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Genetic diversity analysis and marker-trait associations in Amaranthus species

Jamalluddin, N, Massawe, FJ, Mayes, S, Ho, WK and Symonds, RC (2022) Genetic diversity analysis and marker-trait associations in Amaranthus species. PLOS ONE, 17 (5). pp. 1-24. ISSN 1932-6203

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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. 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. datasets, respectively. The release of SNP markers from this panel has produced invaluable preliminary genetic information for phenotyping and cultivar improvement in amaranth species.

Item Type: Article
Uncontrolled Keywords: General Science & Technology
Subjects: G Geography. Anthropology. Recreation > GE Environmental Sciences
T Technology > TX Home economics > TX341 Nutrition. Foods and food supply
Q Science > QH Natural history > QH301 Biology
S Agriculture > S Agriculture (General)
Divisions: Biological & Environmental Sciences (from Sep 19)
Publisher: Public Library of Science (PLoS)
SWORD Depositor: A Symplectic
Date Deposited: 16 May 2022 07:53
Last Modified: 16 May 2022 08:00
DOI or ID number: 10.1371/journal.pone.0267752
URI: https://researchonline.ljmu.ac.uk/id/eprint/16849
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