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De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

View ORCID ProfileYa-Ping Lin, View ORCID ProfileTien-Hor Wu, View ORCID ProfileYan-Kuang Chan, View ORCID ProfileMaarten van Zonneveld, View ORCID ProfileRoland Schafleitner
doi: https://doi.org/10.1101/2021.10.05.463269
Ya-Ping Lin
1Biotechnology, World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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  • For correspondence: ya-ping.lin@worldveg.org roland.schafleitner@worldveg.org
Tien-Hor Wu
2Genetic Resources and Seed Unit, World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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Yan-Kuang Chan
2Genetic Resources and Seed Unit, World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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Maarten van Zonneveld
2Genetic Resources and Seed Unit, World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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Roland Schafleitner
1Biotechnology, World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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  • For correspondence: ya-ping.lin@worldveg.org roland.schafleitner@worldveg.org
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Abstract

Amaranths serve as pseudo cereals and also as traditional leafy vegetables worldwide. In addition to high vigor and richness in nutrients, drought and salinity tolerance of amaranth makes it a promising vegetable to acclimatize to the effects of global climate change. The World Vegetable Center genebank conserves about 1,000 amaranth accessions and various agronomic properties of these accessions were recorded during seed regeneration over decades. In this study, we verified the taxonomic annotation of the germplasm based on a 15K SNP set. Besides, in the assumption that the yield components of grain amaranths are different from those of leaf amaranths, we observed that grain amaranths presented larger inflorescences and earlier flowering than leaf amaranths. Dual-purpose amaranth showed larger leaves than leaf amaranths and later flowering than grain amaranths, which seemed reasonable because farmers can harvest more leaves during the prolonged vegetable stage, which also provides recovery time to enrich grain production. Considering frequent interspecies hybridization among grain amaranth complex, we proposed an interspecies GWAS for days to flowering, identifying a AGL20/SOC1 homolog. Meanwhile, another GWAS using only A. tricolor accessions revealed six candidate genes homologous to lba1, bri1, sgs1 and fca. These homologous genes were involved in the regulation of flowering time in Arabidopsis. This study revealed the usefulness of genotypes for species demarcation in the genus Amaranthus and the potential of interspecies GWAS to detect QTLs across different species, opening up the possibility of targeted introduction of specific genetic variants into different Amaranthus species.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 06, 2021.
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De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus
Ya-Ping Lin, Tien-Hor Wu, Yan-Kuang Chan, Maarten van Zonneveld, Roland Schafleitner
bioRxiv 2021.10.05.463269; doi: https://doi.org/10.1101/2021.10.05.463269
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De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus
Ya-Ping Lin, Tien-Hor Wu, Yan-Kuang Chan, Maarten van Zonneveld, Roland Schafleitner
bioRxiv 2021.10.05.463269; doi: https://doi.org/10.1101/2021.10.05.463269

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