Diversity in Grain Amaranths and Relatives Distinguished by Genotyping by Sequencing (GBS)

Wu, Xiling; Blair, Matthew W.

doi:10.3389/fpls.2017.01960

Cited by 44 publications

(46 citation statements)

References 56 publications

(80 reference statements)

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“…Seed protein analysis would also require producing the seed of the genotypes in either field conditions or in a greenhouse where day length and photoperiod could be controlled and allow the evaluation of seed protein variability [38] as well as provide clean tissues for isozyme analysis [39]. Perhaps most promising, the recent use of next generation sequencing technology of Genotyping by sequencing (GBS), performed by Wu and Blair [40] and Stetter and Schmid [2], was successful at differentiating cultivars from wild accessions and different species from each other.…”

Section: Discussionmentioning

confidence: 99%

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%

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Thapa

Blair

2018

Agronomy

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“…The normalization is validated by clustering of both WGS and GBS ter re .a) S) in S data from A.hyp_Plainsman_PI558499 and A.hyp_Mexico_PI511731 close to each other ( Figure 4.a, red arrow). The tree in Figure 4.a is very similar to that reported using A.hyp.V2.1 as reference 4 . The taxonomy-based classification seems reproducible with green being A. hypochondriacus, light blue being A. cruentus, dark blue being A. caudatus and yellow being A. quitensis.…”

Section: Classification Of Grain Amaranthsmentioning

confidence: 99%

“…For genomics-based crop improvement of local landraces, it is critical to classify these with respect to accession from the germplasm collection. More recently, using genotyping-by-sequencing (GBS), 94 accessions for grain amaranths have been classified 4 . It is of interest to decorate this phylogenetic tree with landraces of importance to India and elsewhere.…”

Section: Introductionmentioning

confidence: 99%

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

Deb

Jayaprasad

Ravi

et al. 2020

Preprint

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In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosomelevel assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

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“…Single-nucleotide polymorphisms (SNPs) are third-generation DNA molecular marker technology defined as single-base changes at a specific nucleotide position across the entire genome of all organisms 12 . Compared to traditional molecular markers, SNPs are abundant, stable, and easily detectable by sequencing technologies such as genotyping-bysequencing (GBS) even without a priori genome sequence information 13 . Thus, SNP markers have been widely used in genetic diversity assessments, molecular evolution studies, and genetic mapping for traits of interest in diverse horticultural crops such as carnation 14 , chrysanthemums 15 , roses 16 , lilies 17 , and tulips 18 .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

Wu¹,

Alexander

2020

Hortic Res

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Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F 1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.

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Diversity in Grain Amaranths and Relatives Distinguished by Genotyping by Sequencing (GBS)

Cited by 44 publications

References 56 publications

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

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