Genetic diversity analysis and marker-trait associations in Amaranthus species

Abstract

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.

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

“…Hoshikawa et al [ 48 ] performed genetic diversity analysis among Amaranthus tricolor accessions using genome-wide SNPs and found a set of 5638 SNPs without missing data in 440 accessions. Similarly, Wu and Blair [ 49 ], and Jamalluddin et al [ 50 ] performed genetic diversity analysis and marker-trait associations in amaranths and relative species using Genotyping By Sequencing (GBS) methods. The identification of allelic variations within economically important genes highlights the practical applications of this research in crop improvement programs.…”

Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics

“…Various studies have reported the development and use of molecular markers such as SSRs ( Suresh S. et al., 2014 ; Delgado and Martín, 2022 ; Vats et al., 2023 ), SNPs ( Jamalluddin et al., 2022 ; Hoshikawa et al., 2023 ); for the diversity analysis but their application in marker-assisted improvement of grain amaranth is very limited. The availability of high-density SNPs information for various amaranth species makes them valuable for genome mapping, analyzing genetic diversity and population structure, constructing ultra-high-density genetic maps, map-based positional cloning, and providing genotypes for genome-wide association analysis ( Xia et al., 2019 ).…”

Genetic resources and breeding approaches for improvement of amaranth (Amaranthus spp.) and quinoa (Chenopodium quinoa)

“…Germplasm from A . hypochondriacus species ( 22 ) and SNP alleles were generated and a genome-wide association study (GWAS) was carried out for the qualitative traits between specific phenotypes and genetic variants within the genome and identified marker-trait associations (MTAs) on 16 amaranthus species. SNP markers were used to produce genetic resources for the phenotyping and development of cultivars.…”

“…These crops can be grown in most countries' environmental conditions and are easily available plant sources of micronutrients to alleviate micronutrient malnutrition ( 21 ). There is a need for their genetic improvement and to explore the breeding behavior of these crops, possibilities to create variations in population, and the use of molecular markers to study diversity in amaranth and quinoa ( 22 – 24 ) ( Table 3 ). We have reviewed genetic mapping studies and DNA barcoding to understand the gene sequence of these crops ( Table 3 ).…”