Analysis of molecular genetic diversity and population structure in<i>Amaranthus</i>germplasm using SSR markers

Suresh, S.; Chung, Jong‐Wook; Cho, G. T.; Sung, Jung Suk; Park, J. H.; Gwag, Jae‐Gyun; Baek, Hyung-Jin

doi:10.1080/11263504.2013.788095

Cited by 36 publications

(32 citation statements)

References 40 publications

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“…SSE is a non-governmental organization that works to preserve America's gardening heritage, so it would be important to determine the species through molecular means. In most studies [1,2,[22][23][24][25][26][27][28][29][30], molecular markers have been able to distinguish South American (A. caudatus, A. quitensis) from Central American (A. cruentus, A. hypochondriacus) species of the subgenus Amaranthus as well as outgroups from other subgenera. The other subgenera of the genus are subgenus Acnida (includes weedy amaranths such as A. palmeri and A. spinosus) and Albersia (includes wild and vegetable species such as A. tricolor and A. viridis).…”

Section: Discussionmentioning

confidence: 99%

“…The use of molecular markers such as Simple Sequence Repeat (SSR) or Single Nucleotide Polmorphism (SNP) seems better than morphological analysis for distinguishing species of grain amaranths [1,2,[22][23][24][25][26][27][28][29][30]. SSR markers in the study by Oo and Park [26] did find clear clustering pattern of geographically close accessions and related species but Suresh et al [1] did not.…”

Section: Discussionmentioning

confidence: 99%

“…Amaranths belong to the dicotyledonous genus Amaranthus L. which is made up of over 70 species [1], and three subgenera [2]. The word Amaranthus originated from the Greek word…”

Section: Introductionmentioning

confidence: 99%

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Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Thapa

Blair

2018

Agronomy

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Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers' Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop's improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Thapa

Blair

2018

Agronomy

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“…Similarly various methods have been used for surveying population structures (Khan et al 2014). Analysis of population structure is critical for collections, conservation, and sustainable utilization of gene bank accessions (Suresh et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Mongolian Wheat Based on SSR Markers: Implications for Conservation and Management

Ya¹,

Raveendar²,

Bayarsukh³

et al. 2017

Plant Breed. Biotech.

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Production of spring wheat, the major crop in Mongolia, accounts for 98% of the cultivated area. Understanding genetic variability in existing gene bank accessions is critical for collection, conservation and use of wheat germplasms. To determine genetic diversity and population structure among a representative collection of Mongolian local wheat cultivars and lines, 200 wheat accessions were analyzed with 15 SSR markers distributed throughout the wheat genome. A total of 85 alleles were detected, with three to five alleles per locus and a mean genetic richness of 5.66. Average genetic diversity index was 0.69, with values ranging from 0.37-0.80. The 200 Mongolian wheat accessions were mainly divided into two subgroups based on structure and phylogenetic analyses, and some phenotypes were divergent by the subgroups. Results from this study will provide valuable information for conservation and sustainable use of Mongolian wheat genetic resources.

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“…GD analysis is important for collections, conservation, and sustainable utilization of Genbank accessions (Suresh et al 2014). Various types of DNA markers studies have been carried out to estimate the GD and phylogenetic relationship among tomato genotypes (Klein-Lankhorst et al 1991;Kwon et al 2009;Geethanjali et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

Raveendar¹,

Chung²,

Lee³

et al. 2016

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The objective of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall FST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.

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Analysis of molecular genetic diversity and population structure inAmaranthusgermplasm using SSR markers

Cited by 36 publications

References 40 publications

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Genetic Diversity and Population Structure of Mongolian Wheat Based on SSR Markers: Implications for Conservation and Management

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

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