Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers

Oo, Win Htet; Park, Yong‐Jin

doi:10.7740/kjcs.2013.58.4.336

Cited by 11 publications

(11 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There is also genetic differentiation between grain and vegetable amaranth in this study, which has also been observed in many molecular markers studies, including AFLP [ 41 ], SSR [ 23 , 42 , 43 ] and GBS [ 15 ], although those studies incorporated far fewer A . tricolor accessions.…”

Section: Discussionsupporting

confidence: 78%

Genetic diversity analysis and marker-trait associations in Amaranthus species

et al. 2022

View full text Add to dashboard Cite

Amaranth (Amaranthus spp.) is a highly nutritious, underutilized vegetable and pseudo-cereal crop. It possesses diverse abiotic stress tolerance traits, is genetically diverse and highly phenotypically plastic, making it an ideal crop to thrive in a rapidly changing climate. Despite considerable genetic diversity there is a lack of detailed characterization of germplasm or population structures. The present study utilized the DArTSeq platform to determine the genetic relationships and population structure between 188 amaranth accessions from 18 agronomically important vegetable, grain, and weedy species. A total of 74, 303 SNP alleles were generated of which 63, 821 were physically mapped to the genome of the grain species A. hypochondriacus. Population structure was inferred in two steps. First, all 188 amaranth accessions comprised of 18 species and second, only 120 A. tricolor accessions. After SNP filtering, a total of 8,688 SNPs were generated on 181 amaranth accessions of 16 species and 9,789 SNPs generated on 118 A. tricolor accessions. Both SNP datasets produced three major sub-populations (K = 3) and generate consistent taxonomic classification of the amaranth sub-genera (Amaranthus Amaranthus, Amaranthus Acnida and Amaranthus albersia), although the accessions were poorly demarcated by geographical origin and morphological traits. A. tricolor accessions were well discriminated from other amaranth species. A genome-wide association study (GWAS) of 10 qualitative traits revealed an association between specific phenotypes and genetic variants within the genome and identified 22 marker trait associations (MTAs) and 100 MTAs (P≤0.01, P≤0.001) on 16 amaranth species and 118 A.tricolor datasets, respectively. The release of SNP markers from this panel has produced invaluable preliminary genetic information for phenotyping and cultivar improvement in amaranth species.

show abstract

Section: Discussionsupporting

confidence: 78%

Genetic diversity analysis and marker-trait associations in Amaranthus species

et al. 2022

View full text Add to dashboard Cite

show abstract

“…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%

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. Vegetable species have been less well studied [31][32][33][34][35][36][37] at least by molecular means than grain amaranths while weedy amaranths have been well studied, especially with recent outbreaks of herbicide resistant amaranths in countries with genetically modified crops and those developing countries transitioning to mechanical weed control.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Thapa

Blair

2018

Agronomy

View full text Add to dashboard Cite

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.

show abstract

“…Several single locus molecular markers have been used for amaranth characterization instead of morphological ones. These range from protein-based ones to DNA-based markers, including isozymes [ 20 , 21 , 22 ], RFLPs [ 23 ], SSRs [ 1 , 24 , 25 ] and SNPs [ 26 , 27 ]. Multi-locus markers have included RAPDs [ 28 , 29 , 30 ] and AFLPs [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Thapa

Edwards

Blair

2021

Genes

View full text Add to dashboard Cite

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies.

show abstract

Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers

Cited by 11 publications

References 34 publications

Genetic diversity analysis and marker-trait associations in Amaranthus species

Genetic diversity analysis and marker-trait associations in Amaranthus species

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Contact Info

Product

Resources

About