Genetic Diversity and Pedigree Analysis of Muscadine Grape Using SSR Markers

Muscadine grape (Vitis rotundifolia) is the first native North American grape to be domesticated. During the past century, breeding programs have created a large collection of muscadine cultivars. Muscadine cultivars are usually identified by evaluating morphological traits and checking breeding records, which can be ambiguous and unauthentic. During this study, simple sequence repeat (SSR) markers were used to generate DNA fingerprinting profiles to identify muscadine cultivars and verify their reported pedigrees. Eighty-nine Vitis accessions were genotyped using 20 SSRs from 13 linkage groups. From these, 81 unique subgenus Muscadinia accessions were identified, and a core set of five SSR markers was able to distinguish all of them. Eighteen misidentifications were found, and five previously unknown accessions were matched with cultivars in the dataset. The profiles of 12 cultivars were not consistent with their reported parentage–progeny relationships. Genetic diversity was analyzed at four levels: all V. rotundifolia cultivars (N = 67); current cultivars (N = 39); historical cultivars (N = 28); and wild V. rotundifolia accessions (N = 9). There was substantial genetic diversity in both wild and historically cultivated muscadines. The principle coordinate analysis (PCoA) showed clear separation among subgenus Vitis cultivars, wild muscadine accessions, and cultivated muscadines, with PCoA1 and PCoA2 explaining 11.0% and 9.3% of the total variation, respectively.

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Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

CABI Agriculture and Bioscience ◽

10.1186/s43170-020-00013-8 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

G. S. V. Prasad ◽

G. Padmavathi ◽

K. Suneetha ◽

M. S. Madhav ◽

K. Muralidharan

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Crop Improvement ◽

Chromosome 6 ◽

Aromatic Rice ◽

Quality Traits ◽

Combined Analysis ◽

The Core ◽

Rice Germplasm ◽

Core Set

Abstract Background Besides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties. Methods The genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement. Results Eighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG. Conclusions Forty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

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KARAKTERISASI KERAGAMAN GENETIK 27 GENOTIPE CABAI BERDASARKAN MARKA SSR (SIMPLE SEQUENCE REPEAT)

BERITA BIOLOGI ◽

10.14203/beritabiologi.v17i2.3313 ◽

2018 ◽

Vol 17 (2) ◽

Author(s):

Rerenstradika Tizar Terryana ◽

Kristianto Nugroho ◽

Habib Rijzaani ◽

Puji Lestari

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Chili Pepper ◽

Sequence Repeat ◽

Average Value ◽

Allele Number ◽

Principle Coordinate Analysis ◽

Simple Sequence

Chili pepper (Capsicum annuum) is one of the high economical horticultural comodity in Indonesia and its genetic diversity contributes to the success of breeding programs. Simple sequence repeat (SSR) markers can be used to analyze genetic diversity among chili pepper genotypes. The aim of this research was to analyze the genetic diversity of twenty-seven genotypes of chili pepper by using 24 SSR markers. The collected data was analyzed using cluster analysis and principle coordinate analysis (PCoA). The result showed that high allele variation (4–17 alleles) was observed among chili pepper genotypes tested, with an average allele number and Polymorphism Information Content (PIC) value was 7.708 and 0.758 (0.598–0.920) respectively. All of SSR markers showed PIC value >0.5 which indicated that these markers were suitable for chili pepper diversity studies with a high differentiation and with the average value of genetic diversity was 0.78. The clustering and principle coordinate analysis showed that twenty-seven genotypes of chili pepper were divided into two groups (coefficient of similarity 0.74 in cluster analysis) indicating a high genetic variability among them. Genetic diversity analysis in this study will be useful as an initial basis of selection for appropriate parents with desired traits to assist the breeding program of chili pepper in Indonesia.

