Genome and Transcriptome of Amaranth Species

Abstract The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For non-model crops the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html.

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Genes ◽

10.3390/genes12121849 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1849

Author(s):

Ranjita Thapa ◽

Matthew Edwards ◽

Matthew W. Blair

Keyword(s):

Wild Species ◽

Germplasm Conservation ◽

Conservation Strategies ◽

South American Species ◽

Amaranthus Cruentus ◽

Amaranthus Hypochondriacus ◽

Major Allele Frequency ◽

Population Structure Analysis ◽

Amaranth Species ◽

Relationship Of

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.

Genetics of Betalain Pigments in Amaranth Species

Compendium of Plant Genomes - The Amaranth Genome ◽

10.1007/978-3-030-72365-1_4 ◽

2021 ◽

pp. 35-54

Author(s):

Erica E. Packard ◽

Isadora Louise Alves da Costa Ribeiro Quintans ◽

Dinesh Adhikary

Keyword(s):

Amaranth Species

Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species

BMC Plant Biology ◽

10.1186/s12870-019-1656-7 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 7

Author(s):

Esaú Bojórquez-Velázquez ◽

Alberto Barrera-Pacheco ◽

Eduardo Espitia-Rangel ◽

Alfredo Herrera-Estrella ◽

Ana Paulina Barba de la Rosa

Keyword(s):

Storage Proteins ◽

Protein Analysis ◽

Late Embryogenesis Abundant ◽

Late Embryogenesis ◽

Amaranth Species ◽

And Storage

Parallel Seed Color Adaptation during Multiple Domestication Attempts of an Ancient New World Grain

Molecular Biology and Evolution ◽

10.1093/molbev/msz304 ◽

2019 ◽

Vol 37 (5) ◽

pp. 1407-1419 ◽

Cited By ~ 5

Author(s):

Markus G Stetter ◽

Mireia Vidal-Villarejo ◽

Karl J Schmid

Keyword(s):

Genomic Region ◽

Color Variation ◽

Chromosome 9 ◽

Seed Color ◽

Color Adaptation ◽

Crop Species ◽

Grain Amaranth ◽

Amaranth Species ◽

Genomic Regions ◽

Selection Of

Abstract Thousands of plants have been selected as crops; yet, only a few are fully domesticated. The lack of adaptation to agroecological environments of many crop plants with few characteristic domestication traits potentially has genetic causes. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. Although three grain amaranth species have been cultivated as crop for millennia, all three lack key domestication traits. We sequenced 121 crop and wild individuals to investigate the genomic signature of repeated incomplete adaptation. Our analysis shows that grain amaranth has been domesticated three times from a single wild ancestor. One trait that has been selected during domestication in all three grain species is the seed color, which changed from dark seeds to white seeds. We were able to map the genetic control of the seed color adaptation to two genomic regions on chromosomes 3 and 9, employing three independent mapping populations. Within the locus on chromosome 9, we identify an MYB-like transcription factor gene, a known regulator for seed color variation in other plant species. We identify a soft selective sweep in this genomic region in one of the crop species but not in the other two species. The demographic analysis of wild and domesticated amaranths revealed a population bottleneck predating the domestication of grain amaranth. Our results indicate that a reduced level of ancestral genetic variation did not prevent the selection of traits with a simple genetic architecture but may have limited the adaptation of complex domestication traits.

A Review of Recent Studies on the Antioxidant Activities of a Third-Millennium Food: Amaranthus spp.

Antioxidants ◽

10.3390/antiox9121236 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1236

Author(s):

Seon-Joo Park ◽

Anshul Sharma ◽

Hae-Jeung Lee

Keyword(s):

Antioxidant Activity ◽

Bioactive Peptides ◽

Antioxidant Activities ◽

Radical Scavenging Activity ◽

Radical Scavenging ◽

Sustainable Food ◽

Amaranth Species ◽

Amaranthus Spp

Amaranth (Amaranthus spp.) plant commonly refers to the sustainable food crop for the 21st century. The crop has witnessed significant attention in recent years due to its high nutritional value and agronomic advantages. It is a relatively well-balanced cosmopolitan food that is a protector against chronic diseases. Usually, the antioxidant activities of amaranth are held responsible for its defensive behavior. Antioxidant activity of plants, generally, is attributed to their phytochemical compounds. The current interest, however, lies in hydrolysates and bioactive peptides because of their numerous biological functions, including antioxidant effect. While the importance of bioactive peptides has been progressively recognized, an integrated review of recent studies on the antioxidant ability of amaranth species, especially their hydrolysates and peptides has not been generated. Hence, in this review, we summarize studies focused on the antioxidant capacity of amaranth renewal over the period 2015–2020. It starts with a background and overall image of the amaranth-related published reviews. The current research focusing on in vitro, in vivo, and chemical assays-based antioxidant activity of different amaranth species are addressed. Finally, the last segment includes the latest studies concerning free radical scavenging activity and metal chelation capacity of amaranth protein hydrolysates and bioactive peptides.

