A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop.

Xiao Ma,Zemin Ning,Willem S Jansen Van Rensburg,Katherine J Denby,Ian A Graham,Yi Li,Allen Van Deynze,Yves Van De Peer,Sydney Mavengahama,Fabián E Vaistij,Michael W Bairu,Sarah Harvey,Sonja L Venter

doi:10.1111/tpj.15298

Abstract

Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internationally traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies, we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.

Highlights

Substantial investment in genetic improvement of crops during the Green Revolution (1960s to 1980s) led to the development of high-yield varieties of staple cereals to feed the world’s population
We demonstrate that the whole genome duplication (WGD) seen in A. hypochondriacus occurred before divergence of this species and A. cruentus, and highlight intraand inter-chromosomal rearrangements compared with A. hypochondriacus
The 17 chromosome-length scaffolds have been named corresponding to the A. hypochondriacus assembly (Lightfoot et al, 2017), based on the degree of synteny between the two genomes

Summary

Introduction

Substantial investment in genetic improvement of crops during the Green Revolution (1960s to 1980s) led to the development of high-yield varieties of staple cereals (predominantly maize, wheat and rice) to feed the world’s population. While these crops provide significant calories for human consumption, they are relatively low in protein (and in particular amino acids), vitamin and micronutrient content. Orphan crops are typically traditional crops grown, traded and consumed within subsistence farming systems They are not traded internationally but can play a major role in the diets and economy of low-income communities across the developing world. Research and advances in orphan crops have lagged significantly behind that of staple crops, but orphan crops are often uniquely adapted to their local environments with enhanced nutritional content compared with more widely cultivated cereals, vegetables and fruits (Jamnadass et al, 2020)

Results

Discussion

Conclusion