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Molecular genetic diversity and population structure of a selected core set in garlic and its relatives using novel SSR markers

Plant Breeding ◽

10.1111/j.1439-0523.2010.01805.x ◽

2010 ◽

Vol 130 (1) ◽

pp. 46-54 ◽

Cited By ~ 32

Author(s):

W.-G. Zhao ◽

J.-W. Chung ◽

G.-A. Lee ◽

K.-H. Ma ◽

H.-H. Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Molecular Genetic ◽

Molecular Genetic Diversity ◽

Core Set

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DNA Fingerprinting and Genetic Diversity Assessment of GM Cotton Genotypes for Protection of Plant Breeder Rights

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1728 ◽

2021 ◽

Vol 25 (04) ◽

pp. 768-776

Author(s):

Shakra Jamil

Keyword(s):

Genetic Diversity ◽

Dna Fingerprinting ◽

Ssr Markers ◽

Polyacrylamide Gel Electrophoresis ◽

Core Set ◽

Diversity Assessment ◽

Cotton Genotypes ◽

Diversity Studies ◽

Selection Of

DNA fingerprinting is rapid, easy, and efficient method for discrimination, identification and characterization of various genotypes for protection of plant breeder’s rights (PBRs). Present study was designed for DNA fingerprinting and genetic diversity assessment of 25 GM cotton genotypes (possessing Cry1Ac gene) using 297 SSR markers through conventional PCR and Polyacrylamide gel electrophoresis. Out of 297 SSR markers, 25 markers were not amplified, 28 were monomorphic and 244 were polymorphic. A total of 1537 alleles were amplified among which 1294 (84.18%) were polymorphic. PIC value in our study ranged from 0.08 to 0.93 with an average of 0.73. Unique allelic pattern was observed for nineteen genotypes whereas six genotypes were identified using two-step identification methods. The UPGMA dendrogram divided the genotypes into two distinct clusters. Cluster I was comprised of 20 genotypes whereas cluster II was comprised of four genotypes. MNH-1020 did not obey any clustering and remained separated. The results of the structure analysis were complementary to cluster analysis and the population was divided into two subgroups. Our results evidenced narrow genetic base of the cotton genotypes cultivated in Punjab Pakistan due to use of common parents in the pedigree/parentage. Further, we proposed a core set of markers for future DNA fingerprinting and genetic diversity studies. The information generated in this study will be helpful in variety registration and subsequent protection under PBRs. Further our findings will be useful in selection of SSR markers for future studies which are focused on DNA fingerprinting and genetic diversity assessment. © 2021 Friends Science Publishers

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Genetic diversity and population structure of the selected core set inAmaranthususing SSR markers

Plant Breeding ◽

10.1111/pbr.12027 ◽

2013 ◽

Vol 132 (2) ◽

pp. 165-173 ◽

Cited By ~ 12

Author(s):

Aye Aye Khaing ◽

Kyaw Thu Moe ◽

Jung-Wook Chung ◽

Hyung-Jin Baek ◽

Yong-Jin Park

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Core Set

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Genealogical Analysis in the Czech Spring Wheat Collection and its Use for the Creation of Core Collection

Czech Journal of Genetics and Plant Breeding ◽

10.17221/3641-cjgpb ◽

2011 ◽

Vol 42 (No. 4) ◽

pp. 117-125 ◽

Cited By ~ 5

Author(s):

Z. Stehno ◽

I. Faberová ◽

L. Dotlačil ◽

S. Martynov ◽

T. Dobrotvorskaya

Keyword(s):

Genetic Diversity ◽

Spring Wheat ◽

Core Collection ◽

Diversity Index ◽

Pedigree Analysis ◽

The Core ◽

Genealogical Analysis ◽

Core Set ◽

Subsequent Calculation ◽

Genetic Profiles

A spring wheat collection of the Czech gene bank included altogether 3270 original accessions in 2005; among them 2123 accessions with pedigree were analyzed using the construction of genetic profiles and subsequent calculation of Renkonen similarity indexes. Genetic diversity was estimated by Shannon diversity index. Subsequently we calculated cluster analysis using coefficients of parentage and in addition, we selected representatives of particular clusters for a core collection. Accessions of the whole analysed set of spring wheat (2123) were progenies of 929 original ancestors and diversity index within the set was H = 4.17. In the selected core set we can trace 718 ancestors and the diversity index is H' = 4.82. The selected core set is composed of 645 accessions (i.e. 30.4% of the whole set) and it represents 77.3% of genetic diversity in the whole set. The diversity between clusters did not decrease in the core set, which shows the representativeness of selected core accessions. Genealogical analysis provided useful information for the choice of cultivars to a core collection. However, pedigree analysis has to be complemented by other generally applicable approaches such as the use of molecular markers, morphological and agronomical characters. The analysis can also provide valuable information for breeders and researchers.  

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