenotypic characterization of their accessions. The complete cataloguing of olive germplasm ensures the correct distribution of identified and authenticated material across national or international institutions.

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