Digestibility and nutritional value of crude oil from three amaranth species

Journal of the American Oil Chemists Society ◽

10.1007/bf02549297 ◽

1987 ◽

Vol 64 (3) ◽

pp. 371-375 ◽

Cited By ~ 13

Author(s):

Luis A. Garcia ◽

Maria Antonieta Alfaro ◽

Ricardo Bressani

Keyword(s):

Crude Oil ◽

Nutritional Value ◽

Amaranth Species

Genetic analysis of three Amaranth species using ISSR markers

Emirates Journal of Food and Agriculture ◽

10.9755/ejfa.v26i1.15911 ◽

2014 ◽

Vol 26 (1) ◽

pp. 35 ◽

Cited By ~ 3

Author(s):

V Stefunova ◽

M Bezo ◽

M Senkova

Keyword(s):

Genetic Analysis ◽

Issr Markers ◽

Amaranth Species

Study and Determination of As, Cr, and Pb in Amaranth Seeds

Journal of Chemistry ◽

10.1155/2013/138391 ◽

2013 ◽

Vol 2013 ◽

pp. 1-4 ◽

Cited By ~ 1

Author(s):

Elba Graciela Aguilar ◽

Miguel Angel Cantarelli ◽

Eduardo Jorge Marchevsky ◽

Nora Lilian Escudero ◽

José Manuel Camiña

Keyword(s):

Inductively Coupled Plasma ◽

Standard Addition ◽

Error Recovery ◽

Atomic Spectroscopy ◽

World Health ◽

Human Beings ◽

High Concentration ◽

Inductively Coupled ◽

Amaranth Species ◽

Health Organization

The concentration of As, Cr, and Pb toxic elements was determined in three species of amaranth seeds:A. hypochondriacus,A. cruentus, andA. dubius. The determinations were carried out by inductively coupled plasma optical atomic spectroscopy (ICP-OES). The result shows that Cr and As were found in minor concentrations than allowed by the World Health Organization (WHO; 120 and 4 mg kg−1resp.); As (mg kg−1):A. dubius(0.76)A. cruentus(<0.50) andA. hypochondriacus(<0.50); Cr (mg kg−1):A. dubius(8.19)A. cruentus(1.15) andA. hypochondriacus(1.20). However, the concentration of Pb was high:A. dubius(19.04)A. cruentus(30.20) andA. hypochondriacus(35.56) more than the maximum of WHO (10 mg kg−1). To avoid systematic error, recovery and validation studies were performed: recovery test: 102.3%; validation (by standard addition): 96.0–103.1%. Due to the fact that amaranth had been proposed as new food due to its nutraceutical properties, the high concentration of Pb found in this study indicates that Pb should be evaluated in these amaranth species to avoid the intake of toxic element by human beings.

Cyanobacteria is uniquely enriched in the roots of grain amaranths

10.1101/540484 ◽

2019 ◽

Author(s):

Suran Nambisan ◽

Meeta Sunil ◽

Bibha Choudhary ◽

Subhashini Srinivasan

Keyword(s):

Abiotic Stress ◽

16S Rrna ◽

Positive Selection ◽

Soil Microbes ◽

Selective Advantage ◽

Negative Control ◽

Relative Increase ◽

Biotic And Abiotic Stress ◽

Amaranthus Hypochondriacus ◽

Amaranth Species

ABSTRACTPlants and microbes have coexisted for millions of years and some have evolved mechanisms to achieve symbiosis driving positive selection. The bartering of chemicals produced by soil microbes and plants favour enrichment of certain types of bacteria near the roots that offers selective advantage to the plant under a given environment. Grain amaranths display certain important agronomic characteristics like C4 dicot, high protein and high lysine grains, resistance to biotic and abiotic stress, which can be translated to other crops. Considering an unusual collection of desirable traits shown by grain amaranths, it is worth pondering if symbiosis with bacteria has played any role in these traits. The objective of this study is to identify bacterial root microflora unique to grain amaranths. Here, by comparing rhizospheric and endophytic composition of 16S rRNA from various sections of roots from selected species under major plant orders including the three varieties of grain amaranths, we report that Cyanobacteria are uniquely enriched by grain amaranths. The diversity in OTUs among the Cyanobacteria also significantly increased among samples from amaranth species compared to negative control. This finding is also validated using root transcriptome of Amaranthus hypochondriacus, where we observe relative increase in Cyanobacterial population between day 15 to day 30 compared to other abundant phylum during this period.